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- PDB-7n4j: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7n4j
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2173.
Components
  • Spike protein S1
  • WRAIR-2173 antibody Fab heavy chain
  • WRAIR-2173 antibody Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Neutralizing antibody / SARS-CoV-2 / WRAIR-2173 / receptor binding domain / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / 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 / 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 / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.207 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: Nat.Immunol. / Year: 2021
Title: Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations.
Authors: Dussupt, V. / Sankhala, R.S. / Mendez-Rivera, L. / Townsley, S.M. / Schmidt, F. / Wieczorek, L. / Lal, K.G. / Donofrio, G.C. / Tran, U. / Jackson, N.D. / Zaky, W.I. / Zemil, M. / Tritsch, S. ...Authors: Dussupt, V. / Sankhala, R.S. / Mendez-Rivera, L. / Townsley, S.M. / Schmidt, F. / Wieczorek, L. / Lal, K.G. / Donofrio, G.C. / Tran, U. / Jackson, N.D. / Zaky, W.I. / Zemil, M. / Tritsch, S.R. / Chen, W.H. / Martinez, E.J. / Ahmed, A. / Choe, M. / Chang, W.C. / Hajduczki, A. / Jian, N. / Peterson, C.E. / Rees, P.A. / Rutkowska, M. / Slike, B.M. / Selverian, C.N. / Swafford, I. / Teng, I.T. / Thomas, P.V. / Zhou, T. / Smith, C.J. / Currier, J.R. / Kwong, P.D. / Rolland, M. / Davidson, E. / Doranz, B.J. / Mores, C.N. / Hatziioannou, T. / Reiley, W.W. / Bieniasz, P.D. / Paquin-Proulx, D. / Gromowski, G.D. / Polonis, V.R. / Michael, N.L. / Modjarrad, K. / Joyce, M.G. / Krebs, S.J.
History
DepositionJun 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 15, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 23, 2022Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 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: Spike protein S1
H: WRAIR-2173 antibody Fab heavy chain
L: WRAIR-2173 antibody Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8434
Polymers71,2573
Non-polymers5871
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Complex migrated as a homogenous species on the Superdex-200 gel-filtration column.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.255, 70.460, 107.255
Angle α, β, γ (deg.)90.000, 98.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Spike protein S1


Mass: 23073.766 Da / Num. of mol.: 1 / 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
#2: Antibody WRAIR-2173 antibody Fab heavy chain


Mass: 25308.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody WRAIR-2173 antibody Fab light chain


Mass: 22874.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.09M NPS (Sodium nitrate, Sodium phosphate dibasic, Ammonium sulfate), 0.1M buffer system 3 (Tris base and BICINE, pH 8.5), 50% precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 34103 / % possible obs: 99.2 % / Redundancy: 6.4 % / CC1/2: 0.95 / Rpim(I) all: 0.06 / Rsym value: 0.14 / Net I/σ(I): 10.6
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 3364 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5w6c

