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- PDB-7xeg: SARS-CoV-2-Beta-RBD and CB6-092-Fab complex -

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Basic information

Entry
Database: PDB / ID: 7xeg
TitleSARS-CoV-2-Beta-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 / membrane fusion / Attachment and Entry / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 ...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 / 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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-Beta-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)148,8816
Polymers148,8816
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)74,4403
Polymers74,4403
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-32 kcal/mol
Surface area27010 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)74,4403
Polymers74,4403
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-30 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.248, 113.236, 102.098
Angle α, β, γ (deg.)90.000, 100.577, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

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
111THRTHRGLYGLY(chain 'A' and resid 333 through 527)AA333 - 52615 - 208
221THRTHRGLYGLYchain 'B'BB333 - 52615 - 208
132GLUGLUVALVALchain 'C'CC1 - 2171 - 217
242GLUGLUVALVALchain 'E'EE1 - 2171 - 217
153ASPASPGLYGLYchain 'D'DD1 - 2141 - 214
263ASPASPGLYGLYchain 'F'FF1 - 2141 - 214

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Spike protein S1


Mass: 25798.023 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: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: Tris pH 8.0, PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 47674 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 42.83 Å2 / Rmerge(I) obs: 0.189 / Net I/σ(I): 10
Reflection shellResolution: 2.69→2.79 Å / Rmerge(I) obs: 0.863 / Num. unique obs: 3714

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C01

7c01


Resolution: 2.69→39.24 Å / SU ML: 0.338 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.3596
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2476 2384 5.01 %
Rwork0.195 45239 -
obs0.1977 47623 95.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.39 Å2
Refinement stepCycle: LAST / Resolution: 2.69→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9667 0 0 0 9667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00429907
X-RAY DIFFRACTIONf_angle_d0.840313485
X-RAY DIFFRACTIONf_chiral_restr0.05461489
X-RAY DIFFRACTIONf_plane_restr0.00541739
X-RAY DIFFRACTIONf_dihedral_angle_d19.08991371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.750.3556940.28251958X-RAY DIFFRACTION70.64
2.75-2.810.31581180.25792317X-RAY DIFFRACTION83.99
2.81-2.870.29751180.2522580X-RAY DIFFRACTION92.24
2.87-2.950.28881320.26222641X-RAY DIFFRACTION96.12
2.95-3.030.3481460.26072710X-RAY DIFFRACTION97.67
3.03-3.110.33561550.2462654X-RAY DIFFRACTION96.1
3.11-3.210.29811370.23152727X-RAY DIFFRACTION98.72
3.22-3.330.31281270.22982792X-RAY DIFFRACTION99.83
3.33-3.460.27131500.21982760X-RAY DIFFRACTION99.69
3.46-3.620.27681410.21332770X-RAY DIFFRACTION99.86
3.62-3.810.24861610.19212765X-RAY DIFFRACTION99.8
3.81-4.050.25191440.17462733X-RAY DIFFRACTION98.87
4.05-4.360.20581630.15692727X-RAY DIFFRACTION98.84
4.36-4.80.18631460.13952768X-RAY DIFFRACTION99.9
4.8-5.490.17911360.15012783X-RAY DIFFRACTION99.83
5.49-6.910.21831510.18792789X-RAY DIFFRACTION98.99
6.92-39.240.21211650.17792765X-RAY DIFFRACTION97.57
Refinement TLS params.Method: refined / Origin x: -10.3390393107 Å / Origin y: -19.6317354866 Å / Origin z: 12.6760251475 Å
111213212223313233
T0.194260767474 Å20.0290405739327 Å2-0.00464168643058 Å2-0.17819479947 Å2-0.0178118396489 Å2--0.204846997737 Å2
L0.23488836746 °2-0.00968004197918 °2-0.0568494290775 °2-0.159101628446 °20.00453987209935 °2--0.253254043057 °2
S-0.0129501442776 Å °-0.0255483148035 Å °-0.00741652954901 Å °0.0288841475813 Å °-0.0198991002613 Å °-0.00677944870391 Å °-0.0182759331933 Å °-0.0276161953763 Å °0.0298002498933 Å °
Refinement TLS groupSelection details: all

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