[English] 日本語
Yorodumi
- PDB-2ms4: Cyclophilin a complexed with a fragment of crk-ii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ms4
TitleCyclophilin a complexed with a fragment of crk-ii
Components
  • Peptide
  • Peptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / CYCLOPHILIN A
Function / homology
Function and homology information


response to hepatocyte growth factor / regulation of intracellular signal transduction / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / postsynaptic specialization assembly / protein phosphorylated amino acid binding / regulation of T cell migration / response to peptide ...response to hepatocyte growth factor / regulation of intracellular signal transduction / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / postsynaptic specialization assembly / protein phosphorylated amino acid binding / regulation of T cell migration / response to peptide / regulation of dendrite development / negative regulation of wound healing / response to yeast / positive regulation of skeletal muscle acetylcholine-gated channel clustering / reelin-mediated signaling pathway / negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / ARMS-mediated activation / MET receptor recycling / negative regulation of viral life cycle / negative regulation of cell motility / heparan sulfate binding / regulation of viral genome replication / negative regulation of natural killer cell mediated cytotoxicity / virion binding / leukocyte chemotaxis / MET activates RAP1 and RAC1 / protein localization to membrane / negative regulation of stress-activated MAPK cascade / endothelial cell activation / regulation of GTPase activity / positive regulation of smooth muscle cell migration / Basigin interactions / protein peptidyl-prolyl isomerization / cyclosporin A binding / p130Cas linkage to MAPK signaling for integrins / Minus-strand DNA synthesis / Plus-strand DNA synthesis / enzyme-linked receptor protein signaling pathway / Uncoating of the HIV Virion / cellular response to insulin-like growth factor stimulus / establishment of cell polarity / Early Phase of HIV Life Cycle / regulation of cell adhesion mediated by integrin / Integration of provirus / negative regulation of protein phosphorylation / dendrite development / APOBEC3G mediated resistance to HIV-1 infection / positive regulation of Rac protein signal transduction / viral release from host cell / Calcineurin activates NFAT / activation of protein kinase B activity / regulation of signal transduction / Binding and entry of HIV virion / ephrin receptor signaling pathway / cellular response to transforming growth factor beta stimulus / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / negative regulation of protein kinase activity / cytoskeletal protein binding / ephrin receptor binding / insulin-like growth factor receptor binding / signaling adaptor activity / phosphotyrosine residue binding / neutrophil chemotaxis / positive regulation of substrate adhesion-dependent cell spreading / cellular response to nitric oxide / Downstream signal transduction / SH2 domain binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / protein tyrosine kinase binding / positive regulation of protein secretion / cell chemotaxis / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / hippocampus development / Regulation of signaling by CBL / positive regulation of JNK cascade / peptidylprolyl isomerase / neuromuscular junction / peptidyl-prolyl cis-trans isomerase activity / response to hydrogen peroxide / Assembly Of The HIV Virion / positive regulation of NF-kappaB transcription factor activity / Budding and maturation of HIV virion / cellular response to nerve growth factor stimulus / receptor tyrosine kinase binding / cerebral cortex development / Regulation of actin dynamics for phagocytic cup formation / platelet activation / SH3 domain binding / lipid metabolic process / platelet aggregation / VEGFA-VEGFR2 Pathway / kinase binding / integrin binding / positive regulation of protein phosphorylation
Similarity search - Function
CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / Variant SH3 domain / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. ...CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / Variant SH3 domain / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Adapter molecule crk / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model detailslowest energy, model1
AuthorsJankowski, W. / Saleh, T. / Rossi, P. / Kalodimos, C.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Cyclophilin A promotes cell migration via the Abl-Crk signaling pathway.
Authors: Saleh, T. / Jankowski, W. / Sriram, G. / Rossi, P. / Shah, S. / Lee, K.B. / Cruz, L.A. / Rodriguez, A.J. / Birge, R.B. / Kalodimos, C.G.
History
DepositionJul 22, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Dec 30, 2015Group: Database references
Revision 1.3Feb 3, 2016Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase A
B: Peptide


Theoretical massNumber of molelcules
Total (without water)18,9922
Polymers18,9922
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A / Peptidyl-prolyl cis-trans ...PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A / Peptidyl-prolyl cis-trans isomerase A / N-terminally processed


Mass: 18036.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase
#2: Protein/peptide Peptide


Mass: 955.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P46108*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCA
1513D HN(CA)CB
1613D HNCO
1713D HN(CO)CA
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11113D 1H-13C NOESY aromatic

-
Sample preparation

DetailsContents: 0.8 mM [U-100% 13C; U-100% 15N] protein_1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: entity_1-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 305 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger A.T. et.al.refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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