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- PDB-7dk2: Crystal structure of SARS-CoV-2 Spike RBD in complex with MW07 Fab -

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Basic information

Entry
Database: PDB / ID: 7dk2
TitleCrystal structure of SARS-CoV-2 Spike RBD in complex with MW07 Fab
Components
  • MW07 heavy chain
  • MW07 light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / SARS-CoV-2 / Spike / RBD / Antibody / ADE / VIRUS / IMMUNE SYSTEM-VIRAL PROTEIN 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 / symbiont-mediated-mediated suppression 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 / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / 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 / 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 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 / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / 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: 3 Å
AuthorsWang, J. / Jiao, S. / Wang, R. / Zhang, J. / Zhang, M. / Wang, M. / Chen, S.
Citation
Journal: To Be Published
Title: Architectural versatility of spike neutralization by a SARS-CoV-2 antibody
Authors: Sun, Y. / Liu, F.J. / Guo, H.T. / Wang, J. / Wang, R. / Zhang, M. / Wang, M. / Chen, S.
#1: Journal: To Be Published
Title: Antibody-dependent enhancement (ADE) of SARS-CoV-2 infection requires FcgammaRIIB-mediated uptake of virus-antibody complex with bivalent interaction
Authors: Wang, J. / Jiao, S. / Wang, R.
History
DepositionNov 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: 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
Revision 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: MW07 heavy chain
B: MW07 light chain
C: Spike protein S1
D: MW07 heavy chain
E: MW07 light chain
F: Spike protein S1
G: MW07 heavy chain
H: MW07 light chain
I: Spike protein S1
J: MW07 heavy chain
K: MW07 light chain
L: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,03316
Polymers289,14812
Non-polymers8854
Water2,540141
1
A: MW07 heavy chain
B: MW07 light chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5084
Polymers72,2873
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-33 kcal/mol
Surface area27350 Å2
MethodPISA
2
D: MW07 heavy chain
E: MW07 light chain
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5084
Polymers72,2873
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-29 kcal/mol
Surface area27340 Å2
MethodPISA
3
G: MW07 heavy chain
H: MW07 light chain
I: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5084
Polymers72,2873
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-29 kcal/mol
Surface area27100 Å2
MethodPISA
4
J: MW07 heavy chain
K: MW07 light chain
L: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5084
Polymers72,2873
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-30 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.730, 102.810, 163.420
Angle α, β, γ (deg.)90.000, 107.160, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 1 through 221)
21(chain D and resid 1 through 221)
31chain G
41chain J
12(chain B and resid 1 through 213)
22chain E
32(chain H and resid 1 through 213)
42(chain K and resid 1 through 213)
13(chain C and (resid 336 through 524 or resid 601))
23(chain F and (resid 336 through 524 or resid 601))
33chain I
43(chain L and (resid 336 through 524 or resid 601))

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
111GLUGLULYSLYS(chain A and resid 1 through 221)AA1 - 2211 - 221
211GLUGLULYSLYS(chain D and resid 1 through 221)DD1 - 2211 - 221
311GLUGLULYSLYSchain GGG1 - 2211 - 221
411GLUGLULYSLYSchain JJJ1 - 2211 - 221
112ASPASPGLUGLU(chain B and resid 1 through 213)BB1 - 2131 - 213
212ASPASPGLUGLUchain EEE1 - 2131 - 213
312ASPASPGLUGLU(chain H and resid 1 through 213)HH1 - 2131 - 213
412ASPASPGLUGLU(chain K and resid 1 through 213)KK1 - 2131 - 213
113CYSCYSVALVAL(chain C and (resid 336 through 524 or resid 601))CC336 - 52418 - 206
123NAGNAGNAGNAG(chain C and (resid 336 through 524 or resid 601))CM601
213CYSCYSVALVAL(chain F and (resid 336 through 524 or resid 601))FF336 - 52418 - 206
223NAGNAGNAGNAG(chain F and (resid 336 through 524 or resid 601))FN601
313CYSCYSVALVALchain III336 - 52418 - 206
413CYSCYSVALVAL(chain L and (resid 336 through 524 or resid 601))LL336 - 52418 - 206
423NAGNAGNAGNAG(chain L and (resid 336 through 524 or resid 601))LP601

