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- PDB-7n4m: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7n4m
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2151.
Components
  • Spike protein S1
  • WRAIR-2151 antibody Fab heavy chain
  • WRAIR-2151 antibody Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Neutralizing antibody / SARS-CoV-2 / WRAIR-2151 / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.79 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 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 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
H: WRAIR-2151 antibody Fab heavy chain
A: Spike protein S1
L: WRAIR-2151 antibody Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7234
Polymers70,2993
Non-polymers4241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Complex eluted as a homogenous species on the Superdex-200 column.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.913, 112.913, 239.508
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody WRAIR-2151 antibody Fab heavy chain


Mass: 24015.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: 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
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#3: Antibody WRAIR-2151 antibody Fab light chain


Mass: 23209.432 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 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
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: 5.43 Å3/Da / Density % sol: 77.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.57→119.75 Å / Num. obs: 35105 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.99 / Rpim(I) all: 0.06 / Rsym value: 0.2 / Net I/σ(I): 13
Reflection shellResolution: 3.57→3.78 Å / Redundancy: 13.2 % / Num. unique obs: 5627 / CC1/2: 0.14 / % possible all: 98.3

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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: 5xwd, 4rir

5xwd

4rir


Resolution: 3.79→19.994 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3168 774 4.99 %
Rwork0.2575 14724 -
obs0.2604 15498 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 431.26 Å2 / Biso mean: 200.6336 Å2 / Biso min: 95.57 Å2
Refinement stepCycle: final / Resolution: 3.79→19.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 28 0 4170
Biso mean--303.17 --
Num. residues----537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024291
X-RAY DIFFRACTIONf_angle_d0.55859
X-RAY DIFFRACTIONf_chiral_restr0.041641
X-RAY DIFFRACTIONf_plane_restr0.003751
X-RAY DIFFRACTIONf_dihedral_angle_d12.8392518
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.79-4.02570.3511000.3019205583
4.0257-4.33360.33661290.27222473100
4.3336-4.76440.26581300.23962486100
4.7644-5.44160.28891360.24752494100
5.4416-6.81050.32661300.27072551100
6.8105-100.33021490.2512665100
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)
16.2385.70171.33546.25-1.70165.92491.0847-4.3485-0.5627-1.3222-1.9351-1.3213-1.48910.2397-0.16511.9335-0.14710.00341.7913-0.58341.5666-10.139-14.20647.776
25.77357.3553-4.42568.4522-5.92974.2247-0.3072-1.18030.7934-0.1433-1.0316-0.05660.22541.1331.55171.351-0.0382-0.06031.6469-0.14821.4346-9.12-21.14343.893
