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- PDB-8f2j: Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV... -

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Basic information

Entry
Database: PDB / ID: 8f2j
TitleCrystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain
Components
  • Spike protein S1
  • WRAIR-2134 Fab Heavy Chain
  • WRAIR-2134 Fab Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Neutralizing antibody / SARS-CoV-2 / WRAIR-2134 / receptor binding domain / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / 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 / membrane fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / 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 / membrane fusion / entry receptor-mediated virion attachment to host cell / 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 / endocytosis involved in viral entry into host cell / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 (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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus spike glycoprotein S1, receptor binding / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsSankhala, R.S. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-18-2-0040 United States
CitationJournal: To Be Published
Title: Antibody Targeting of Conserved Sites of Vulnerability on the SARS-CoV-2 Spike Receptor-Binding Domain.
Authors: Sankhala, R.S. / Dussupt, V. / Jensen, J. / Modjarrad, K. / Joyce, M.G.
History
DepositionNov 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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: WRAIR-2134 Fab Heavy Chain
B: WRAIR-2134 Fab Light Chain
D: WRAIR-2134 Fab Heavy Chain
F: WRAIR-2134 Fab Light Chain
H: WRAIR-2134 Fab Heavy Chain
I: WRAIR-2134 Fab Heavy Chain
J: WRAIR-2134 Fab Light Chain
L: WRAIR-2134 Fab Light Chain
C: Spike protein S1
E: Spike protein S1
G: Spike protein S1
K: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,56716
Polymers284,27612
Non-polymers1,2914
Water00
1
A: WRAIR-2134 Fab Heavy Chain
B: WRAIR-2134 Fab Light Chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2904
Polymers71,0693
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: WRAIR-2134 Fab Heavy Chain
F: WRAIR-2134 Fab Light Chain
G: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4934
Polymers71,0693
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: WRAIR-2134 Fab Heavy Chain
L: WRAIR-2134 Fab Light Chain
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2904
Polymers71,0693
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: WRAIR-2134 Fab Heavy Chain
J: WRAIR-2134 Fab Light Chain
K: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4934
Polymers71,0693
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.190, 154.430, 165.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody
WRAIR-2134 Fab Heavy Chain


Mass: 25186.064 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Antibody Heavy Chain Fab fragment / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
WRAIR-2134 Fab Light Chain


Mass: 22809.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Antibody Light Chain / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein
Spike protein S1


Mass: 23073.766 Da / Num. of mol.: 4 / Fragment: receptor binding domain (RBD)
Source method: isolated from a genetically manipulated source
Details: Viral protein
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#4: 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.: 2
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
#5: 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.: 2
Source method: isolated from a genetically manipulated source
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
Has ligand of interestN
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: 3.21 Å3/Da / Density % sol: 61.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 121509 / % possible obs: 99.7 % / Redundancy: 3.57 % / CC1/2: 0.99 / Rsym value: 0.149 / Net I/σ(I): 7.15
Reflection shellResolution: 3.15→3.33 Å / Mean I/σ(I) obs: 1.05 / Num. unique obs: 19496 / CC1/2: 0.428 / Rsym value: 1.43 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GGU, 6B0W, 7N4J

