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- PDB-8gf2: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 8gf2
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies eCR3022.20 and CC12.3
Components
  • (eCR3022.20 Fab ...) x 2
  • CC12.3 Fab heavy chain
  • CC12.3 Fab light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Antibody / SARS-CoV-2 / SARS-CoV / Coronavirus / Spike / IMMUNE SYSTEM / 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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / 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 / membrane / identical protein binding / 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: 2.851 Å
AuthorsYuan, M. / Zhu, X. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI132317 United States
Bill & Melinda Gates FoundationOPP1170236 United States
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Sci.Signal. / Year: 2023
Title: Broadening a SARS-CoV-1-neutralizing antibody for potent SARS-CoV-2 neutralization through directed evolution.
Authors: Zhao, F. / Yuan, M. / Keating, C. / Shaabani, N. / Limbo, O. / Joyce, C. / Woehl, J. / Barman, S. / Burns, A. / Tran, Q. / Zhu, X. / Ricciardi, M. / Peng, L. / Smith, J. / Huang, D. / ...Authors: Zhao, F. / Yuan, M. / Keating, C. / Shaabani, N. / Limbo, O. / Joyce, C. / Woehl, J. / Barman, S. / Burns, A. / Tran, Q. / Zhu, X. / Ricciardi, M. / Peng, L. / Smith, J. / Huang, D. / Briney, B. / Sok, D. / Nemazee, D. / Teijaro, J.R. / Wilson, I.A. / Burton, D.R. / Jardine, J.G.
History
DepositionMar 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
C: CC12.3 Fab heavy chain
D: CC12.3 Fab light chain
H: eCR3022.20 Fab heavy chain
L: eCR3022.20 Fab light chain
B: Spike protein S1
E: CC12.3 Fab heavy chain
F: CC12.3 Fab light chain
X: eCR3022.20 Fab heavy chain
Y: eCR3022.20 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,18012
Polymers241,53410
Non-polymers6462
Water00
1
A: Spike protein S1
C: CC12.3 Fab heavy chain
D: CC12.3 Fab light chain
H: eCR3022.20 Fab heavy chain
L: eCR3022.20 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9886
Polymers120,7675
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-56 kcal/mol
Surface area45740 Å2
MethodPISA
2
B: Spike protein S1
E: CC12.3 Fab heavy chain
F: CC12.3 Fab light chain
X: eCR3022.20 Fab heavy chain
Y: eCR3022.20 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,1916
Polymers120,7675
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-55 kcal/mol
Surface area46310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.570, 161.220, 230.117
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 334 through 445 or resid 449 through 528 or resid 529))
12chain C
22(chain E and (resid 1 through 128 or resid 134 through 214))
13(chain D and (resid 2 or resid 4 through 8...
23(chain F and (resid 2 or resid 4 through 8...
33(chain L and (resid 2 or resid 4 through 8...
43(chain Y and (resid 2 or resid 4 through 8...
14(chain H and (resid 1 through 129 or resid 135 through 215))
24(chain X and resid 1 through 215)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA334 - 528
211(chain B and (resid 334 through 445 or resid 449 through 528 or resid 529))B334 - 445
221(chain B and (resid 334 through 445 or resid 449 through 528 or resid 529))B449 - 528
231(chain B and (resid 334 through 445 or resid 449 through 528 or resid 529))B529
112chain CC1 - 214
212(chain E and (resid 1 through 128 or resid 134 through 214))E1 - 128
222(chain E and (resid 1 through 128 or resid 134 through 214))E134 - 214
113(chain D and (resid 2 or resid 4 through 8...D2
123(chain D and (resid 2 or resid 4 through 8...D4 - 8
133(chain D and (resid 2 or resid 4 through 8...D11
