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- PDB-7c01: Molecular basis for a potent human neutralizing antibody targetin... -

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Basic information

Entry
Database: PDB / ID: 7c01
TitleMolecular basis for a potent human neutralizing antibody targeting SARS-CoV-2 RBD
Components
  • CB6 heavy chain
  • CB6 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / RBD / neutralizing antibodies / molecular basis
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, 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, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsShi, R. / Qi, J. / Wang, Q. / Gao, F.G. / Yan, J.
Funding support China, 4items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29040201 China
Ministry of Science and Technology (MoST, China)2018ZX09711003 China
Ministry of Science and Technology (MoST, China)2020YFC0841400 China
National Natural Science Foundation of China (NSFC)81922044 China
CitationJournal: Nature / Year: 2020
Title: A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2.
Authors: Shi, R. / Shan, C. / Duan, X. / Chen, Z. / Liu, P. / Song, J. / Song, T. / Bi, X. / Han, C. / Wu, L. / Gao, G. / Hu, X. / Zhang, Y. / Tong, Z. / Huang, W. / Liu, W.J. / Wu, G. / Zhang, B. / ...Authors: Shi, R. / Shan, C. / Duan, X. / Chen, Z. / Liu, P. / Song, J. / Song, T. / Bi, X. / Han, C. / Wu, L. / Gao, G. / Hu, X. / Zhang, Y. / Tong, Z. / Huang, W. / Liu, W.J. / Wu, G. / Zhang, B. / Wang, L. / Qi, J. / Feng, H. / Wang, F.S. / Wang, Q. / Gao, G.F. / Yuan, Z. / Yan, J.
History
DepositionApr 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 19, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Mar 10, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description / _entity_name_com.name
Revision 1.5Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
H: CB6 heavy chain
L: CB6 light chain
B: Spike protein S1
C: CB6 heavy chain
D: CB6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,6838
Polymers149,2416
Non-polymers4422
Water0
1
A: Spike protein S1
H: CB6 heavy chain
L: CB6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8424
Polymers74,6203
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-26 kcal/mol
Surface area27090 Å2
MethodPISA
2
B: Spike protein S1
C: CB6 heavy chain
D: CB6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8424
Polymers74,6203
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-27 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.400, 106.730, 170.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein / SARS-Cov-2 Spike protein S1


Mass: 25951.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody CB6 heavy chain


Mass: 24950.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody CB6 light chain


Mass: 23718.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 24 % w/v PEG 1500, 20 % v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 36863 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 63.8 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.2
Reflection shellResolution: 2.88→2.95 Å / Num. unique obs: 2670 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Blu-Ice1.15.2_3472data collection
HKL-2000data reduction
UCSD-systemHKL-2000data processing
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LGZ, 4TSA

6lgz

4tsa


Resolution: 2.88→34.83 Å / SU ML: 0.3529 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2768
RfactorNum. reflection% reflection
Rfree0.2651 1790 4.87 %
Rwork0.2181 --
obs0.2204 36767 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 63.69 Å2
Refinement stepCycle: LAST / Resolution: 2.88→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9670 0 0 0 9670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00369906
X-RAY DIFFRACTIONf_angle_d0.776513480
X-RAY DIFFRACTIONf_chiral_restr0.04851498
X-RAY DIFFRACTIONf_plane_restr0.00431738
X-RAY DIFFRACTIONf_dihedral_angle_d22.19743580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.960.31441390.29182634X-RAY DIFFRACTION99.89
2.96-3.040.38741120.29732690X-RAY DIFFRACTION100
3.04-3.140.33211410.28612666X-RAY DIFFRACTION99.96
3.14-3.260.3171630.27612612X-RAY DIFFRACTION100
3.26-3.390.32991430.25732643X-RAY DIFFRACTION99.96
3.39-3.540.29831350.24692684X-RAY DIFFRACTION99.93
3.54-3.730.32191270.25462683X-RAY DIFFRACTION99.96
3.73-3.960.2961460.22832660X-RAY DIFFRACTION99.79
3.96-4.260.26071360.19542682X-RAY DIFFRACTION99.82
4.26-4.690.21191400.16942691X-RAY DIFFRACTION99.75
4.69-5.370.23131310.17712719X-RAY DIFFRACTION99.89
5.37-6.760.2331440.20262751X-RAY DIFFRACTION99.97
6.76-34.830.21231330.20062862X-RAY DIFFRACTION99.11
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6362888698380.05476774355660.3809189952561.25742763256-0.004378556119231.155733561680.0821418355939-0.0410054995272-0.0705532865420.232087447356-0.0267297876168-0.161094913380.003530693490670.007048336130194.9349391853E-90.382781112735-0.00832195334504-0.0147733384830.3272775448890.00532971392620.376515757416-19.6538135277-28.3406707137-21.2742774673
20.340514689379-0.162269114476-0.2066158298890.99198947292-0.5895344069181.073791588560.03366459941310.1208651784740.0235307898508-0.228560867202-0.009752091442890.05190610718960.236234956372-0.0923794346351-1.59848684794E-90.4595477663020.0335644699729-0.02605620327840.4288088978690.04059333882030.380652397699-11.3879249168-7.14385917026-73.8021523136
30.1713911858780.0793363431488-0.1466657847170.5501257012120.6923970797841.385472718720.0185685046351-0.0373947786778-0.1209148114080.0399145426509-0.0180672647963-0.01223736440620.06858466570910.108162347906-2.91322580866E-100.291895019375-0.007016813962970.02117233037740.3264050022510.03662843310610.3510665209567.212441942144.07502190234-33.4373446854
40.5436741603250.309965445150.4724176378670.6437546999880.5859603100251.434328081450.0927330811861-0.0404093142079-0.02313503568540.109660028288-0.06982453345630.0699411433452-0.0287132741097-0.160828295372-3.7309282398E-90.397545100934-0.0123041651030.03779258404450.3276863411510.008224552927220.366154441059-6.581886661813.5722468947-26.3574161521
50.775613837726-0.5493121656960.6264545491181.1058967602-0.6442034382920.756792347324-0.0687026169866-0.167046044113-0.3485410691190.04821269505820.1393680605540.2439787782820.0616180023309-0.1547879396212.90566863008E-90.3363974390230.01476653424580.0364270277120.4312680028360.03201419025990.482095452136-54.9937999707-18.4428217181-49.9435359169
60.516356008474-0.7518993398950.6682776260240.772409802581-0.1802858192250.401586933760.03189022573120.0495334716215-0.116056327675-0.155072654792-0.03151588915950.0303606110480.03195563762320.0182290994163-7.62644554844E-90.392280300508-0.0108079453750.01464275331890.4265808873250.03614392766930.354840311437-45.9097047936-7.99604789676-61.4311448059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain H
6X-RAY DIFFRACTION6chain L

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