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

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Basic information

Entry
Database: PDB / ID: 8fah
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with SARS-CoV-2 reactive human antibody CR3022
Components
  • CR3022 Fab heavy chain
  • CR3022 Fab light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / viral protein / immune system / human antibody / SARS-CoV-2 / VIRAL PROTEIN-IMMUNE SYSTEM 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.22 Å
AuthorsSankhala, R.S. / Jensen, J.L. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-18-2-0040 United States
CitationJournal: Structure / Year: 2024
Title: Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain.
Authors: Sankhala, R.S. / Dussupt, V. / Chen, W.H. / Bai, H. / Martinez, E.J. / Jensen, J.L. / Rees, P.A. / Hajduczki, A. / Chang, W.C. / Choe, M. / Yan, L. / Sterling, S.L. / Swafford, I. / Kuklis, ...Authors: Sankhala, R.S. / Dussupt, V. / Chen, W.H. / Bai, H. / Martinez, E.J. / Jensen, J.L. / Rees, P.A. / Hajduczki, A. / Chang, W.C. / Choe, M. / Yan, L. / Sterling, S.L. / Swafford, I. / Kuklis, C. / Soman, S. / King, J. / Corbitt, C. / Zemil, M. / Peterson, C.E. / Mendez-Rivera, L. / Townsley, S.M. / Donofrio, G.C. / Lal, K.G. / Tran, U. / Green, E.C. / Smith, C. / de Val, N. / Laing, E.D. / Broder, C.C. / Currier, J.R. / Gromowski, G.D. / Wieczorek, L. / Rolland, M. / Paquin-Proulx, D. / van Dyk, D. / Britton, Z. / Rajan, S. / Loo, Y.M. / McTamney, P.M. / Esser, M.T. / Polonis, V.R. / Michael, N.L. / Krebs, S.J. / Modjarrad, K. / Joyce, M.G.
History
DepositionNov 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CR3022 Fab heavy chain
L: CR3022 Fab light chain
A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4464
Polymers71,0213
Non-polymers4241
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-36 kcal/mol
Surface area30710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.176, 151.176, 192.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Antibody CR3022 Fab heavy chain


Mass: 23668.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody CR3022 Fab light chain


Mass: 24278.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Protein Spike protein S1


Mass: 23073.766 Da / Num. of mol.: 1 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): Expi293F / 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.: 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

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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: 7.76 Å3/Da / Density % sol: 84.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1M Succinic acid, 0.1M HEPES pH 7.0 and 2% PEG MME2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.2→50 Å / Num. obs: 13814 / % possible obs: 82.2 % / Redundancy: 6.1 % / CC1/2: 0.98 / Net I/σ(I): 5.57
Reflection shellResolution: 4.2→4.35 Å / Num. unique obs: 800 / CC1/2: 0.47