143(chain D and (resid 2 or resid 4 through 8...D14
153(chain D and (resid 2 or resid 4 through 8...D16 - 20
163(chain D and (resid 2 or resid 4 through 8...D1 - 211
173(chain D and (resid 2 or resid 4 through 8...D26 - 42
183(chain D and (resid 2 or resid 4 through 8...D1 - 211
193(chain D and (resid 2 or resid 4 through 8...D5
1103(chain D and (resid 2 or resid 4 through 8...D78
1113(chain D and (resid 2 or resid 4 through 8...D81 - 82
1123(chain D and (resid 2 or resid 4 through 8...D84 - 9
1133(chain D and (resid 2 or resid 4 through 8...D1 - 211
1143(chain D and (resid 2 or resid 4 through 8...D97 - 103
1153(chain D and (resid 2 or resid 4 through 8...D105 - 211
213(chain F and (resid 2 or resid 4 through 8...F2
223(chain F and (resid 2 or resid 4 through 8...F4 - 8
233(chain F and (resid 2 or resid 4 through 8...F11
243(chain F and (resid 2 or resid 4 through 8...F14
253(chain F and (resid 2 or resid 4 through 8...F16 - 20
263(chain F and (resid 2 or resid 4 through 8...F1 - 213
273(chain F and (resid 2 or resid 4 through 8...F26 - 42
283(chain F and (resid 2 or resid 4 through 8...F1 - 213
293(chain F and (resid 2 or resid 4 through 8...F5
2103(chain F and (resid 2 or resid 4 through 8...F78
2113(chain F and (resid 2 or resid 4 through 8...F81 - 82
2123(chain F and (resid 2 or resid 4 through 8...F84 - 9
2133(chain F and (resid 2 or resid 4 through 8...F1 - 213
2143(chain F and (resid 2 or resid 4 through 8...F97 - 103
2153(chain F and (resid 2 or resid 4 through 8...F105 - 211
313(chain L and (resid 2 or resid 4 through 8...L2
323(chain L and (resid 2 or resid 4 through 8...L4 - 8
333(chain L and (resid 2 or resid 4 through 8...L11
343(chain L and (resid 2 or resid 4 through 8...L1
353(chain L and (resid 2 or resid 4 through 8...L26 - 27
363(chain L and (resid 2 or resid 4 through 8...L1 - 215
373(chain L and (resid 2 or resid 4 through 8...L27
383(chain L and (resid 2 or resid 4 through 8...L1 - 215
393(chain L and (resid 2 or resid 4 through 8...L44 - 42
3103(chain L and (resid 2 or resid 4 through 8...L51 - 52
3113(chain L and (resid 2 or resid 4 through 8...L57
3123(chain L and (resid 2 or resid 4 through 8...L76
3133(chain L and (resid 2 or resid 4 through 8...L81 - 82
3143(chain L and (resid 2 or resid 4 through 8...L1 - 215
3153(chain L and (resid 2 or resid 4 through 8...L84 - 91
3163(chain L and (resid 2 or resid 4 through 8...L95
3173(chain L and (resid 2 or resid 4 through 8...L97 - 10
3183(chain L and (resid 2 or resid 4 through 8...L105 - 211
413(chain Y and (resid 2 or resid 4 through 8...Y2
423(chain Y and (resid 2 or resid 4 through 8...Y4 - 8
433(chain Y and (resid 2 or resid 4 through 8...Y11
443(chain Y and (resid 2 or resid 4 through 8...Y1
453(chain Y and (resid 2 or resid 4 through 8...Y26 - 27
463(chain Y and (resid 2 or resid 4 through 8...Y1 - 214
473(chain Y and (resid 2 or resid 4 through 8...Y27
483(chain Y and (resid 2 or resid 4 through 8...Y1 - 214
493(chain Y and (resid 2 or resid 4 through 8...Y44 - 42
4103(chain Y and (resid 2 or resid 4 through 8...Y51 - 52
4113(chain Y and (resid 2 or resid 4 through 8...Y57
4123(chain Y and (resid 2 or resid 4 through 8...Y76
4133(chain Y and (resid 2 or resid 4 through 8...Y81 - 82
4143(chain Y and (resid 2 or resid 4 through 8...Y1 - 214
4153(chain Y and (resid 2 or resid 4 through 8...Y84 - 91
4163(chain Y and (resid 2 or resid 4 through 8...Y95
4173(chain Y and (resid 2 or resid 4 through 8...Y97 - 10
4183(chain Y and (resid 2 or resid 4 through 8...Y105 - 211
114(chain H and (resid 1 through 129 or resid 135 through 215))H1 - 129
124(chain H and (resid 1 through 129 or resid 135 through 215))H135 - 215
214(chain X and resid 1 through 215)X1 - 215

