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- PDB-7f7h: SARS-CoV-2 S protein RBD in complex with A8-1 Fab -

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Basic information

Entry
Database: PDB / ID: 7f7h
TitleSARS-CoV-2 S protein RBD in complex with A8-1 Fab
Components
  • Heavy chain of A8-1 Fab
  • Light chain of A8-1 Fab
  • Spike glycoprotein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / SARS-CoV-2 / VIRUS / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / symbiont-mediated suppression of host innate immune response / 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 / 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 / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsDou, Y. / Wang, X. / Wang, K. / Liu, P. / Lu, B.
CitationJournal: To Be Published
Title: High throughput isolation of potent neutralizing antibodies from convalescent COVID-19 patients.
Authors: Dou, Y. / Jia, Z. / Deng, Y. / Lan, J. / Liu, H.
History
DepositionJun 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain of A8-1 Fab
B: Light chain of A8-1 Fab
E: Spike glycoprotein S1
C: Heavy chain of A8-1 Fab
D: Light chain of A8-1 Fab
F: Spike glycoprotein S1


Theoretical massNumber of molelcules
Total (without water)133,1096
Polymers133,1096
Non-polymers00
Water00
1
A: Heavy chain of A8-1 Fab
B: Light chain of A8-1 Fab
E: Spike glycoprotein S1


Theoretical massNumber of molelcules
Total (without water)66,5543
Polymers66,5543
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-26 kcal/mol
Surface area26580 Å2
MethodPISA
2
C: Heavy chain of A8-1 Fab
D: Light chain of A8-1 Fab
F: Spike glycoprotein S1


Theoretical massNumber of molelcules
Total (without water)66,5543
Polymers66,5543
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-27 kcal/mol
Surface area26600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.772, 75.660, 181.544
Angle α, β, γ (deg.)90.000, 92.260, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain C and (resid 1 through 132 or (resid 138 and (name C or name O )) or resid 139 through 217))
12(chain B and resid 2 through 211)
22chain D
13(chain E and (resid 336 through 382 or resid 393 through 515))
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUPROPROchain AAA1 - 2171 - 217
211GLUGLUSERSER(chain C and (resid 1 through 132 or (resid 138 and (name C or name O )) or resid 139 through 217))CD1 - 1321 - 132
221GLYGLYGLYGLY(chain C and (resid 1 through 132 or (resid 138 and (name C or name O )) or resid 139 through 217))CD138138
231GLUGLULYSLYS(chain C and (resid 1 through 132 or (resid 138 and (name C or name O )) or resid 139 through 217))CD1 - 2181 - 218
112ILEILEARGARG(chain B and resid 2 through 211)BB2 - 2111 - 210
212ILEILEARGARGchain DDE2 - 2111 - 210
113CYSCYSVALVAL(chain E and (resid 336 through 382 or resid 393 through 515))EC336 - 3823 - 49
123THRTHRPHEPHE(chain E and (resid 336 through 382 or resid 393 through 515))EC393 - 51560 - 182
213CYSCYSPHEPHEchain FFF336 - 5153 - 182

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Heavy chain of A8-1 Fab


Mass: 23002.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Light chain of A8-1 Fab


Mass: 22969.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Spike glycoprotein S1


Mass: 20581.994 Da / Num. of mol.: 2 / Fragment: RBD domain
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

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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: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris, PEG 6000, 100mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.071 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 25319 / % possible obs: 99.23 % / Redundancy: 3.7 % / CC1/2: 0.969 / Net I/σ(I): 7.065
Reflection shellResolution: 3.19→3.304 Å / Num. unique obs: 2432 / CC1/2: 0.585

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VSB

6vsb


Resolution: 3.19→36.28 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2753 1190 4.7 %
Rwork0.2054 24112 -
obs0.2087 25302 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.13 Å2 / Biso mean: 61.3607 Å2 / Biso min: 41.68 Å2
Refinement stepCycle: final / Resolution: 3.19→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9218 0 0 0 9218
Num. residues----1204
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1842X-RAY DIFFRACTION12.806TORSIONAL
12C1842X-RAY DIFFRACTION12.806TORSIONAL
21B1919X-RAY DIFFRACTION12.806TORSIONAL
22D1919X-RAY DIFFRACTION12.806TORSIONAL
31E1500X-RAY DIFFRACTION12.806TORSIONAL
32F1500X-RAY DIFFRACTION12.806TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.19-3.340.4221340.29812910304496
3.34-3.510.32741410.252330243165100
3.51-3.730.35191480.240930133161100
3.73-4.020.29691430.217830173160100
4.02-4.420.23941590.178129913150100
4.42-5.060.24511290.153330853214100
5.06-6.370.23351410.196130313172100
6.37-36.280.25171950.20423041323699
Refinement TLS params.Method: refined / Origin x: -14.4637 Å / Origin y: 4.5365 Å / Origin z: 46.0971 Å
111213212223313233
T0.4179 Å2-0.0166 Å20.1443 Å2-0.6186 Å20.0242 Å2--0.5638 Å2
L0.017 °20.0645 °20.3876 °2-0.2873 °20.1743 °2--1.1901 °2
S-0.0913 Å °0.0742 Å °0.0406 Å °-0.0441 Å °-0.0308 Å °0.0356 Å °-0.075 Å °-0.0557 Å °0.1216 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 217
2X-RAY DIFFRACTION1allB2 - 213
3X-RAY DIFFRACTION1allE334 - 515
4X-RAY DIFFRACTION1allC1 - 218
5X-RAY DIFFRACTION1allD2 - 211
6X-RAY DIFFRACTION1allF336 - 515

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