37.6563-1.6959-1.14868.0489-2.67893.8144-0.5016-0.4060.55040.68870.0826-0.8138-0.8657-2.073-0.17420.96810.2012-0.01261.5726-0.0721.3254-14.687-17.08635.447
45.45170.341-2.35078.1524-1.21042.99720.80810.02190.11180.97610.62421.1884-0.25561.2403-1.1541.0490.0135-0.0681.7471-0.32481.3851-8.899-25.4837.823
53.7112.52162.18717.54280.51276.3527-0.8847-1.08112.0864-0.46530.05561.4582-0.126-0.70590.85971.15650.1667-0.14491.3491-0.17791.2013-12.848-14.70138.553
63.90190.0888-4.09513.71550.84684.75652.8183-2.82071.4436-0.38970.98493.07732.69774.9518-2.74961.61190.0310.20512.0688-0.10471.5464-34.064-46.4736.896
74.97942.24760.35724.3822-2.9243.04981.2005-1.2466-4.0583-1.46381.09090.31091.4734-1.2324-2.27011.8130.0196-0.08742.3081-0.11191.3275-36.714-44.52117.998
87.0031-1.720.83334.41711.80737.2820.0347-0.44270.45640.29490.2147-0.5196-0.1475-0.3114-0.17541.03850.1090.08331.49310.08011.2601-37.218-34.41126.595
97.9596-0.2397-2.39798.17794.50358.37270.13732.229-0.6617-1.7938-0.2916-0.7135-1.0193-0.70410.34971.2216-0.1697-0.11261.8663-0.26671.7922-38.574-39.9976.883
103.7832-5.5305-2.75438.27113.30772.68241.060.5603-0.593-0.52840.33920.3687-0.62650.2231-1.4421.25130.0490.01671.7119-0.06151.4947-52.898-388.553
115.15943.70323.93130.4681-0.34625.5618-0.42560.7787-0.65-0.38840.3128-0.3960.2751.58870.23641.13840.27220.19481.3894-0.25971.2656-38.681-37.4728.238
129.723-5.25326.09214.0912-3.19273.5852-1.7587-4.07062.5876-2.12770.9393-1.03471.5172-1.18990.40991.99840.30990.74862.3123-0.10181.7421-43.285-39.57745.497
136.3909-1.68022.93623.1042-5.07458.4934-1.1328-0.54931.7832-1.78110.0082-3.1269-0.07840.20421.00211.68210.1251-0.24821.20480.65522.0531-23.238-11.23222.384
149.2765-5.8627-0.67213.78690.9213.8163-3.5569-0.7084.18023.64081.32950.7384-1.4363-2.97512.83241.83250.2922-0.5122.7998-0.5013.4481-36.2494.02831.185
151.4905-1.9115-3.04162.17351.7676.9169-0.53222.21470.7557-2.9635-1.8479-0.67221.0219-1.9431.62520.74710.3062-0.48982.11870.33092.0705-29.976-15.69323.405
161.4979-0.13990.23258.20233.39362.98220.28822.804-1.49640.5479-0.27430.0279-0.38991.06220.70311.0868-0.0774-0.09471.5282-0.44291.2673-26.348-9.4437.608
173.2933-3.5797-6.61725.28088.07782.0270.7295-1.77495.08071.8233-0.5746-0.56521.5692-1.2314-0.71021.30040.4653-0.17982.7491-0.38971.9877-36.787-14.08538.624
183.59365.3137-0.58062.00252.6532.6186-0.5977-1.67962.6273-2.16330.5436-0.6459-2.8336-4.52331.62671.55791.257-0.11582.6117-0.79173.0028-37.721-11.50328.842
192.2514-2.7472-1.61043.83892.18151.81212.4131-0.11690.7414-4.3656-1.5791-2.0171-3.5233-2.80210.14771.78780.8722-0.35441.7929-0.38142.9042-34.97-11.27223.878
204.96252.89543.32743.63130.06464.1399-3.7369-3.73790.9242-0.19611.2783-2.6266-1.6463-4.5612.3621.71020.5946-0.3362.6826-0.94933.2041-33.781.12138.977
214.3827-1.9289-3.08954.28474.28834.8525-2.5588-3.73761.26130.87124.1271-2.38020.63383.3595-0.54781.22340.5378-0.21111.6783-0.0381.4537-24.85-12.51531.124
222.50872.5273-1.90254.2511-3.66913.6111-1.05660.3982.0512-1.701-0.1103-3.03570.63751.4941.33771.20010.23490.03351.6718-0.10261.4622-21.144-17.8827.735
236.35291.7153-3.64192.47980.89463.81542.35152.81581.5176-2.1471-0.81552.2767-4.4069-6.60320.57242.17680.9535-0.55032.86320.05063.5162-29.8425.47233.127
249.77798.41755.699.04966.75854.21210.4721-3.5572-1.2033-0.8785-0.09460.2707-1.149-1.7771-0.31712.36940.4861-1.01872.3865-0.89123.0974-16.85418.60247.164