5ggu

6b0w

7n4j


Resolution: 3.16→19.96 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2453 2974 5.07 %
Rwork0.2088 --
obs0.2106 58671 92.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.16→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19573 0 84 0 19657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.799
X-RAY DIFFRACTIONf_dihedral_angle_d13.7487165
X-RAY DIFFRACTIONf_chiral_restr0.0513019
X-RAY DIFFRACTIONf_plane_restr0.0053542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.210.3606250.2987402X-RAY DIFFRACTION
3.21-3.270.2502841411X-RAY DIFFRACTION50
3.27-3.330.32951390.31092419X-RAY DIFFRACTION87
3.33-3.390.3671410.30322845X-RAY DIFFRACTION100
3.39-3.460.35571440.28022802X-RAY DIFFRACTION100
3.46-3.530.3191440.26622848X-RAY DIFFRACTION100
3.53-3.610.31281330.25282838X-RAY DIFFRACTION100
3.61-3.70.28191640.25422813X-RAY DIFFRACTION100
3.7-3.80.30831440.24242829X-RAY DIFFRACTION100
3.8-3.910.23971630.23022825X-RAY DIFFRACTION100
3.91-4.040.23651610.21242851X-RAY DIFFRACTION100
4.04-4.180.22721410.19992830X-RAY DIFFRACTION100
4.18-4.350.2051610.17912853X-RAY DIFFRACTION100
4.35-4.540.22861640.17162809X-RAY DIFFRACTION100
4.54-4.780.1841240.17162909X-RAY DIFFRACTION100
4.78-5.080.21781580.17682848X-RAY DIFFRACTION100
5.08-5.460.2121490.18252868X-RAY DIFFRACTION100
5.46-60.23561680.20622865X-RAY DIFFRACTION100
6-6.830.23371530.21582905X-RAY DIFFRACTION100
6.84-8.50.26791600.19412917X-RAY DIFFRACTION100
8.5-19.960.20271540.17343010X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.39471.5542-0.45282.711-0.15681.101-0.203-0.10930.389-0.130.16280.0123-0.0912-0.066800.53930.1521-0.14980.4408-0.06360.69175.33-39.32713.358
21.80411.6524-0.16343.1172-0.39381.24670.2936-0.47770.16040.7978-0.2634-0.1036-0.16470.05190.01110.89460.0759-0.12420.7008-0.14110.635111.468-41.25829.809
31.5236-0.0078-0.09621.81590.80631.0129-0.0638-0.31620.0750.00560.0097-0.2638-0.00770.20720.02750.4774-0.0105-0.1070.51410.06460.4714-24.4073.40616.781
41.6424-0.3873-0.37132.5485-0.04730.6116-0.0717-0.229-0.06910.1401-0.0499-0.00920.02860.07660.07490.48370.0258-0.13420.44010.04340.3598-38.3-1.87924.317
52.0131-1.351-0.21942.6340.7270.7998-0.13250.1633-0.1087-0.03340.02360.15460.1339-0.00440.06050.5186-0.07550.03860.39760.02330.4142-37.438-38.07767.897
61.6944-0.72160.59513.0113-1.08010.90140.0966-0.2653-0.28760.0078-0.00670.53750.0354-0.1937-0.00670.48280.02390.08120.5498-0.03840.5407-78.761-1.91814.91
71.6127-0.42050.34892.612-0.70590.8351-0.1355-0.1532-0.20610.24620.0920.1964-0.0147-0.11550.03420.44590.04770.05540.48590.00120.4478-65.3193.84222.863
81.2071-1.2590.07842.73830.1191.11230.13390.6566-0.0192-0.505-0.22070.06630.191-0.20520.04320.6812-0.06740.00960.66980.10320.4309-33.832-35.87650.684
93.36231.2690.68572.78160.24392.07050.2827-0.3061-0.8621.3261-0.07140.48640.3616-0.2413-0.1231.0828-0.09980.1080.60220.02780.9067-20.858-77.28221.106
102.6777-2.16020.15724.21860.02721.7606-0.12320.36071.11530.35570.04290.0541-0.5894-0.2994-0.06020.7860.1334-0.15880.45560.1941.114-63.7810.79565.721
112.20140.46281.06713.72690.82443.4268-0.28020.1468-0.096-0.17880.2970.2056-0.21110.1637-0.03450.5580.00260.10090.37420.04620.8262-30.163-39.925-2.598
122.17420.6717-0.65612.78790.24132.885-0.20.11390.0885-0.38710.1367-0.00170.0745-0.10950.02760.42410.0752-0.10940.4148-0.00770.561-70.17139.909-7.947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:229 )A1 - 229
2X-RAY DIFFRACTION2( CHAIN B AND RESID 10:220 )B10 - 220
3X-RAY DIFFRACTION3( CHAIN D AND RESID 1:231 )D1 - 231
4X-RAY DIFFRACTION4( CHAIN F AND RESID 10:220 )F10 - 220
5X-RAY DIFFRACTION5( CHAIN H AND RESID 1:231 )H1 - 231
6X-RAY DIFFRACTION6( CHAIN I AND RESID 1:230 )I1 - 230
7X-RAY DIFFRACTION7( CHAIN J AND RESID 9:220 )J9 - 220
8X-RAY DIFFRACTION8( CHAIN L AND RESID 10:220 )L10 - 220
9X-RAY DIFFRACTION9( CHAIN C AND ( RESID 334:532 OR RESID 601:601 ) )C334 - 532
10X-RAY DIFFRACTION9( CHAIN C AND ( RESID 334:532 OR RESID 601:601 ) )C601
11X-RAY DIFFRACTION10( CHAIN E AND ( RESID 334:531 OR RESID 601:601 ) )E334 - 531
12X-RAY DIFFRACTION10( CHAIN E AND ( RESID 334:531 OR RESID 601:601 ) )E601
13X-RAY DIFFRACTION11( CHAIN G AND RESID 334:529 )G334 - 529
14X-RAY DIFFRACTION12( CHAIN K AND RESID 333:529 )K333 - 529

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