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- PDB-7n4i: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7n4i
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2057.
Components
  • (WRAIR-2057 Antibody Fab ...) x 2
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Neutralizing antibody / SARS-CoV-2 / WRAIR-2057 / 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: 2.284 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 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 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
H: WRAIR-2057 Antibody Fab Heavy Chain
L: WRAIR-2057 Antibody Fab Light Chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2256
Polymers70,4553
Non-polymers7713
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Homogenous migration over the Superdex-200 gel-filtration coulm.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.931, 73.931, 149.176
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody WRAIR-2057 Antibody Fab Heavy Chain


Mass: 24108.049 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: Antibody WRAIR-2057 Antibody Fab Light Chain


Mass: 23272.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules C

#3: 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
#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

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Non-polymers , 2 types, 253 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 36098 / % possible obs: 99.3 % / Redundancy: 5.1 % / CC1/2: 0.99 / Rpim(I) all: 0.05 / Rsym value: 0.1 / Net I/σ(I): 19
Reflection shellResolution: 2.28→2.46 Å / Num. unique obs: 3406 / CC1/2: 0.87

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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: 4zd3

4zd3


Resolution: 2.284→19.871 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 1800 5 %
Rwork0.1999 34188 -
obs0.2018 35988 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 388.49 Å2 / Biso mean: 60.7314 Å2 / Biso min: 17.82 Å2
Refinement stepCycle: final / Resolution: 2.284→19.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4850 0 105 251 5206
Biso mean--166.52 46.36 -
Num. residues----632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055042
X-RAY DIFFRACTIONf_angle_d0.7556867
X-RAY DIFFRACTIONf_chiral_restr0.052759
X-RAY DIFFRACTIONf_plane_restr0.006875
X-RAY DIFFRACTIONf_dihedral_angle_d11.6822999
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2841-2.34520.30661300.2365246393
2.3452-2.41410.28911400.23742641100
2.4141-2.49190.32311400.24092632100
2.4919-2.58080.29271410.23822613100
2.5808-2.68390.32421410.24322666100
2.6839-2.80570.29761350.23422615100
2.8057-2.95320.2821360.24462658100
2.9532-3.13750.25981360.23132642100
3.1375-3.37870.26181410.20982662100
3.3787-3.71670.22171390.19942631100
3.7167-4.250.21541380.1742632100
4.25-5.33730.15991430.14662670100
5.3373-100.21541400.18962663100
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)
12.90230.20910.09936.395.91479.7047-0.16350.8494-0.8359-0.9521-0.0061-0.06090.24350.4186-0.09730.62150.2480.02910.7949-0.27990.774112.867-3.536-7.581
20.7987-0.20790.13441.61370.4021.89110.19790.4562-0.7093-0.160.1178-0.60740.89550.3761-0.28140.76770.1743-0.15040.5847-0.27690.84888.68-9.594-2.926
