[English] 日本語
Yorodumi
- PDB-6u7e: HCoV-229E RBD Class III in complex with human APN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u7e
TitleHCoV-229E RBD Class III in complex with human APN
Components
  • Aminopeptidase NAlanine aminopeptidase
  • Spike glycoproteinPeplomer
KeywordsHYDROLASE/VIRAL PROTEIN / CoV / coronavirus / 229E / spike glycoprotein / APN / S-protein / HYDROLASE-VIRAL PROTEIN complex
Function / homology
Function and homology information


membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / endoplasmic reticulum-Golgi intermediate compartment / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / aminopeptidase activity / receptor-mediated virion attachment to host cell / secretory granule membrane / peptide binding / metallopeptidase activity ...membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / endoplasmic reticulum-Golgi intermediate compartment / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / aminopeptidase activity / receptor-mediated virion attachment to host cell / secretory granule membrane / peptide binding / metallopeptidase activity / endocytosis involved in viral entry into host cell / virus receptor activity / lysosomal membrane / angiogenesis / fusion of virus membrane with host plasma membrane / signaling receptor activity / fusion of virus membrane with host endosome membrane / cell differentiation / viral envelope / external side of plasma membrane / pathogenesis / proteolysis / virion membrane / neutrophil degranulation / extracellular space / extracellular exosome / zinc ion binding / integral component of membrane / plasma membrane / cytoplasm
Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Spike glycoprotein S1, coronavirus / Peptidase M1 N-terminal domain / ERAP1-like C-terminal domain / Peptidase family M1 domain / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein, Alphacoronavirus / Aminopeptidase N-like , N-terminal ...Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Spike glycoprotein S1, coronavirus / Peptidase M1 N-terminal domain / ERAP1-like C-terminal domain / Peptidase family M1 domain / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein, Alphacoronavirus / Aminopeptidase N-like , N-terminal / Aminopeptidase N-type / ERAP1-like C-terminal domain / Peptidase M1, membrane alanine aminopeptidase / Spike glycoprotein S2, coronavirus / Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Zincin-like fold / tricorn interacting facor f3 domain / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Alpha Horseshoe / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
polysac:dmanpb1-4dglcpnacb1-4dglcpnacb1-: / polysac:dglcpnacb1-4dglcpnacb1-: / Spike glycoprotein / Aminopeptidase N
Biological speciesHomo sapiens (human)
Human coronavirus 229E
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTomlinson, A.C.A. / Li, Z. / Rini, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 6, 2020Group: Data collection / Database references / Category: chem_comp / pdbx_related_exp_data_set / Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminopeptidase N
B: Aminopeptidase N
C: Spike glycoprotein
D: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,18122
Polymers238,3744
Non-polymers4,80718
Water905
1
A: Aminopeptidase N
C: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,59111
Polymers119,1872
Non-polymers2,4049
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminopeptidase N
D: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,59111
Polymers119,1872
Non-polymers2,4049
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)99.320, 98.520, 153.620
Angle α, β, γ (deg.)90.000, 104.440, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Aminopeptidase N / Alanine aminopeptidase / hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid plasma ...hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid plasma membrane glycoprotein CD13 / gp150


Mass: 103522.031 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 66-967)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANPEP, APN, CD13, PEPN / Plasmid: PB-T-PAF / Cell line (production host): HEK293S GnT1-minus / Production host: Homo sapiens (human) / References: UniProt: P15144, membrane alanyl aminopeptidase
#2: Protein Spike glycoprotein / Peplomer


Mass: 15664.968 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus 229E / Plasmid: PB-T-PAF / Cell line (production host): HEK293S GnT1-minus / Production host: Homo sapiens (human) / References: UniProt: Q1HVL8*PLUS

-
Sugars , 3 types, 16 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 2 types, 7 molecules

