[English] 日本語
Yorodumi
- PDB-8fah: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

+
Open data


ID or keywords:

Loading...

-
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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 / 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 S1 subunit, receptor binding domain superfamily, 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / 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: 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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

-
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

Read more