256.76361.633-5.50177.1242-1.83974.72564.0839-2.3076-1.88462.0559-2.24331.662-5.7009-0.4908-1.43413.20770.24880.66722.77830.54342.09653.87117.96453.001
265.8935-5.71645.48685.8534-5.62965.35690.07381.11925.6589-1.09541.2413-0.0286-3.03732.3851-3.24122.24370.57440.19543.8974-1.16323.4584-17.22316.02444.978
275.4411-2.0422-1.68518.0541-3.20538.76497.4253-0.3607-0.32126.7214-4.57891.3590.8793-0.3733-1.43623.60040.20670.10342.0105-0.70373.8885-14.11921.15738.468
281.76430.4864-5.6761.9819-2.48367.36352.73180.69492.21938.55950.8746-1.05360.8791.92083.61155.9720.7618-1.32411.92582.6523-1.8616-2.45126.86540.254
295.0972-4.3095-4.29723.8244.1295.42041.0112-0.4638-3.25580.7587-4.02035.2403-1.22940.58751.99121.8188-0.2299-0.99513.1002-1.35913.3198-17.8768.62841.281
301.9934-1.369-0.13384.005-3.56163.26520.5062-0.8726-1.9874-0.69323.55995.1038-0.59871.2563-0.05452.34111.5736-2.05425.0186-0.95883.1623-17.10412.22342.121
311.4689-1.1253-2.7650.5811.96394.7431-0.5235-0.8744-0.2555-1.3841-1.11030.0871-2.5082-3.40152.33252.76440.3174-0.32423.44150.17193.9638-2.33425.8446.634
323.72474.51960.55227.408-2.35083.1058-0.39675.92044.48261.0043-2.05691.85833.49552.56831.11112.711-0.0530.09543.8053-0.39552.8532-12.93527.23446.986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 2:11 )H2 - 11
2X-RAY DIFFRACTION2( CHAIN H AND RESID 12:34 )H12 - 34
3X-RAY DIFFRACTION3( CHAIN H AND RESID 35:54 )H35 - 54
4X-RAY DIFFRACTION4( CHAIN H AND RESID 55:84 )H55 - 84
5X-RAY DIFFRACTION5( CHAIN H AND RESID 85:122 )H85 - 122
6X-RAY DIFFRACTION6( CHAIN A AND RESID 331:342 )A331 - 342
7X-RAY DIFFRACTION7( CHAIN A AND RESID 343:353 )A343 - 353
8X-RAY DIFFRACTION8( CHAIN A AND RESID 354:442 )A354 - 442
9X-RAY DIFFRACTION9( CHAIN A AND RESID 443:459 )A443 - 459
10X-RAY DIFFRACTION10( CHAIN A AND RESID 460:479 )A460 - 479
11X-RAY DIFFRACTION11( CHAIN A AND RESID 480:516 )A480 - 516
12X-RAY DIFFRACTION12( CHAIN A AND RESID 517:532 )A517 - 532
13X-RAY DIFFRACTION13( CHAIN L AND RESID 1:8 )L1 - 8
14X-RAY DIFFRACTION14( CHAIN L AND RESID 9:18 )L9 - 18
15X-RAY DIFFRACTION15( CHAIN L AND RESID 19:32 )L19 - 32
16X-RAY DIFFRACTION16( CHAIN L AND RESID 33:48 )L33 - 48
17X-RAY DIFFRACTION17( CHAIN L AND RESID 49:61 )L49 - 61
18X-RAY DIFFRACTION18( CHAIN L AND RESID 62:66 )L62 - 66
19X-RAY DIFFRACTION19( CHAIN L AND RESID 67:75 )L67 - 75
20X-RAY DIFFRACTION20( CHAIN L AND RESID 76:84 )L76 - 84
21X-RAY DIFFRACTION21( CHAIN L AND RESID 85:91 )L85 - 91
22X-RAY DIFFRACTION22( CHAIN L AND RESID 92:102 )L92 - 102
23X-RAY DIFFRACTION23( CHAIN L AND RESID 103:108 )L103 - 108
24X-RAY DIFFRACTION24( CHAIN L AND RESID 109:122 )L109 - 122
25X-RAY DIFFRACTION25( CHAIN L AND RESID 123:134 )L123 - 134
26X-RAY DIFFRACTION26( CHAIN L AND RESID 135:140 )L135 - 140
27X-RAY DIFFRACTION27( CHAIN L AND RESID 141:151 )L141 - 151
28X-RAY DIFFRACTION28( CHAIN L AND RESID 152:161 )L152 - 161
29X-RAY DIFFRACTION29( CHAIN L AND RESID 162:171 )L162 - 171
30X-RAY DIFFRACTION30( CHAIN L AND RESID 172:177 )L172 - 177
31X-RAY DIFFRACTION31( CHAIN L AND RESID 178:198 )L178 - 198
32X-RAY DIFFRACTION32( CHAIN L AND RESID 199:211 )L199 - 211

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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