[English] 日本語
Yorodumi
- PDB-7e3o: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e3o
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody nCoV617
Components
  • Spike protein S1
  • nCoV617 Heigh Chain
  • nCoV617 Light Chain
KeywordsVIRAL PROTEIN / SARS-CoV-2 / S-RBD / RBS-C / native human monoclonal antibody / therapeutic antibody
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 / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsChen, S.D. / Yang, M.
CitationJournal: Microbiol Spectr / Year: 2021
Title: Structural Basis of a Human Neutralizing Antibody Specific to the SARS-CoV-2 Spike Protein Receptor-Binding Domain.
Authors: Yang, M. / Li, J. / Huang, Z. / Li, H. / Wang, Y. / Wang, X. / Kang, S. / Huang, X. / Wu, C. / Liu, T. / Jia, Z. / Liang, J. / Yuan, X. / He, S. / Chen, X. / Zhou, Z. / Chen, Q. / Liu, S. / ...Authors: Yang, M. / Li, J. / Huang, Z. / Li, H. / Wang, Y. / Wang, X. / Kang, S. / Huang, X. / Wu, C. / Liu, T. / Jia, Z. / Liang, J. / Yuan, X. / He, S. / Chen, X. / Zhou, Z. / Chen, Q. / Liu, S. / Li, J. / Zheng, H. / Liu, X. / Li, K. / Yao, X. / Lang, B. / Liu, L. / Liao, H.X. / Chen, S.
History
DepositionFeb 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: nCoV617 Light Chain
H: nCoV617 Heigh Chain
R: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)69,3773
Polymers69,3773
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-36 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.093, 60.367, 77.296
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Antibody nCoV617 Light Chain


Mass: 22551.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector HA-MCS-pcDNA3.1 (others)
#2: Antibody nCoV617 Heigh Chain


Mass: 24278.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector HA-MCS-pcDNA3.1 (others)
#3: Protein Spike protein S1


Mass: 22547.164 Da / Num. of mol.: 1 / Fragment: UNP residues 337-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: unidentified baculovirus / References: UniProt: P0DTC2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 152 mM NH4Cl, 22.8% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: SDMS / Detector: CMOS / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.51→40.67 Å / Num. obs: 25491 / % possible obs: 94.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.897 / Net I/σ(I): -0.6
Reflection shellResolution: 2.514→2.603 Å / Num. unique obs: 2495 / CC1/2: 0.868

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J, 7K8Z

6m0j

7k8z


Resolution: 2.51→40.67 Å / SU ML: 0.3431 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.0598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2589 1996 7.84 %
Rwork0.204 23468 -
obs0.2083 25464 94.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.17 Å2
Refinement stepCycle: LAST / Resolution: 2.51→40.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 0 63 4741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00974801
X-RAY DIFFRACTIONf_angle_d1.2146542
X-RAY DIFFRACTIONf_chiral_restr0.0667725
X-RAY DIFFRACTIONf_plane_restr0.0089842
X-RAY DIFFRACTIONf_dihedral_angle_d14.15666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.580.33091380.23991623X-RAY DIFFRACTION94.83
2.58-2.650.36431450.26171706X-RAY DIFFRACTION97.78
2.65-2.720.30811450.24871702X-RAY DIFFRACTION96.8
2.72-2.810.32051440.25321680X-RAY DIFFRACTION96.46
2.81-2.910.33131440.24781693X-RAY DIFFRACTION96.38
2.91-3.030.34751440.23881702X-RAY DIFFRACTION95.9
3.03-3.170.29741420.23961671X-RAY DIFFRACTION95.17
3.17-3.330.28241420.23091673X-RAY DIFFRACTION94.98
3.33-3.540.30041430.22571672X-RAY DIFFRACTION94.63
3.54-3.820.29031430.21081687X-RAY DIFFRACTION94.87
3.82-4.20.25821450.19191683X-RAY DIFFRACTION93.94
4.2-4.810.19761410.15861671X-RAY DIFFRACTION92.69
4.81-6.050.20681410.17081668X-RAY DIFFRACTION90.95
6.05-40.670.20841390.19091637X-RAY DIFFRACTION85.22
Refinement TLS params.Method: refined / Origin x: -17.2087125013 Å / Origin y: 8.26329743651 Å / Origin z: -6.48148426029 Å
111213212223313233
T0.474870565229 Å2-0.0121177394775 Å20.0189358203883 Å2-0.48066937301 Å2-0.0094058205698 Å2--0.457613974792 Å2
L1.06121900395 °20.190912061987 °20.726946367854 °2-0.19017607079 °20.112790840697 °2--0.545442535615 °2
S-0.00638252055348 Å °0.116984759717 Å °-0.06776808289 Å °0.00828757034323 Å °0.048553685888 Å °-0.0165248554962 Å °-0.0450550366404 Å °0.106107057303 Å °-0.000347990682264 Å °
Refinement TLS groupSelection details: all

+
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