[English] 日本語
Yorodumi
- PDB-6mnt: CUS-3 coat protein I-domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mnt
TitleCUS-3 coat protein I-domain
ComponentsPutative coat protein
KeywordsVIRAL PROTEIN / anti-parallel beta-barrel
Function / homologyMajor capsid protein Gp5 / P22 coat protein - gene protein 5 / viral capsid / Putative coat protein
Function and homology information
Biological speciesEnterobacteria phage CUS-3 (virus)
MethodSOLUTION NMR / molecular dynamics
AuthorsTripler, T.N. / Kaplan, A.R. / Alexandrescu, A.T. / Teschke, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentR01 GM076661 United States
CitationJournal: To Be Published
Title: CUS-3 and Sf6 coat protein I-domains
Authors: Tripler, T.N. / Kaplan, A.R. / Alexandrescu, A.T. / Teschke, C.M.
History
DepositionOct 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative coat protein


Theoretical massNumber of molelcules
Total (without water)13,2731
Polymers13,2731
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6910 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Putative coat protein


Mass: 13272.730 Da / Num. of mol.: 1 / Fragment: I-domain, residues 223-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage CUS-3 (virus) / Gene: ECRS218_0018 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A5VW72

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic13D HN(CA)CB
121isotropic12D 1H-15N HSQC
132isotropic13D HN(CO)CA
142isotropic1HN(CA)CO
152isotropic13D HNCO
161isotropic13D 1H-15N NOESY
172isotropic13D 1H-13C NOESY
183isotropic23D 1H-15N TOCSY
192isotropic13D HBHA(CO)NH
1102isotropic13D (H)CCH-TOCSY
1112isotropic13D CCH-TOCSY
1122isotropic13D 1H-13C NOESY aliphatic
1133isotropic22D DQF-COSY
1143isotropic22D 1H-1H NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.99 mM [U-99% 15N] CUS-3 coat protein I-domain, 20 mM sodium phosphate, 90% H2O/10% D2O15N sample90% H2O/10% D2O
solution21.9 mM [U-99% 15N], U-99% 13C CUS-3 coat protein I-domain, 20 mM sodium phosphate, 90% H2O/10% D2O15N13C sample90% H2O/10% D2O
solution31.9 mM [U-99% 15N] CUS-3 coat protein I-domain, 20 mM sodium phosphate, 100% D2OD20100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.99 mMCUS-3 coat protein I-domain[U-99% 15N]1
20 mMsodium phosphatenatural abundance1
1.9 mMCUS-3 coat protein I-domain[U-99% 15N], U-99% 13C2
20 mMsodium phosphatenatural abundance2
1.9 mMCUS-3 coat protein I-domain[U-99% 15N]3
20 mMsodium phosphatenatural abundance3
Sample conditionsIonic strength: 20 mM / Label: 1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298.13 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.processing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNMRCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesrefinement
CcpNMRCCPNpeak picking
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 6
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 25

+
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