[English] 日本語
Yorodumi
- PDB-5zxv: Structural definition of a unique neutralization epitope on the r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zxv
TitleStructural definition of a unique neutralization epitope on the receptor-binding domain of MERS-CoV spike glycoprotein
Components
  • MERS-CoV RBD
  • heavy chain
  • light chain
KeywordsVIRAL PROTEIN / Antibody
Function / homology
Function and homology information


membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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. ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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
Similarity search - Domain/homology
Biological speciesMiddle East respiratory syndrome coronavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.482 Å
AuthorsZhang, S. / Wang, X.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Cell Rep / Year: 2018
Title: Structural Definition of a Unique Neutralization Epitope on the Receptor-Binding Domain of MERS-CoV Spike Glycoprotein
Authors: Zhang, S. / Zhou, P. / Wang, P. / Li, Y. / Jiang, L. / Jia, W. / Wang, H. / Fan, A. / Wang, D. / Shi, X. / Fang, X. / Hammel, M. / Wang, S. / Wang, X. / Zhang, L.
History
DepositionMay 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MERS-CoV RBD
B: MERS-CoV RBD
H: heavy chain
L: light chain
C: heavy chain
D: light chain


Theoretical massNumber of molelcules
Total (without water)136,8016
Polymers136,8016
Non-polymers00
Water00
1
A: MERS-CoV RBD
H: heavy chain
L: light chain


Theoretical massNumber of molelcules
Total (without water)68,4003
Polymers68,4003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MERS-CoV RBD
C: heavy chain
D: light chain


Theoretical massNumber of molelcules
Total (without water)68,4003
Polymers68,4003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.647, 138.647, 228.736
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein MERS-CoV RBD


Mass: 22929.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome coronavirus
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: K9N5Q8*PLUS
#2: Antibody heavy chain


Mass: 22745.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody light chain


Mass: 22724.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 2%(v/v) tacsimate pH 5.0, 0.1M sodium citrate tribasic dihydrate pH 5.6, 16%(w/v) polyethylene glycol 3,350 and 2M sodium thiocyanate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 4.482→50 Å / Num. obs: 9351 / % possible obs: 96.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 8.4
Reflection shellResolution: 4.5→4.6 Å / Redundancy: 3.1 % / Num. unique obs: 9351 / CC1/2: 0.541 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L72

4l72


Resolution: 4.482→35.438 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 52.66
RfactorNum. reflection% reflection
Rfree0.343 474 5.07 %
Rwork0.3072 --
obs0.3104 9351 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.482→35.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9488 0 0 0 9488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069750
X-RAY DIFFRACTIONf_angle_d0.97513326
X-RAY DIFFRACTIONf_dihedral_angle_d12.2495836
X-RAY DIFFRACTIONf_chiral_restr0.0491518
X-RAY DIFFRACTIONf_plane_restr0.0061696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.4921-5.13640.40441730.39362869X-RAY DIFFRACTION88
5.1364-6.45020.39811340.36773004X-RAY DIFFRACTION93
6.4502-23.88340.32121570.26882978X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: -37.7227 Å / Origin y: 91.9355 Å / Origin z: -3.3713 Å
111213212223313233
T2.4933 Å20.1823 Å2-0.092 Å2-2.5291 Å2-0.3317 Å2--2.1425 Å2
L1.7421 °21.1809 °2-0.1946 °2-2.3504 °2-0.2263 °2--1.3357 °2
S0.0536 Å °-0.3159 Å °0.8561 Å °0.1458 Å °0.2548 Å °0.6626 Å °-0.1947 Å °-0.3761 Å °-0 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://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