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- PDB-7xei: SARS-CoV-2-prototyped-RBD and CB6-092-Fab complex -

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Basic information

Entry
Database: PDB / ID: 7xei
TitleSARS-CoV-2-prototyped-RBD and CB6-092-Fab complex
Components
  • CB6-092-Fab heavy chain
  • CB6-092-Fab light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / complex / antibody / receptor / IMMUNE SYSTEM / 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 / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsWang, Y. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171274 China
CitationJournal: To Be Published
Title: SARS-CoV-2-prototyped-RBD and CB6-092-Fab complex
Authors: Wang, Y. / Feng, Y.
History
DepositionMar 31, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike protein S1
B: Spike protein S1
C: CB6-092-Fab heavy chain
D: CB6-092-Fab light chain
E: CB6-092-Fab heavy chain
F: CB6-092-Fab light chain


Theoretical massNumber of molelcules
Total (without water)148,8126
Polymers148,8126
Non-polymers00
Water00
1
A: Spike protein S1
C: CB6-092-Fab heavy chain
D: CB6-092-Fab light chain


Theoretical massNumber of molelcules
Total (without water)74,4063
Polymers74,4063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-29 kcal/mol
Surface area27000 Å2
MethodPISA
2
B: Spike protein S1
E: CB6-092-Fab heavy chain
F: CB6-092-Fab light chain


Theoretical massNumber of molelcules
Total (without water)74,4063
Polymers74,4063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-32 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.046, 112.197, 101.741
Angle α, β, γ (deg.)90.000, 100.900, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 333 through 527)
21chain B
12chain C
22(chain E and (resid 1 through 136 or resid 139 through 218))
13chain D
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
111THRTHRPROPRO(chain A and resid 333 through 527)AA333 - 52715 - 209
211THRTHRPROPROchain BBB333 - 52715 - 209
112GLUGLUGLUGLUchain CCC1 - 2181 - 218
212GLUGLUSERSER(chain E and (resid 1 through 136 or resid 139 through 218))EE1 - 1361 - 136
222GLYGLYGLUGLU(chain E and (resid 1 through 136 or resid 139 through 218))EE139 - 218139 - 218
113ASPASPGLUGLUchain DDD1 - 2151 - 215
213ASPASPGLUGLUchain FFF1 - 2151 - 215

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Spike protein S1


Mass: 25763.961 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 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody CB6-092-Fab heavy chain


Mass: 25044.105 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: Antibody CB6-092-Fab light chain


Mass: 23598.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 3.27 Å3/Da / Density % sol: 62.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: Ammonium nitrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.76→74.61 Å / Num. obs: 41517 / % possible obs: 91.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 53.46 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.1
Reflection shellResolution: 2.76→2.91 Å / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4309

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C01

7c01


Resolution: 2.76→49.95 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2629 2011 4.85 %
Rwork0.2153 39460 -
obs0.2176 41471 91.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.76 Å2 / Biso mean: 61.5672 Å2 / Biso min: 29.82 Å2
Refinement stepCycle: final / Resolution: 2.76→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9648 0 0 0 9648
Num. residues----1255
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1178X-RAY DIFFRACTION4.827TORSIONAL
12B1178X-RAY DIFFRACTION4.827TORSIONAL
21C1294X-RAY DIFFRACTION4.827TORSIONAL
22E1294X-RAY DIFFRACTION4.827TORSIONAL
31D1298X-RAY DIFFRACTION4.827TORSIONAL
32F1298X-RAY DIFFRACTION4.827TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.76-2.830.41891380.32352932307096
2.83-2.910.32741700.28342941311196
2.91-2.990.33221380.26722961309996
2.99-3.090.3671660.26832984315098
3.09-3.20.30231310.26623068319998
3.2-3.330.30321520.24832983313598
3.33-3.480.3152850.2471650173554
3.48-3.660.30181390.23682534267383
3.66-3.890.28091230.24012386250977
3.89-4.190.28391530.20332890304394
4.19-4.620.23551650.16572943310896
4.62-5.280.19161480.16853043319198
5.28-6.650.23461450.19533060320598
6.66-49.950.20591580.1953085324398
Refinement TLS params.Method: refined / Origin x: 29.6898 Å / Origin y: -19.5424 Å / Origin z: 12.5092 Å
111213212223313233
T0.2535 Å20.0247 Å20.0479 Å2-0.4025 Å2-0.0399 Å2--0.5061 Å2
L0.2872 °2-0.0103 °2-0.0401 °2-0.157 °2-0.0109 °2--0.2744 °2
S-0.0104 Å °-0.0721 Å °0.0034 Å °0.0537 Å °-0.0112 Å °-0.0037 Å °-0.0342 Å °-0.0239 Å °0.0351 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA333 - 528
2X-RAY DIFFRACTION1allB333 - 527
3X-RAY DIFFRACTION1allC1 - 218
4X-RAY DIFFRACTION1allD1 - 215
5X-RAY DIFFRACTION1allE1 - 218
6X-RAY DIFFRACTION1allF1 - 215

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