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.22→48.98 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2862 824 5 %
Rwork0.2461 --
obs0.2481 11132 53.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.22→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4933 0 28 0 4961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d6.132707
X-RAY DIFFRACTIONf_chiral_restr0.054768
X-RAY DIFFRACTIONf_plane_restr0.005887
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
4.22-4.490.4439340.3237693
4.49-4.830.3814590.2833109923
4.83-5.320.3284920.2824181837
5.32-6.090.32541690.2842307363
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)
10.7891-0.3826-0.0242.6479-1.34563.9817-0.0602-0.24320.4301-1.02470.8648-0.75540.0532-0.53851.7750.52310.05390.110.307-0.18070.3707-64.579-29.0669.656
21.2088-0.4595-2.17520.13180.44162.911-0.48610.2971-0.30020.1657-0.33450.04981.24960.6408-1.6868-0.4777-0.5202-0.02380.3266-0.14510.7422-74.453-24.5422.977
32.07060.07540.4490.41270.67321.13021.05290.35930.62580.1997-0.2292-0.1158-1.24570.43030.08890.9795-0.20410.09840.5718-0.14690.6874-81.922-12.55337.632
40.50580.66710.20341.53060.30670.60690.6052-0.204-0.0327-0.3703-0.5651-0.215-0.6062-0.05070.02631.09610.201-0.10870.84350.30750.9997-56.495-46.00627.788
50.49520.0515-0.56060.19090.02220.69260.112-1.21010.31560.20190.95920.0176-0.49620.69650.14521.01020.4085-0.17770.9864-0.28180.9516-52.999-33.66926.875
61.07071.3411-0.67991.5278-0.78860.5465-0.3136-0.6543-0.3268-0.4938-0.15310.58461.30750.45210.00010.99540.2152-0.21120.82530.01350.8631-58.568-39.40130.949
70.70170.3201-0.7840.5229-0.39381.23270.6311-0.7272-0.4030.3771-0.45370.1951-0.19070.42120.00110.882-0.2081-0.09280.6321-0.12720.774-84.991-26.24543.357
80.45240.4487-0.12070.7675-0.65760.9860.2640.29130.20420.0117-0.7211-0.22890.17080.115-0.27820.44820.35470.23050.2041-0.19950.8853-92.233-26.97846.907
90.4414-0.2982-0.27230.41610.03420.2310.50040.5790.587-0.1678-0.0373-0.25850.7185-0.5217-0.00021.2031-0.13820.3381.1294-0.10691.1492-31.293-37.103-1.627
101.0149-0.2034-0.0719-0.0091-0.0212-0.0023-0.308-0.219-0.4605-0.18470.73840.0393-0.8745-0.5608-0.00011.0675-0.0657-0.13930.9948-0.17571.082-41.922-36.3834.166
110.62210.48550.32060.5101-0.00950.38730.3508-0.36020.17750.2823-0.82910.4326-0.07710.29850.00021.2261-0.1377-0.010.7979-0.16630.8632-43.42-41.012-10.502
120.00270.009-0.005-0.00360.0080.01530.4083-0.8925-1.0402-0.22990.3074-0.08790.39940.62410.00111.4408-0.08850.11711.2542-0.00910.7859-40.003-52.366-7.353
131.8420.51080.75421.34660.41870.7592-0.63250.18360.5675-0.7908-0.03740.56080.2329-0.1691-0.41832.12970.3239-0.01580.6019-0.62510.7325-44.176-56.161-25.302
140.91020.6105-0.14810.9394-0.58680.4854-0.4322-0.2538-0.35270.2754-0.4377-0.9217-0.5666-0.4795-0.24131.14490.15630.03490.6585-0.38951.0139-43.879-34.181-10.168
150.20370.1523-0.06460.1222-0.04070.01161.1193-0.4593-0.05470.90970.60840.1510.15131.1888-0.00041.43970.0650.07781.97960.16391.5096-32.013-41.32218.375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:79 )H1 - 79
2X-RAY DIFFRACTION2( CHAIN H AND RESID 80:136 )H80 - 136
3X-RAY DIFFRACTION3( CHAIN H AND RESID 137:217 )H137 - 217
4X-RAY DIFFRACTION4( CHAIN L AND RESID 1:38 )L1 - 38
5X-RAY DIFFRACTION5( CHAIN L AND RESID 39:67 )L39 - 67
6X-RAY DIFFRACTION6( CHAIN L AND RESID 68:116 )L68 - 116
7X-RAY DIFFRACTION7( CHAIN L AND RESID 117:178 )L117 - 178
8X-RAY DIFFRACTION8( CHAIN L AND RESID 179:213 )L179 - 213
9X-RAY DIFFRACTION9( CHAIN A AND RESID 332:358 )A332 - 358
10X-RAY DIFFRACTION10( CHAIN A AND RESID 359:416 )A359 - 416
11X-RAY DIFFRACTION11( CHAIN A AND RESID 417:459 )A417 - 459
12X-RAY DIFFRACTION12( CHAIN A AND RESID 460:469 )A460 - 469
13X-RAY DIFFRACTION13( CHAIN A AND RESID 470:494 )A470 - 494
14X-RAY DIFFRACTION14( CHAIN A AND RESID 495:516 )A495 - 516
15X-RAY DIFFRACTION15( CHAIN A AND RESID 517:532 )A517 - 532

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