[English] 日本語
Yorodumi
- PDB-1m0v: NMR STRUCTURE OF THE TYPE III SECRETORY DOMAIN OF YERSINIA YOPH C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m0v
TitleNMR STRUCTURE OF THE TYPE III SECRETORY DOMAIN OF YERSINIA YOPH COMPLEXED WITH THE SKAP-HOM PHOSPHO-PEPTIDE N-acetyl-DEpYDDPF-NH2
Components
  • PROTEIN-TYROSINE PHOSPHATASE YOPH
  • SKAP55 homologue
KeywordsHYDROLASE / high resolution structure
Function / homology
Function and homology information


Signal regulatory protein family interactions / B cell activation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of cell population proliferation / extracellular region / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
YopH tyrosine phosphatase N-terminal domain / Protein-tyrosine phosphatase, YopH, N-terminal domain / SKAP family / Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. ...YopH tyrosine phosphatase N-terminal domain / Protein-tyrosine phosphatase, YopH, N-terminal domain / SKAP family / Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / PH domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Tyrosine-protein phosphatase YopH / Src kinase-associated phosphoprotein 2
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKhandelwal, P. / Keliikuli, K. / Smith, C.L. / Saper, M.A. / Zuiderweg, E.R.P.
Citation
Journal: Biochemistry / Year: 2002
Title: Solution structure and phosphopeptide binding to the N-terminal domain of Yersinia YopH: comparison with a crystal structure
Authors: Khandelwal, P. / Keliikuli, K. / Smith, C.L. / Saper, M.A. / Zuiderweg, E.R.P.
#1: Journal: MOL.MICROBIOL. / Year: 2001
Title: STRUCTURE OF THE TYPE III SECRETION AND SUBSTRATE-BINDING DOMAIN OF YERSINIA YOPH PHOSPHATASE
Authors: SMITH, C.L. / KHANDELWAL, P. / KELIIKULI, K. / ZUIDERWEG, E.R.P. / SAPER, M.A.
#2: Journal: J.BIOMOL.NMR / Year: 2001
Title: 1H, 15N AND 13C ASSIGNMENTS OF THE N-TERMINAL DOMAIN OF YERSINIA OUTER PROTEIN H IN ITS APO FORM AND IN COMPLEX WITH A PHOSPHOTYROSINE PEPTIDE
Authors: KHANDELWAL, P. / KELIIKULI, K. / SMITH, C.L. / SAPER, M.A. / ZUIDERWEG, E.R.P.
History
DepositionJun 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN-TYROSINE PHOSPHATASE YOPH
B: SKAP55 homologue


Theoretical massNumber of molelcules
Total (without water)15,8862
Polymers15,8862
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 360structures with the least restraint violations
RepresentativeModel #9best ramachandran plot

-
Components

#1: Protein PROTEIN-TYROSINE PHOSPHATASE YOPH / VIRULENCE PROTEIN


Mass: 14882.599 Da / Num. of mol.: 1 / Fragment: AMINO-TERMINAL DOMAIN (RESIDUES 1-129)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: p08538, UniProt: P08538*PLUS, protein-tyrosine-phosphatase
#2: Protein/peptide SKAP55 homologue / SKAP-HOM PEPTIDE


Mass: 1003.879 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS peptide WAS CHEMICALLY synthesiZED. It is naturally found in Mus musculus (mouse).
References: GenBank: 13277602, UniProt: Q3UND0*PLUS
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-resolved NOESY
1213D 15N-resolved NOESY
1313D (H)CCH
1413D 15N/13C filtered/edited NOESY
NMR detailsText: 15N HSQC titrations

-
Sample preparation

DetailsContents: 0.6 mM YopHNT U-15N,13C complexed with 0.72 mM unlabeled peptide; 50mM phosphate buffer NA
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mm phosphate / pH: 6.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AVANCEBrukerAVANCE5002

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeprocessing
XEASYdata analysis
CNSstructure solution
ARIA1Nilges, M. and O'Donoghue, S.I.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 3472 restraints, 3222 are NOE-derived distance constraints, 152 dihedral angle restraints, 98 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: best ramachandran plot
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 360 / 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