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- PDB-7l7d: Crystal structure of SARS-CoV-2 spike RBD in complex with human m... -

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Basic information

Entry
Database: PDB / ID: 7l7d
TitleCrystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibody AZD8895
Components
  • Spike protein S1
  • heavy chain of human monoclonal antibody Fab AZD8895
  • light chain of human monoclonal antibody Fab AZD8895
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / spike protein / receptor binding domain / human monoclonal antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
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: 2.5 Å
AuthorsDong, J. / Crowe, J.E.
CitationJournal: Nat Microbiol / Year: 2021
Title: Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail.
Authors: Dong, J. / Zost, S.J. / Greaney, A.J. / Starr, T.N. / Dingens, A.S. / Chen, E.C. / Chen, R.E. / Case, J.B. / Sutton, R.E. / Gilchuk, P. / Rodriguez, J. / Armstrong, E. / Gainza, C. / Nargi, ...Authors: Dong, J. / Zost, S.J. / Greaney, A.J. / Starr, T.N. / Dingens, A.S. / Chen, E.C. / Chen, R.E. / Case, J.B. / Sutton, R.E. / Gilchuk, P. / Rodriguez, J. / Armstrong, E. / Gainza, C. / Nargi, R.S. / Binshtein, E. / Xie, X. / Zhang, X. / Shi, P.Y. / Logue, J. / Weston, S. / McGrath, M.E. / Frieman, M.B. / Brady, T. / Tuffy, K.M. / Bright, H. / Loo, Y.M. / McTamney, P.M. / Esser, M.T. / Carnahan, R.H. / Diamond, M.S. / Bloom, J.D. / Crowe Jr., J.E.
History
DepositionDec 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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

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Assembly

Deposited unit
H: heavy chain of human monoclonal antibody Fab AZD8895
L: light chain of human monoclonal antibody Fab AZD8895
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,74710
Polymers71,9743
Non-polymers7747
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-28 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.118, 81.583, 101.157
Angle α, β, γ (deg.)90.00, 94.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody heavy chain of human monoclonal antibody Fab AZD8895


Mass: 24100.277 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 light chain of human monoclonal antibody Fab AZD8895


Mass: 23644.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules E

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


Mass: 24229.189 Da / Num. of mol.: 1 / Fragment: receptor binding domain (UNP residues 330-529)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#5: 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 natural 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

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Non-polymers , 2 types, 225 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 16% PEG3350, 0.2 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 17, 2020
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→43.98 Å / Num. obs: 24896 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 19.2
Reflection shellResolution: 2.5→2.63 Å / Rmerge(I) obs: 0.245 / Num. unique obs: 3598

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6XC2

6xc2


Resolution: 2.5→43.98 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1232 4.95 %
Rwork0.1846 --
obs0.1869 24875 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 50 220 5064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034955
X-RAY DIFFRACTIONf_angle_d0.5636730
X-RAY DIFFRACTIONf_dihedral_angle_d16.304703
X-RAY DIFFRACTIONf_chiral_restr0.043737
X-RAY DIFFRACTIONf_plane_restr0.004869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.31521060.25062643X-RAY DIFFRACTION99
2.6-2.720.34041450.25782583X-RAY DIFFRACTION100
2.72-2.860.27281440.23832600X-RAY DIFFRACTION100
2.86-3.040.26951350.2242602X-RAY DIFFRACTION100
3.04-3.270.26771520.21592608X-RAY DIFFRACTION100
3.27-3.60.22921330.1872642X-RAY DIFFRACTION100
3.6-4.130.20921320.16782638X-RAY DIFFRACTION100
4.13-5.190.18131370.13662643X-RAY DIFFRACTION100
5.2-43.980.20481480.16492684X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.4857 Å / Origin y: 15.6466 Å / Origin z: 53.4486 Å
111213212223313233
T0.1859 Å2-0.0393 Å2-0.0557 Å2-0.2393 Å20.0642 Å2--0.3286 Å2
L0.8354 °2-0.5098 °2-0.5137 °2-0.6809 °20.7017 °2--1.3552 °2
S-0.0049 Å °-0.0451 Å °-0.0546 Å °0.0382 Å °-0.0038 Å °0.0112 Å °0.0451 Å °-0.1573 Å °0.0167 Å °
Refinement TLS groupSelection details: all

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