33.33581.8725-1.09341.57180.13771.3556-0.8949-0.3579-1.02490.56860.6258-0.85110.37740.18980.28461.21040.2262-0.22870.6237-0.1691.03743.453-20.71-5.422
43.401-0.0170.53061.85930.77682.36240.17920.2636-0.52130.21620.1636-0.36290.63640.4303-0.28970.39940.1177-0.140.3148-0.09090.40944.8811.5287.512
55.4291-1.27361.13876.1323-2.33825.4116-0.00970.11040.16330.1384-0.0891-0.0935-0.50760.30150.02650.31550.0622-0.03560.3566-0.03010.3252-3.91723.20817.571
61.94390.131-0.35481.75410.40111.04190.03520.3871-0.6901-0.28760.4021-0.510.44110.6133-0.40040.52990.1917-0.13520.4812-0.15850.63347.407-4.0981.611
77.3913-2.65331.41223.24850.24712.98090.27670.28580.3067-0.3645-0.1480.17670.2303-0.248-0.07220.2406-0.0172-0.05170.27830.01090.1612-24.6136.197-15.094
82.50510.62481.62882.3738-0.19042.645-0.02490.0592-0.15940.10930.1448-0.04020.1529-0.1382-0.09150.2166-0.03360.01160.2159-0.00970.1866-18.0517.402-4.301
94.6152-1.2796-1.63348.68023.01559.4505-0.481-0.7552-0.32110.98280.42540.78560.22280.112-0.07360.3736-0.04140.0920.3919-0.01610.3214-28.8998.242.018
102.15760.68110.6471.59040.26491.7511-0.1130.1142-0.06730.06920.1955-0.00920.1822-0.1255-0.04190.286-0.00390.02830.2440.00810.2295-21.0528.342-7.323
112.7641.1159-0.044.1784-0.72233.1930.07690.06850.17630.0470.27790.5783-0.0946-0.4967-0.30470.24020.0114-0.04440.37250.00330.2381-41.65132.267-34.24
120.53840.176-0.42453.051-0.14871.35420.2392-0.1794-0.2701-0.2726-0.0772-0.00250.17970.0173-0.15280.3465-0.0152-0.08930.44570.05260.3011-34.08325.287-32.193
133.69222.7104-1.68234.1299-1.0242.57680.3817-0.3279-0.23510.4639-0.33940.1609-0.2716-0.25270.01650.3537-0.0532-0.06170.40060.04280.3575-37.3125.503-25.506
141.4902-0.51240.25392.2146-5.77145.39880.0086-0.0424-0.0486-0.1773-0.0596-0.03890.0547-0.1895-0.03710.43310.0211-0.05860.428-0.04330.2375-35.94826.922-39.57
152.0941.94611.85272.003-4.71375.75290.93560.6001-0.399-1.7181-0.84731.1044-0.2192-0.0928-0.11490.52920.0779-0.13170.58920.13620.3918-41.28725.22-40.346
166.70245.32-8.46622.07362.01642.16780.06640.58740.22860.11280.12820.9831-0.4604-0.8723-0.23550.36350.08160.00370.3490.03890.3179-21.66127.5383.922
172.03191.2762-2.30914.3612-5.00686.7751-0.0677-0.1090.33490.33460.0493-0.1296-0.90910.24230.01480.2857-0.0254-0.06180.2397-0.00770.3117-13.89137.126-6.571
181.04630.08830.41871.2161.08572.1579-0.0682-0.05360.03770.138-0.02660.0944-0.0429-0.1856-0.00650.29160.059-0.01610.24710.00280.2289-13.19424.3152.397
192.08143.57728.70642.51222.8015.5091-0.43850.53210.5056-0.10830.06120.4877-0.02310.63590.46170.2684-0.0278-0.02180.3353-0.03640.2988-13.31321.909-11.831
201.2069-0.3422-2.41530.3813-1.069.4296-0.04850.25520.23810.0349-0.1092-0.36940.73680.55680.21280.32490.0527-0.00290.36570.06210.2651-2.89824.401-5.522
215.11783.1765-6.67053.8559-5.03922.0413-0.01940.00810.47250.14320.2043-0.0807-0.03660.396-0.05360.3163-0.0305-0.11410.3720.02870.3248-8.84731.7620.783
222.57411.0854-0.51393.5313-1.93073.2672-0.26680.18180.0949-0.06920.1655-0.0753-0.1717-0.07840.07240.29270.0152-0.04040.251-0.0160.2483-12.10729.75-10.455