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody
MW07 heavy chain


Mass: 23867.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
MW07 light chain


Mass: 23296.830 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein
Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 25122.336 Da / Num. of mol.: 4 / Fragment: Receptor Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DTC2
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% (w/v) polyethylene glycol 20000, 100 mM MES, pH 6.5, and 0.01 M TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 70845 / % possible obs: 98.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.092 / Rrim(I) all: 0.22 / Χ2: 1.109 / Net I/σ(I): 4 / Num. measured all: 381223
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.115.50.9870130.7480.4461.0810.94198.6
3.11-3.235.40.73770210.8470.3390.8151.04898.7
3.23-3.385.20.56670790.880.2680.6291.03598.7
3.38-3.565.10.50170980.9250.2380.5571.08298.6
3.56-3.785.60.4270540.9190.190.4631.2298.5
3.78-4.075.50.25269810.980.1140.2781.14197.9
4.07-4.485.20.15470860.990.0720.1711.21798.3
4.48-5.135.50.12670810.990.0570.1391.17798.3
5.13-6.465.50.11870880.9910.0540.131.09898.3
6.46-505.40.07873440.9970.0380.0871.12699.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG, 6JJP

6lzg

6jjp


Resolution: 3→46.468 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3039 3437 4.87 %
Rwork0.2577 67160 -
obs0.26 70597 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.15 Å2 / Biso mean: 49.9434 Å2 / Biso min: 6.42 Å2
Refinement stepCycle: final / Resolution: 3→46.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19262 0 56 141 19459
Biso mean--89.37 23.38 -
Num. residues----2503
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4107X-RAY DIFFRACTION9.067TORSIONAL
12D4107X-RAY DIFFRACTION9.067TORSIONAL
13G4107X-RAY DIFFRACTION9.067TORSIONAL
14J4107X-RAY DIFFRACTION9.067TORSIONAL
21B4036X-RAY DIFFRACTION9.067TORSIONAL
22E4036X-RAY DIFFRACTION9.067TORSIONAL
23H4036X-RAY DIFFRACTION9.067TORSIONAL
24K4036X-RAY DIFFRACTION9.067TORSIONAL
31C2743X-RAY DIFFRACTION9.067TORSIONAL
32F2743X-RAY DIFFRACTION9.067TORSIONAL
33I2743X-RAY DIFFRACTION9.067TORSIONAL
34L2743X-RAY DIFFRACTION9.067TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.04110.38121330.3423222182
3.0411-3.08460.38791360.3508270098
3.0846-3.13060.39571530.3337271899
3.1306-3.17950.40131490.3279263699
3.1795-3.23160.37131450.3268268499
3.2316-3.28730.42461390.3196270199
3.2873-3.34710.36261360.3092272299
3.3471-3.41140.37521320.308272798
3.4114-3.4810.34941550.308266799
3.481-3.55670.32971310.2903273098
3.5567-3.63940.37221150.3275270199
3.6394-3.73040.40141370.3558266598
3.7304-3.83120.36931270.2931269698
3.8312-3.94390.32711300.2527270498
3.9439-4.07110.30461320.2627268598
4.0711-4.21650.25281280.2283271598
4.2165-4.38520.24931380.1975270098
4.3852-4.58460.2061300.1899268798
4.5846-4.82610.22381150.1928274998
4.8261-5.12810.24871200.1884274199
5.1281-5.52350.22521820.197265598
5.5235-6.07830.24491440.2096271698
6.0783-6.95530.27561280.2193274899
6.9553-8.75330.23131470.2195277599
8.7533-46.4680.28461550.2324271796

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