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- PDB-7vn9: Crystal structure of human coronavirus 229E spike protein recepto... -

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Basic information

Entry
Database: PDB / ID: 7vn9
TitleCrystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with C04 Fab
Components
  • C04 Fab heavy chain
  • C04 Fab light chain
  • Spike glycoprotein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Neutralizing antibody / human coronavirus 229E / C04 Fab. / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Human coronavirus 229E
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.49 Å
AuthorsXiang, J.C. / Yang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32070170 China
CitationJournal: Commun Biol / Year: 2022
Title: Antigenic mapping reveals sites of vulnerability on alpha-HCoV spike protein.
Authors: Xiang, J. / Su, J. / Lan, Q. / Zhao, W. / Zhou, Y. / Xu, Y. / Niu, J. / Xia, S. / Qi, Q. / Sidhu, S. / Lu, L. / Miersch, S. / Yang, B.
History
DepositionOct 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: C04 Fab heavy chain
L: C04 Fab light chain
E: Spike glycoprotein S1
A: C04 Fab heavy chain
B: C04 Fab light chain
C: Spike glycoprotein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,50310
Polymers127,6856
Non-polymers1,8194
Water00
1
H: C04 Fab heavy chain
L: C04 Fab light chain
E: Spike glycoprotein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8535
Polymers63,8423
Non-polymers1,0112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: C04 Fab heavy chain
B: C04 Fab light chain
C: Spike glycoprotein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6505
Polymers63,8423
Non-polymers8082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.732, 183.732, 255.988
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 136 or resid 144 through 147 or resid 149 through 222))
21(chain H and (resid 2 through 136 or resid 144 through 147 or resid 149 through 222))
12chain B
22(chain L and (resid 1 through 180 or resid 186 through 203))
13(chain C and (resid 296 through 310 or resid 317 through 431 or resid 432 or resid 435))
23(chain E and (resid 296 through 431 or resid 437 or resid 440))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 136 or resid 144 through 147 or resid 149 through 222))A2 - 136
121(chain A and (resid 2 through 136 or resid 144 through 147 or resid 149 through 222))A144 - 147
131(chain A and (resid 2 through 136 or resid 144 through 147 or resid 149 through 222))A149 - 222
211(chain H and (resid 2 through 136 or resid 144 through 147 or resid 149 through 222))H2 - 136
221(chain H and (resid 2 through 136 or resid 144 through 147 or resid 149 through 222))H144 - 147
231(chain H and (resid 2 through 136 or resid 144 through 147 or resid 149 through 222))H149 - 222
112chain BB1 - 203
212(chain L and (resid 1 through 180 or resid 186 through 203))L1 - 180
222(chain L and (resid 1 through 180 or resid 186 through 203))L186 - 203
113(chain C and (resid 296 through 310 or resid 317 through 431 or resid 432 or resid 435))C296 - 310
123(chain C and (resid 296 through 310 or resid 317 through 431 or resid 432 or resid 435))C317 - 431
133(chain C and (resid 296 through 310 or resid 317 through 431 or resid 432 or resid 435))C432
143(chain C and (resid 296 through 310 or resid 317 through 431 or resid 432 or resid 435))C435
213(chain E and (resid 296 through 431 or resid 437 or resid 440))E296 - 431
223(chain E and (resid 296 through 431 or resid 437 or resid 440))E437
233(chain E and (resid 296 through 431 or resid 437 or resid 440))E440

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules EC

#3: Protein Spike glycoprotein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 16194.324 Da / Num. of mol.: 2 / Fragment: receptor-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus 229E / Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15423

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Antibody , 2 types, 4 molecules HALB

#1: Antibody C04 Fab heavy chain


Mass: 24304.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Antibody C04 Fab light chain


Mass: 23343.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Sugars , 3 types, 4 molecules

#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
#5: 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.: 1
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
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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

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Details

Has ligand of interestN
Has protein modificationY

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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: 5.09 Å3/Da / Density % sol: 75.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.6M AmSO4, 0.1M Critic Acid pH 5.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 4.49→50 Å / Num. obs: 15864 / % possible obs: 100 % / Redundancy: 16.6 % / Biso Wilson estimate: 174 Å2 / CC1/2: 0.992 / CC star: 0.998 / Net I/σ(I): 6.75
Reflection shellResolution: 4.49→4.66 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1514 / CC1/2: 0.527 / CC star: 0.831 / Rpim(I) all: 0.544 / Rrim(I) all: 1.802 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ATK, 6DF2

6atk

6df2


Resolution: 4.49→42.66 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2885 797 5.06 %
Rwork0.2734 14946 -
obs0.2742 15743 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 286.51 Å2 / Biso mean: 199.1161 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 4.49→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8422 0 120 0 8542
Biso mean--243.94 --
Num. residues----1113
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1760X-RAY DIFFRACTION21.313TORSIONAL
12H1760X-RAY DIFFRACTION21.313TORSIONAL
21B1654X-RAY DIFFRACTION21.313TORSIONAL
22L1654X-RAY DIFFRACTION21.313TORSIONAL
31C1091X-RAY DIFFRACTION21.313TORSIONAL
32E1091X-RAY DIFFRACTION21.313TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.49-4.770.36041300.34042407253799
4.77-5.140.32541280.304924532581100
5.14-5.650.31711360.289924582594100
5.65-6.470.28321380.294924802618100
6.47-8.140.32891200.29225342654100
8.14-42.660.23991450.22862614275998
Refinement TLS params.Method: refined / Origin x: 40.738 Å / Origin y: 55.9337 Å / Origin z: 50.1939 Å
111213212223313233
T1.7886 Å20.2635 Å2-0.1361 Å2-1.4945 Å2-0.0999 Å2--1.7116 Å2
L0.6686 °20.2233 °2-0.5838 °2-0.3389 °2-0.0253 °2--0.7328 °2
S0.0661 Å °0.0278 Å °-0.1547 Å °-0.2862 Å °-0.069 Å °0.056 Å °0.1618 Å °-0.0518 Å °0.0281 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH2 - 223
2X-RAY DIFFRACTION1allL1 - 213
3X-RAY DIFFRACTION1allE296 - 435
4X-RAY DIFFRACTION1allE436 - 440
5X-RAY DIFFRACTION1allA2 - 222
6X-RAY DIFFRACTION1allB1 - 203
7X-RAY DIFFRACTION1allC297 - 431
8X-RAY DIFFRACTION1allC432 - 435

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