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- PDB-7cjf: Crystal structure of SARS-CoV-2 RBD in complex with a neutralizin... -

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Basic information

Entry
Database: PDB / ID: 7cjf
TitleCrystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody Fab
Components
  • Spike protein S1
  • antibody heavy chain
  • antibody light chain
KeywordsVIRAL PROTEIN / SARS-CoV-2 / RBD / antibody
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / 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 / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.108 Å
AuthorsGuo, Y. / Li, X. / Zhang, G. / Fu, D. / Schweizer, L. / Zhang, H. / Rao, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)31670731 China
National Science Foundation (NSF, United States)31870733 China
CitationJournal: Nat Commun / Year: 2021
Title: A SARS-CoV-2 neutralizing antibody with extensive Spike binding coverage and modified for optimal therapeutic outcomes.
Authors: Guo, Y. / Huang, L. / Zhang, G. / Yao, Y. / Zhou, H. / Shen, S. / Shen, B. / Li, B. / Li, X. / Zhang, Q. / Chen, M. / Chen, D. / Wu, J. / Fu, D. / Zeng, X. / Feng, M. / Pi, C. / Wang, Y. / ...Authors: Guo, Y. / Huang, L. / Zhang, G. / Yao, Y. / Zhou, H. / Shen, S. / Shen, B. / Li, B. / Li, X. / Zhang, Q. / Chen, M. / Chen, D. / Wu, J. / Fu, D. / Zeng, X. / Feng, M. / Pi, C. / Wang, Y. / Zhou, X. / Lu, M. / Li, Y. / Fang, Y. / Lu, Y.Y. / Hu, X. / Wang, S. / Zhang, W. / Gao, G. / Adrian, F. / Wang, Q. / Yu, F. / Peng, Y. / Gabibov, A.G. / Min, J. / Wang, Y. / Huang, H. / Stepanov, A. / Zhang, W. / Cai, Y. / Liu, J. / Yuan, Z. / Zhang, C. / Lou, Z. / Deng, F. / Zhang, H. / Shan, C. / Schweizer, L. / Sun, K. / Rao, Z.
History
DepositionJul 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description / _entity_name_com.name
Revision 1.2May 26, 2021Group: 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 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 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
A: antibody heavy chain
B: antibody light chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5474
Polymers69,3253
Non-polymers2211
Water10,647591
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-21 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.958, 148.575, 144.655
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-775-

HOH

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Components

#1: Antibody antibody heavy chain


Mass: 24271.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody antibody light chain


Mass: 23281.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein / Spike glycoprotein


Mass: 21772.391 Da / Num. of mol.: 1 / Fragment: receptor binding domain, RBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2
#4: 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: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 20%(w/v)PEG 3350 0.2M potassium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 49623 / % possible obs: 92.7 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.031 / Rrim(I) all: 0.097 / Χ2: 0.958 / Net I/σ(I): 7.9 / Num. measured all: 475973
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.149.70.826390.8950.2640.8440.91799.8
2.14-2.189.80.81226630.890.2670.8560.91799.7
2.18-2.229.40.82923210.9030.2770.8760.91488.7
2.22-2.263.20.1384030.9670.0820.1623.06315.2
2.26-2.319.10.62826360.9440.2160.6650.93699.2
2.31-2.379.50.48926410.9550.1650.5160.92299.9
2.37-2.4210.10.43326420.9660.1410.4560.973100
2.42-2.49100.35226490.9740.1150.3710.96100
2.49-2.569.90.31126360.9780.1020.3280.953100
2.56-2.659.70.24326700.9830.0810.2570.965100
2.65-2.749.40.20126750.9870.0680.2120.98499.9
2.74-2.8510.20.15926600.9940.0520.1680.99100
2.85-2.9810.10.12626590.9960.0410.1320.995100
2.98-3.149.90.09726710.9960.0320.1021.009100
3.14-3.339.60.07426740.9980.0250.0791.05100
3.33-3.599.40.0625890.9980.020.0631.03396.3
3.59-3.958.50.06314990.9910.0240.0681.24955.8
3.95-4.529.60.03927280.9990.0130.0420.9399.8
4.52-5.79.60.03527240.9990.0120.0370.82399.7
5.7-509.20.03328440.9990.0110.0350.74799.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BWJ

7bwj


Resolution: 2.108→36.164 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1991 4.16 %
Rwork0.1846 45922 -
obs0.1864 47913 89.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.34 Å2 / Biso mean: 39.1355 Å2 / Biso min: 16.38 Å2
Refinement stepCycle: final / Resolution: 2.108→36.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 14 591 5423
Biso mean--82.9 50.18 -
Num. residues----627
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.108-2.16050.24641290.2236288279
2.1605-2.21890.28891420.247316088
2.2189-2.28420.4314330.329278822
2.2842-2.35790.2931560.2357351996
2.3579-2.44220.27021590.2295360799
2.4422-2.53990.26991570.21853612100
2.5399-2.65550.31581570.21253643100
2.6555-2.79540.28651540.20773669100
2.7954-2.97050.24021590.20233675100
2.9705-3.19970.25491590.1993670100
3.1997-3.52150.22241560.17983675100
3.5215-4.03050.23171020.1948244666
4.0305-5.07570.15411670.12713732100
5.0757-36.1640.19051610.1599384499
Refinement TLS params.Method: refined / Origin x: 1.5016 Å / Origin y: -32.9337 Å / Origin z: -5.522 Å
111213212223313233
T0.1721 Å20.0113 Å2-0.0112 Å2-0.2342 Å2-0.0038 Å2--0.2128 Å2
L0.0671 °20.1611 °2-0.1233 °2-0.8778 °2-0.4499 °2--0.525 °2
S-0.0042 Å °-0.0398 Å °-0.0227 Å °-0.1182 Å °0.0032 Å °0.0425 Å °0.0764 Å °0.0253 Å °0.001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 220
2X-RAY DIFFRACTION1ALLA305 - 515
3X-RAY DIFFRACTION1ALLB1 - 213
4X-RAY DIFFRACTION1ALLB306 - 525
5X-RAY DIFFRACTION1ALLC334 - 878

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