[English] 日本語
Yorodumi
- PDB-6xkp: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xkp
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-270
Components
  • CV07-270 Heavy Chain
  • CV07-270 Light Chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Antibody / Spike / Coronavirus / COVID-19 / IMMUNE SYSTEM / 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 / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / 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 / 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 / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsLiu, H. / Yuan, M. / Zhu, X. / Wu, N.C. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI139445 United States
CitationJournal: Cell / Year: 2020
Title: A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model.
Authors: Kreye, J. / Reincke, S.M. / Kornau, H.C. / Sanchez-Sendin, E. / Corman, V.M. / Liu, H. / Yuan, M. / Wu, N.C. / Zhu, X. / Lee, C.D. / Trimpert, J. / Holtje, M. / Dietert, K. / Stoffler, L. / ...Authors: Kreye, J. / Reincke, S.M. / Kornau, H.C. / Sanchez-Sendin, E. / Corman, V.M. / Liu, H. / Yuan, M. / Wu, N.C. / Zhu, X. / Lee, C.D. / Trimpert, J. / Holtje, M. / Dietert, K. / Stoffler, L. / von Wardenburg, N. / van Hoof, S. / Homeyer, M.A. / Hoffmann, J. / Abdelgawad, A. / Gruber, A.D. / Bertzbach, L.D. / Vladimirova, D. / Li, L.Y. / Barthel, P.C. / Skriner, K. / Hocke, A.C. / Hippenstiel, S. / Witzenrath, M. / Suttorp, N. / Kurth, F. / Franke, C. / Endres, M. / Schmitz, D. / Jeworowski, L.M. / Richter, A. / Schmidt, M.L. / Schwarz, T. / Muller, M.A. / Drosten, C. / Wendisch, D. / Sander, L.E. / Osterrieder, N. / Wilson, I.A. / Pruss, H.
History
DepositionJun 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: 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_PubMed / _citation.title
Revision 1.2Nov 25, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike protein S1
B: Spike protein S1
H: CV07-270 Heavy Chain
L: CV07-270 Light Chain
M: CV07-270 Heavy Chain
N: CV07-270 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,46116
Polymers147,2506
Non-polymers1,21110
Water00
1
A: Spike protein S1
H: CV07-270 Heavy Chain
L: CV07-270 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3279
Polymers73,6253
Non-polymers7026
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-84 kcal/mol
Surface area27240 Å2
MethodPISA
2
B: Spike protein S1
M: CV07-270 Heavy Chain
N: CV07-270 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1357
Polymers73,6253
Non-polymers5094
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-66 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.020, 151.785, 66.015
Angle α, β, γ (deg.)90.000, 95.440, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12H
22M
13L
23N

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNPROPROAA334 - 52716 - 209
21ASNASNPROPROBB334 - 52716 - 209
12GLNGLNLYSLYSHC1 - 2141 - 230
22GLNGLNLYSLYSME1 - 2141 - 230
13ALAALATHRTHRLD3 - 2103 - 213
23ALAALATHRTHRNF3 - 2103 - 213

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Spike protein S1


Mass: 26095.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Antibody CV07-270 Heavy Chain


Mass: 24817.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody CV07-270 Light Chain


Mass: 22711.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 6.5 0.2 M sodium chloride 2 M ammonium sulfate 15% (v/v) ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 41624 / % possible obs: 90.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.099 / Rrim(I) all: 0.222 / Χ2: 0.7 / Net I/σ(I): 3.7 / Num. measured all: 195146
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.60.89320890.6760.5051.0310.39790.8
2.75-2.83.90.87421130.7210.4720.9970.40292.6
2.8-2.854.20.76121310.8010.3990.8630.40992.7
2.85-2.914.40.7720690.7880.3980.870.41192.3
2.91-2.974.60.6921320.7820.350.7760.43392.2
2.97-3.044.70.60620530.8230.3040.680.45991
3.04-3.124.70.47720400.8920.2390.5360.45888.4
3.12-3.24.70.39518740.9140.1980.4430.51282.2
3.2-3.34.80.3219310.9430.1580.3580.53684.3
3.3-3.44.90.28421880.960.1390.3170.55696.1
3.4-3.5250.2521710.9640.1210.2780.58495
3.52-3.6650.20721860.9750.1010.230.65994.8
3.66-3.834.90.17321490.980.0850.1930.72393.8
3.83-4.034.90.14921080.9810.0730.1660.85392.9
4.03-4.294.90.12220820.990.060.1370.9690.8
4.29-4.624.80.10519630.9910.0510.1171.10785.3
4.62-5.084.90.10219120.9920.0490.1131.07783.4
5.08-5.815.10.10122170.9920.0480.1120.89295.9
5.81-7.3250.09821480.9910.0470.1090.87793.3
7.32-504.90.06120680.9960.0290.0681.39688.2

-
Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41
Resolution: 2.72→49.73 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.866 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.195 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2694 2055 4.9 %RANDOM
Rwork0.2199 ---
obs0.2223 39568 89.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.71 Å2 / Biso mean: 37.534 Å2 / Biso min: 8.26 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å20 Å2-0.64 Å2
2---0.4 Å20 Å2
3----2.61 Å2
Refinement stepCycle: final / Resolution: 2.72→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9177 0 68 0 9245
Biso mean--67.74 --
Num. residues----1253
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A52220.16
12B52220.16
21H61150.14
22M61150.14
31L52330.16
32N52330.16
LS refinement shellResolution: 2.72→2.786 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.391 137 -
Rwork0.32 2581 -
obs--79.66 %

+
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://pdbjlvh1.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