#5: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 21, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.99→48.092 Å / Num. obs: 58215 / % possible obs: 99.8 % / Redundancy: 3.642 % / Biso Wilson estimate: 81.905 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.083 / Χ2: 1.024 / Net I/σ(I): 11.06 / Num. measured all: 212045 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.99-3.073.8560.6422.1516357424842420.8590.74699.9
3.07-3.153.8570.4852.7916180419741950.9090.565100
3.15-3.243.8440.3843.5315499404140320.9420.44799.8
3.24-3.343.8410.2814.5915327399639900.9690.32899.8
3.34-3.453.8290.2275.714448377937730.9740.26499.8
3.45-3.573.7940.1747.114302377637700.9840.20399.8
3.57-3.713.7610.1358.8613264353335270.9890.15899.8
3.71-3.863.6890.1110.3712716344734470.9920.129100
3.86-4.033.6390.09311.6912100333833250.9930.10999.6
4.03-4.233.5580.07913.6811236315831580.9940.093100
4.23-4.463.4840.06715.410428300129930.9960.07999.7
4.46-4.733.3960.05817.039751287828710.9950.06999.8
4.73-5.053.3830.05517.558972265826520.9960.06499.8
5.05-5.463.3860.05318.438503251125110.9960.062100
5.46-5.983.3820.05318.547781230823010.9950.06299.7
5.98-6.693.3890.04919.357160212221130.9960.05899.6
6.69-7.723.3430.04221.326142183818370.9970.0599.9
7.72-9.463.3790.03823.135291157215660.9970.04599.6
9.46-13.373.4370.03724.224207122912240.9970.04499.6
13.37-48.0923.4610.03524.7323817076880.9980.04197.3

-
Processing

Software
NameVersionClassification
PHENIX1.16rc1_3535refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4FYQ
Resolution: 3→48.092 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 2881 5 %
Rwork0.2035 54700 -
Obs0.2055 57581 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 227.29 Å2 / Biso mean: 97.7358 Å2 / Biso min: 46.4 Å2
Refinement stepCycle: final / Resolution: 3→48.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16234 0 304 5 16543
Biso mean--124.91 55.76 -
Num. residues----2026
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.04920.32521350.31222544100
3.0492-3.10180.4121370.29982604100
3.1018-3.15820.35141360.2972584100
3.1582-3.21890.32861360.28442581100
3.2189-3.28460.31441370.27732601100
3.2846-3.3560.28391360.27862582100
3.356-3.4340.34481380.2622615100
3.434-3.51990.29351360.24662588100
3.5199-3.6150.25831360.23582571100
3.615-3.72130.27261370.2242602100
3.7213-3.84140.29181360.21482607100
3.8414-3.97860.24751370.22022605100
3.9786-4.13790.24771370.20832612100
4.1379-4.32610.26631370.18612601100
4.3261-4.5540.20021370.17452588100
4.554-4.83910.22231370.17322610100
4.8391-5.21230.23131390.17192635100
5.2123-5.7360.23371360.18682597100
5.736-6.56430.25381390.19612633100
6.5643-8.26350.19231400.18692650100
8.2635-48.0920.191420.1691269099
Refinement TLS params.Method: refined / Origin x: -24.614 Å / Origin y: -18.6671 Å / Origin z: -38.2449 Å
111213212223313233
T0.5522 Å20.0082 Å2-0.0379 Å2-0.6031 Å2-0.0288 Å2--0.5069 Å2
L0.9241 °2-0.2648 °2-0.0451 °2-0.2534 °2-0.0215 °2--0.4836 °2
S-0.0576 Å °-0.1874 Å °-0.1049 Å °-0.0216 Å °0.1076 Å °-0.0035 Å °-0.0073 Å °-0.0122 Å °-0.0501 Å °
Refinement TLS group
IDRefinement-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA68 - 967
2X-RAY DIFFRACTION1allA5001 - 5011
3X-RAY DIFFRACTION1allB68 - 967
4X-RAY DIFFRACTION1allB5001 - 5010
5X-RAY DIFFRACTION1allC302 - 416
6X-RAY DIFFRACTION1allC2001 - 2002
7X-RAY DIFFRACTION1allD298 - 417
8X-RAY DIFFRACTION1allD2001 - 2002
9X-RAY DIFFRACTION1allS1 - 5

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more