5w6c


Resolution: 2.207→44.403 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 1686 5 %
Rwork0.172 32025 -
obs0.1738 33711 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.63 Å2 / Biso mean: 43.9268 Å2 / Biso min: 12.1 Å2
Refinement stepCycle: final / Resolution: 2.207→44.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4957 0 39 281 5277
Biso mean--90.54 42.15 -
Num. residues----652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035141
X-RAY DIFFRACTIONf_angle_d0.7037029
X-RAY DIFFRACTIONf_chiral_restr0.047786
X-RAY DIFFRACTIONf_plane_restr0.005900
X-RAY DIFFRACTIONf_dihedral_angle_d13.173053
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.207-2.27180.28951380.2063236888
2.2718-2.34520.25971300.2007267098
2.3452-2.4290.24681410.1884269799
2.429-2.52620.22891430.1904266199
2.5262-2.64120.24851400.1943264898
2.6412-2.78040.21841410.1844271599
2.7804-2.95460.25881440.1873268999
2.9546-3.18260.19221340.1772267798
3.1826-3.50280.19511440.16572729100
3.5028-4.00940.19091460.1583271899
4.0094-5.05020.16971450.1403271098
5.0502-100.18821400.1772274398
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)
11.2999-1.06180.13121.54950.89695.3920.5844-1.7275-0.27691.156-0.5382-0.20270.51941.153-0.28610.7157-0.3383-0.07581.0010.11450.3074-26.247-6.025233.9718
20.33730.09610.09560.2581-0.03040.11830.6722-2.12261.24921.7512-0.7842-0.3233-0.87050.9882-0.43351.3621-0.69630.07941.3459-0.43610.2721-29.39284.13939.7476
33.30340.8767-0.84921.94110.39373.89740.2676-0.45180.45340.3681-0.15430.3652-0.3074-0.0636-0.00640.2882-0.03520.07010.1581-0.03350.293-37.7789-2.097921.0287
45.82961.20892.59626.53791.83936.73960.1560.25850.0013-0.1133-0.14430.62860.3726-0.72180.02280.195-0.05920.01640.24760.04650.2778-44.543-12.14096.6851
52.7985-0.3590.6172.70940.73632.6350.3249-1.21840.30781.1421-0.27360.3621-0.1143-0.02510.03080.6884-0.28640.16830.6444-0.14580.2985-30.67681.352832.8959
64.8613-3.57475.0863.2042-4.40627.33760.2060.5491-1.0786-0.66290.294-0.09250.7030.1147-0.35750.43890.08060.02010.2039-0.00090.4104-27.8634-20.8065-14.6248
72.3993-0.56630.69283.2408-1.14172.98350.0050.3175-0.1787-0.1453-0.0260.05410.2609-0.07370.04260.18380.0062-0.02930.1794-0.03090.2441-36.9096-15.9527-14.0803
82.27050.3005-0.77547.8147-5.55854.7563-0.05620.0859-0.1993-0.00710.1240.12350.2547-0.2672-0.34630.1605-0.0099-0.04250.1467-0.00470.2914-39.6433-14.2425-3.8715
94.579-2.10310.27217.7424-0.77233.9760.080.3737-0.3858-0.2987-0.06550.40590.3115-0.3530.00970.1763-0.0264-0.02630.2087-0.03560.2416-42.5376-17.522-10.0922
100.97680.6232-0.98030.73540.19712.0519-0.0270.2825-0.1436-0.12710.11660.06730.05560.1085-0.08130.22180.0302-0.02920.09930.02360.2419-34.4836-11.6015-8.7244
110.83280.2820.3030.85451.06436.18220.05280.0788-0.09070.0096-0.0171-0.02750.4233-0.27020.03030.17370.0232-0.02640.12070.01570.2101-32.4915-11.0879-8.6627
125.11643.0703-3.01253.1275-4.43767.1368-0.160.3927-0.1585-0.32340.4844-0.20510.17590.1113-0.09760.5935-0.1552-0.10170.6253-0.07810.4116-47.2415-9.5865-39.2412
135.2913-1.5635-0.69511.6396-1.98494.53280.3370.73660.1578-0.326-0.34780.0832-0.1768-0.7691-0.03960.46790.01180.05860.3964-0.06860.2093-41.77637.8018-45.9044
