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- PDB-6u7g: HCoV-229E RBD Class V in complex with human APN -

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Basic information

Entry
Database: PDB / ID: 6u7g
TitleHCoV-229E RBD Class V in complex with human APN
Components
  • Aminopeptidase NAlanine aminopeptidase
  • Spike protein
KeywordsHYDROLASE/VIRAL PROTEIN / CoV / coronavirus / 229E / spike glycoprotein / APN / S-protein / HYDROLASE-VIRAL PROTEIN complex
Function / homology
Function and homology information


membrane alanyl aminopeptidase / receptor-mediated virion attachment to host cell / metalloaminopeptidase activity / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / aminopeptidase activity / secretory granule membrane / metallopeptidase activity / peptide binding / virus receptor activity ...membrane alanyl aminopeptidase / receptor-mediated virion attachment to host cell / metalloaminopeptidase activity / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / aminopeptidase activity / secretory granule membrane / metallopeptidase activity / peptide binding / virus receptor activity / lysosomal membrane / fusion of virus membrane with host plasma membrane / signaling receptor activity / angiogenesis / cell differentiation / viral envelope / external side of plasma membrane / proteolysis / neutrophil degranulation / extracellular space / zinc ion binding / extracellular exosome / integral component of membrane / plasma membrane / cytoplasm
Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Coronavirus S1 glycoprotein / Peptidase M1 N-terminal domain / ERAP1-like C-terminal domain / Peptidase family M1 domain / 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 / Coronavirus S1 glycoprotein / Peptidase M1 N-terminal domain / ERAP1-like C-terminal domain / Peptidase family M1 domain / Aminopeptidase N-like , N-terminal / Aminopeptidase N-type / ERAP1-like C-terminal domain / Peptidase M1, membrane alanine aminopeptidase / Coronavirus S2 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 protein / Spike glycoprotein
Biological speciesHomo sapiens (human)
Human coronavirus 229E
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsTomlinson, 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 protein
D: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,51727
Polymers238,7404
Non-polymers4,77623
Water14,430801
1
A: Aminopeptidase N
C: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,86914
Polymers119,3702
Non-polymers2,49912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminopeptidase N
D: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,64813
Polymers119,3702
Non-polymers2,27711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)99.555, 98.682, 147.525
Angle α, β, γ (deg.)90.000, 104.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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 protein


Mass: 15848.161 Da / Num. of mol.: 2 / Fragment: receptor-binding domain (UNP residues 292-432)
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: H1AG31, UniProt: Q1HVK2*PLUS
#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.: 21
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 801 / Source method: isolated from a natural source / Formula: H2O
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: 2.96 Å3/Da / Density % sol: 58.41 % / Mosaicity: 0.58 °
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: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.349→200 Å / Num. obs: 114608 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Rrim(I) all: 0.062 / Χ2: 0.84 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.392.90.37756190.8720.2580.4590.82399
2.39-2.433.20.3457130.9120.2190.4060.78799.7
2.43-2.483.70.30757240.9350.1850.360.8100
2.48-2.533.70.2657250.9480.1550.3030.807100
2.53-2.593.80.23456940.9510.1380.2720.81899.9
2.59-2.653.70.19857340.9610.1180.2310.822100
2.65-2.713.70.16957020.9710.1010.1970.849100
2.71-2.793.60.13957440.9750.0850.1640.868100
2.79-2.873.50.11357030.980.070.1330.902100
2.87-2.963.20.09257420.9820.060.1110.886100
2.96-3.073.50.07857390.9880.0480.0920.89499.9
3.07-3.193.40.06657300.9890.0410.0780.97399.9
3.19-3.333.80.05757190.9910.0330.0661.0399.7
3.33-3.513.80.04957160.9930.0290.0571.02399.6
3.51-3.733.70.04357280.9930.0260.0511.01599.9
3.73-4.023.50.03857650.9930.0240.0450.90999.7
4.02-4.423.30.03357100.9940.0210.0390.7799.3
4.42-5.063.50.03257450.9950.0190.0370.7599.3
5.06-6.383.80.02957930.9960.0170.0340.59699.7
6.38-2003.40.02458630.9970.0150.0280.44398.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16rc1_3535refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4FYQ
Resolution: 2.35→45.614 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.4
RfactorNum. reflection% reflection
Rfree0.2184 5552 5.02 %
Rwork0.1786 --
Obs0.1806 110683 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.15 Å2 / Biso mean: 43.2781 Å2 / Biso min: 12.71 Å2
Refinement stepCycle: final / Resolution: 2.35→45.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16260 0 533 801 17594
Biso mean--67.87 37.99 -
Num. residues----2027
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.35-2.37610.31921120.2302228163
2.3761-2.4040.2921500.2194266574
2.404-2.43340.28051390.2239294981
2.4334-2.46420.28831690.217316786
2.4642-2.49660.24841870.209330592
2.4966-2.53080.26481690.2053340594
2.5308-2.56690.26732050.2064353398
2.5669-2.60520.24271880.2026362799
2.6052-2.64590.25971790.20643634100
2.6459-2.68930.23571880.20463637100
2.6893-2.73570.26371920.20353650100
2.7357-2.78540.2341990.19713611100
2.7854-2.8390.25491880.20373666100
2.839-2.89690.27731700.20133630100
2.8969-2.95990.261980.20133632100
2.9599-3.02880.23612000.20473648100
3.0288-3.10450.24841900.20283630100
3.1045-3.18840.26732200.20133630100
3.1884-3.28220.20681860.19013624100
3.2822-3.38810.22152050.18543602100
3.3881-3.50910.22411910.17973636100
3.5091-3.64960.20022120.1753628100
3.6496-3.81560.21711710.16723688100
3.8156-4.01670.20281840.16433648100
4.0167-4.26820.17031930.144362699
4.2682-4.59740.16621940.1352362699
4.5974-5.05950.15961900.1355365599
5.0595-5.79040.18821970.15463676100
5.7904-7.29050.20812000.1763680100
7.2905-45.6140.19011860.1711374298
Refinement TLS params.Method: refined / Origin x: 23.9331 Å / Origin y: -24.6026 Å / Origin z: -35.288 Å
111213212223313233
T0.1766 Å2-0.0095 Å2-0.0264 Å2-0.1469 Å20.0067 Å2--0.1714 Å2
L0.5855 °2-0.1047 °2-0.0588 °2-0.1373 °2-0.055 °2--0.3867 °2
S-0.0247 Å °-0.0864 Å °-0.0913 Å °0.0044 Å °0.0459 Å °0.016 Å °-0.0038 Å °-0.0241 Å °-0.0274 Å °
Refinement TLS group

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

IDAuth asym-IDAuth seq-ID
1A66 - 967
2A5001 - 5010
3B66 - 967
4B5001 - 5010
5C299 - 2002
6D302 - 417
7D2002 - 2001
8S1 - 814

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