[English] 日本語
Yorodumi
- PDB-6okx: Solution structure of VEK50RH1/AA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6okx
TitleSolution structure of VEK50RH1/AA
ComponentsPlasminogen-binding group A streptococcal M-like protein PAM
KeywordsPROTEIN BINDING / Plasminogen binding peptide
Function / homologyStreptococcal M proteins C repeat profile. / Streptococcal M proteins D repeats region profile. / Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / YSIRK Gram-positive signal peptide / plasminogen activation / extracellular region / Plasminogen-binding group A streptococcal M-like protein PAM
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsYuan, Y. / Castellino, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HL013423 United States
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Solution structural model of the complex of the binding regions of human plasminogen with its M-protein receptor from Streptococcus pyogenes.
Authors: Yuan, Y. / Ayinuola, Y.A. / Singh, D. / Ayinuola, O. / Mayfield, J.A. / Quek, A. / Whisstock, J.C. / Law, R.H.P. / Lee, S.W. / Ploplis, V.A. / Castellino, F.J.
History
DepositionApr 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plasminogen-binding group A streptococcal M-like protein PAM


Theoretical massNumber of molelcules
Total (without water)6,0211
Polymers6,0211
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5780 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein Plasminogen-binding group A streptococcal M-like protein PAM


Mass: 6020.606 Da / Num. of mol.: 1 / Fragment: residues 85-133 / Mutation: R101A, H102A
Source method: isolated from a genetically manipulated source
Details: AP53 / Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: pam, emm / Plasmid: pET15b / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P49054

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D NOESY
131isotropic13D CBCA(CO)NH
141isotropic13D C(CO)NH
151isotropic13D HNCO
161isotropic13D HNCA
181isotropic13D HN(CA)CB

-
Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-99% 13C; U-99% 15N] VEK50RH1/AA, 2 ug/mL DSS, 1 ug/mL DTT, 20 mM [U-2H] Bis-Tris-d19, 93% H2O/7% D2O
Label: 15N, 13C_sample / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMVEK50RH1/AA[U-99% 13C; U-99% 15N]1
2 ug/mLDSSnatural abundance1
1 ug/mLDTTnatural abundance1
20 mMBis-Tris-d19[U-2H]1
Sample conditionsIonic strength: 20 mM / Label: condition_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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