142.68343.40621.37124.42.17443.1449-1.0772.84670.9054-3.30091.0382-1.8233-0.2791.08770.01991.8341-0.10910.21431.0635-0.02861.3337-34.486324.4494-45.1373
158.58874.862-5.0673.6724-5.08838.26040.21110.96050.4573-0.14450.1290.0542-0.4710.0966-0.36570.4328-0.04820.03320.42930.00330.3174-36.91149.5418-43.6582
163.8719-1.00920.47350.2677-0.11370.4469-0.02810.4586-1.3612-1.52430.1549-0.58220.92550.02820.60390.74080.11470.22510.2839-0.2060.2833-35.0718-2.3392-44.8587
171.9843-0.14170.23932.2943.68856.04370.21460.40960.0954-0.8758-0.0984-0.768-0.20580.7758-0.36430.81670.04180.36770.4143-0.07710.605-25.34087.0498-47.7855
188.22997.1549-6.9617.1379-5.25126.59240.04640.73450.5066-0.40920.21080.20030.2477-0.6818-0.19690.25360.029-0.01630.27380.02910.2863-38.89660.0511-34.1811
194.52232.8754-1.70056.0788-3.79075.66750.26610.35930.1411-0.382-0.2135-0.0974-0.28910.5301-0.10750.36190.00510.11250.3717-0.05480.217-33.67758.3228-43.2082
202.2491-0.09091.15037.00612.03461.2442-0.48770.9435-0.2951-1.74490.5006-0.47490.677-0.10530.1440.7635-0.00240.1320.5903-0.15080.3319-36.28392.564-52.0053
218.04841.50270.65351.96451.92391.9949-0.68421.15420.8541-0.96470.32181.3185-0.3668-0.49060.38760.7094-0.0139-0.04180.53460.05410.5051-40.876915.7844-52.3517
221.8040.5613-0.51961.6365-1.52014.71460.03750.17820.1150.02170.0193-0.0446-0.08570.3202-0.05390.14020.0028-0.02660.16580.01230.2396-23.78242.5808-9.6924
234.0673-1.5867-0.01022.4424-0.53373.50850.1270.4672-0.0591-0.1372-0.26330.0444-0.18160.21340.11960.2426-0.00040.02050.2262-0.02010.1703-38.93313.3952-32.3348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 331 through 353 )A331 - 353
2X-RAY DIFFRACTION2chain 'A' and (resid 354 through 394 )A354 - 394
3X-RAY DIFFRACTION3chain 'A' and (resid 395 through 479 )A395 - 479
4X-RAY DIFFRACTION4chain 'A' and (resid 480 through 494 )A480 - 494
5X-RAY DIFFRACTION5chain 'A' and (resid 495 through 532 )A495 - 532
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 8 )H1 - 8
7X-RAY DIFFRACTION7chain 'H' and (resid 9 through 46 )H9 - 46
8X-RAY DIFFRACTION8chain 'H' and (resid 47 through 61 )H47 - 61
9X-RAY DIFFRACTION9chain 'H' and (resid 62 through 84 )H62 - 84
10X-RAY DIFFRACTION10chain 'H' and (resid 85 through 108 )H85 - 108
11X-RAY DIFFRACTION11chain 'H' and (resid 109 through 130 )H109 - 130
12X-RAY DIFFRACTION12chain 'H' and (resid 131 through 136 )H131 - 136
13X-RAY DIFFRACTION13chain 'H' and (resid 137 through 144 )H137 - 144
14X-RAY DIFFRACTION14chain 'H' and (resid 145 through 151 )H145 - 151
15X-RAY DIFFRACTION15chain 'H' and (resid 152 through 162 )H152 - 162
16X-RAY DIFFRACTION16chain 'H' and (resid 163 through 174 )H163 - 174
17X-RAY DIFFRACTION17chain 'H' and (resid 175 through 182 )H175 - 182
18X-RAY DIFFRACTION18chain 'H' and (resid 183 through 192 )H183 - 192
19X-RAY DIFFRACTION19chain 'H' and (resid 193 through 205 )H193 - 205
20X-RAY DIFFRACTION20chain 'H' and (resid 206 through 227 )H206 - 227
21X-RAY DIFFRACTION21chain 'H' and (resid 228 through 233 )H228 - 233
22X-RAY DIFFRACTION22chain 'L' and (resid 1 through 119 )L1 - 119
23X-RAY DIFFRACTION23chain 'L' and (resid 120 through 216 )L120 - 216

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