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Spike protein S1


Mass: 26095.348 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: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2

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Antibody , 4 types, 8 molecules CEDFHXLY

#2: Antibody CC12.3 Fab heavy chain


Mass: 23377.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody CC12.3 Fab light chain


Mass: 23431.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#4: Antibody eCR3022.20 Fab heavy chain


Mass: 23480.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody eCR3022.20 Fab light chain


Mass: 24382.021 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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Sugars , 2 types, 2 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: 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: obtained synthetically / 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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Details

Has ligand of interestN

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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: 3.03 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate - citric acid buffer pH 5.0, 15% (v/v) ethylene glycol, 1 M lithium chloride, and 10% (w/v) polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 67940 / % possible obs: 99.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.062 / Rrim(I) all: 0.158 / Χ2: 0.791 / Net I/σ(I): 4.7 / Num. measured all: 434051
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.96.41.06134180.660.4521.1550.38499.9
2.9-2.956.70.88133650.7240.3670.9560.39699.9
2.95-3.016.80.77333650.8020.3180.8370.402100
3.01-3.076.90.64633720.8550.2640.6980.41699.9
3.07-3.1470.52434050.8930.2130.5660.426100
3.14-3.216.80.43633660.9240.1790.4720.44399.9
3.21-3.296.70.36334050.9380.150.3930.46499.8
3.29-3.386.60.29233660.9520.1230.3170.51899.9
3.38-3.485.30.26833470.9280.1280.2980.74498.8
3.48-3.595.80.18933960.9770.0840.2070.63599.5
3.59-3.724.90.18833040.9540.0930.2110.87997.3
3.72-3.876.70.15833820.9840.0650.1710.71899.2
3.87-4.045.90.1432450.9640.0630.1541.02194.9
4.04-4.266.80.11134020.9910.0460.120.96699.8
4.26-4.526.60.09734210.9920.0410.1051.16499.8
4.52-4.876.40.08734240.9930.0380.0951.299.9
4.87-5.365.70.0834320.9940.0360.0881.1699.4
5.36-6.146.80.08334180.9940.0340.091.08599.8
6.14-7.736.90.07635020.9950.0310.0831.17399.9
7.73-5060.05836050.9970.0250.0631.80399.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6xc7

6xc7


Resolution: 2.851→46.827 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 3440 5.07 %
Rwork0.209 64412 -
obs0.2111 67852 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.73 Å2 / Biso mean: 59.969 Å2 / Biso min: 26.06 Å2
Refinement stepCycle: final / Resolution: 2.851→46.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16244 0 42 0 16286
Biso mean--84.76 --
Num. residues----2118
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1170X-RAY DIFFRACTION6.794TORSIONAL
12B1170X-RAY DIFFRACTION6.794TORSIONAL
21C1278X-RAY DIFFRACTION6.794TORSIONAL
22E1278X-RAY DIFFRACTION6.794TORSIONAL
31D1988X-RAY DIFFRACTION6.794TORSIONAL
32F1988X-RAY DIFFRACTION6.794TORSIONAL
33L1988X-RAY DIFFRACTION6.794TORSIONAL
34Y1988X-RAY DIFFRACTION6.794TORSIONAL
41H1288X-RAY DIFFRACTION6.794TORSIONAL
42X1288X-RAY DIFFRACTION6.794TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.851-2.88970.36691340.3157250496
2.8897-2.93090.32271540.2962532100
2.9309-2.97470.30311360.28442586100
2.9747-3.02110.33531390.28152552100
3.0211-3.07070.41521200.2932578100
3.0707-3.12360.36861200.29432626100
3.1236-3.18040.33561560.27632511100
3.1804-3.24150.3291490.2722587100
3.2415-3.30770.3011440.25952561100
3.3077-3.37960.29291380.25132567100
3.3796-3.45820.3131210.2619255799
3.4582-3.54460.28111440.2462256699
3.5446-3.64040.29671270.2314258999
3.6404-3.74750.27721400.2296251997
3.7475-3.86840.27281320.2276255699
3.8684-4.00660.25781140.2154241993
4.0066-4.16690.28461280.19422628100
4.1669-4.35650.22491450.17522583100
4.3565-4.5860.20341460.1542565100
4.586-4.8730.19111370.14222627100
4.873-5.24880.20411490.1457257499
5.2488-5.77610.1761470.16412619100
5.7761-6.610.21771080.18032668100
6.61-8.32020.21341520.18852649100
8.3202-46.8270.2091600.1985268998
Refinement TLS params.Method: refined / Origin x: 6.171 Å / Origin y: -50.4832 Å / Origin z: -28.0993 Å
111213212223313233
T0.3585 Å20.0286 Å20.0056 Å2-0.3499 Å20.0194 Å2--0.2736 Å2
L0.1429 °20.1109 °2-0.0559 °2-0.1815 °2-0.0819 °2--0.0814 °2
S-0.0036 Å °0.0158 Å °0.0165 Å °-0.0382 Å °0.0201 Å °-0.0162 Å °0.0333 Å °0.0097 Å °-0.0006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA334 - 528
2X-RAY DIFFRACTION1allA529
3X-RAY DIFFRACTION1allC1 - 214
4X-RAY DIFFRACTION1allD1 - 211
5X-RAY DIFFRACTION1allH1 - 215
6X-RAY DIFFRACTION1allL1 - 215
7X-RAY DIFFRACTION1allB334 - 528
8X-RAY DIFFRACTION1allB529 - 530
9X-RAY DIFFRACTION1allE1 - 216
10X-RAY DIFFRACTION1allF1 - 213
11X-RAY DIFFRACTION1allX1 - 216
12X-RAY DIFFRACTION1allY1 - 214

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