234.9582-1.313.34463.388-1.53419.02-0.0716-0.0585-0.0597-0.1652-0.3354-0.05560.720.030.40290.1880.02420.04260.187-0.02370.2549-18.89221.0153.135
241.8187-5.64843.57951.94731.91531.9788-0.24580.55090.69180.6360.37590.4967-0.54380.0606-0.33560.295-0.0460.0560.3730.1020.3316-18.27838.68-16.92
252.34695.9893.1935.31890.89634.2871-0.12250.83330.48890.15340.18740.3241-0.3504-0.08580.13790.39610.0576-0.0080.3324-0.03990.401-37.50340.39-26.188
262.01895.5863-3.06832.0242-6.99612.00911.10340.764-2.0669-1.38470.08331.55171.3937-1.1724-0.89650.5865-0.1277-0.22941.0105-0.04370.7718-53.19524.958-31.364
272.44083.23030.60941.8047-1.12842.1569-0.1051-0.3561-0.12520.09110.0950.1138-0.1327-0.2843-0.17570.30690.0356-0.02980.36830.00430.2666-37.64437.686-19.712
282.1602-3.2262-3.95551.79171.40551.46540.2716-1.2750.14040.04620.23640.0192-0.5048-0.1598-0.31960.49390.10120.01240.73330.04870.3226-45.08134.278-15.22
292.23052.15160.92993.25660.42041.33390.03960.08390.0319-0.00340.06670.20750.0147-0.4743-0.15620.2853-0.0191-0.02120.51770.12130.2578-36.20233.061-22.989
302.32467.8572.06058.91561.39014.71250.4336-1.31961.81750.0438-0.66161.15820.0407-0.78220.22680.34440.10920.0340.5559-0.10850.3772-44.78742.51-18.989
312.01761.71134.11785.68461.55718.025-0.3855-0.47910.4814-0.03480.38380.2375-0.0102-0.51580.05450.47510.225-0.01480.78350.02220.3391-49.33442.56-25.484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 334:349 )C334 - 349
2X-RAY DIFFRACTION2( CHAIN C AND RESID 350:380 )C350 - 380
3X-RAY DIFFRACTION3( CHAIN C AND RESID 381:393 )C381 - 393
4X-RAY DIFFRACTION4( CHAIN C AND RESID 394:474 )C394 - 474
5X-RAY DIFFRACTION5( CHAIN C AND RESID 475:487 )C475 - 487
6X-RAY DIFFRACTION6( CHAIN C AND RESID 488:532 )C488 - 532
7X-RAY DIFFRACTION7( CHAIN H AND RESID 1:17 )H1 - 17
8X-RAY DIFFRACTION8( CHAIN H AND RESID 18:60 )H18 - 60
9X-RAY DIFFRACTION9( CHAIN H AND RESID 61:69 )H61 - 69
10X-RAY DIFFRACTION10( CHAIN H AND RESID 70:122 )H70 - 122
11X-RAY DIFFRACTION11( CHAIN H AND RESID 123:144 )H123 - 144
12X-RAY DIFFRACTION12( CHAIN H AND RESID 145:174 )H145 - 174
13X-RAY DIFFRACTION13( CHAIN H AND RESID 175:193 )H175 - 193
14X-RAY DIFFRACTION14( CHAIN H AND RESID 194:212 )H194 - 212
15X-RAY DIFFRACTION15( CHAIN H AND RESID 213:221 )H213 - 221
16X-RAY DIFFRACTION16( CHAIN L AND RESID 1:7 )L1 - 7
17X-RAY DIFFRACTION17( CHAIN L AND RESID 8:25 )L8 - 25
18X-RAY DIFFRACTION18( CHAIN L AND RESID 26:38 )L26 - 38
19X-RAY DIFFRACTION19( CHAIN L AND RESID 39:48 )L39 - 48
20X-RAY DIFFRACTION20( CHAIN L AND RESID 49:61 )L49 - 61
21X-RAY DIFFRACTION21( CHAIN L AND RESID 62:75 )L62 - 75
22X-RAY DIFFRACTION22( CHAIN L AND RESID 76:90 )L76 - 90
23X-RAY DIFFRACTION23( CHAIN L AND RESID 91:102 )L91 - 102
24X-RAY DIFFRACTION24( CHAIN L AND RESID 103:108 )L103 - 108
25X-RAY DIFFRACTION25( CHAIN L AND RESID 109:121 )L109 - 121
26X-RAY DIFFRACTION26( CHAIN L AND RESID 122:128 )L122 - 128
27X-RAY DIFFRACTION27( CHAIN L AND RESID 129:150 )L129 - 150
28X-RAY DIFFRACTION28( CHAIN L AND RESID 151:163 )L151 - 163
29X-RAY DIFFRACTION29( CHAIN L AND RESID 164:186 )L164 - 186
30X-RAY DIFFRACTION30( CHAIN L AND RESID 187:204 )L187 - 204
31X-RAY DIFFRACTION31( CHAIN L AND RESID 205:212 )L205 - 212

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