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- PDB-6u7e: HCoV-229E RBD Class III in complex with human APN -

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Basic information

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


membrane alanyl aminopeptidase / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / metalloaminopeptidase activity / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / aminopeptidase activity / endocytosis involved in viral entry into host cell / secretory granule membrane / metallopeptidase activity ...membrane alanyl aminopeptidase / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / metalloaminopeptidase activity / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / aminopeptidase activity / endocytosis involved in viral entry into host cell / secretory granule membrane / metallopeptidase activity / peptide binding / virus receptor activity / lysosomal membrane / fusion of virus membrane with host plasma membrane / signaling receptor activity / angiogenesis / fusion of virus membrane with host endosome membrane / cell differentiation / viral envelope / external side of plasma membrane / virion membrane / proteolysis / pathogenesis / neutrophil degranulation / extracellular space / zinc ion binding / extracellular exosome / integral component of membrane / plasma membrane / cytoplasm
Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1 N-terminal domain / ERAP1-like C-terminal domain / Peptidase family M1 domain / Spike glycoprotein, Alphacoronavirus / Aminopeptidase N-like , N-terminal / Aminopeptidase N-type / ERAP1-like C-terminal domain / Peptidase M1, membrane alanine aminopeptidase / Coronavirus S2 glycoprotein ...Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1 N-terminal domain / ERAP1-like C-terminal domain / Peptidase family M1 domain / Spike glycoprotein, Alphacoronavirus / Aminopeptidase N-like , N-terminal / Aminopeptidase N-type / ERAP1-like C-terminal domain / Peptidase M1, membrane alanine aminopeptidase / Coronavirus S2 glycoprotein / Coronavirus S1 glycoprotein / ct:1.25.50.20: / ct:2.60.40.1910: / 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
Aminopeptidase N / Spike glycoprotein
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)243,28928
Polymers238,3744
Non-polymers4,91524
Water905
1
A: Aminopeptidase N
C: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,64514
Polymers119,1872
Non-polymers2,45812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminopeptidase N
D: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,64514
Polymers119,1872
Non-polymers2,45812
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

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Components

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Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein/peptide Aminopeptidase N / Alanine aminopeptidase / 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/peptide Spike glycoprotein


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

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Non-polymers , 4 types, 29 molecules

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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Mass: 221.208 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
#5: Chemical ChemComp-BMA / BETA-D-MANNOSE / Mannose


Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#6: Water ChemComp-HOH / water / Water


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

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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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

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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

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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

Refinement-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection details: all

IDAuth asym-IDAuth seq-ID
1A68 - 967
2A5001 - 5011
3B68 - 967
4B5001 - 5010
5C302 - 416
6C2001 - 2002
7D298 - 417
8D2001 - 2002
9S1 - 5

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