[English] 日本語
Yorodumi
- PDB-1x67: Solution structure of the cofilin homology domain of HIP-55 (dreb... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1x67
TitleSolution structure of the cofilin homology domain of HIP-55 (drebrin-like protein)
ComponentsDrebrin-like protein
KeywordsPROTEIN BINDING / cell-free protein synthesis / actin-binding protein / SH3P7 / mAbp1 / T-cell lymphocyte signaling and regulation / T-cell antigen receptor regulation / HPK-1 activation / c-JUN N-terminal kinase activation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


podosome assembly / clathrin-coated vesicle membrane / structural constituent of postsynaptic actin cytoskeleton / membrane organization / podosome / Neurexins and neuroligins / anchoring junction / Rac protein signal transduction / Caspase-mediated cleavage of cytoskeletal proteins / synapse assembly ...podosome assembly / clathrin-coated vesicle membrane / structural constituent of postsynaptic actin cytoskeleton / membrane organization / podosome / Neurexins and neuroligins / anchoring junction / Rac protein signal transduction / Caspase-mediated cleavage of cytoskeletal proteins / synapse assembly / neuron projection morphogenesis / ruffle / enzyme activator activity / endocytosis / actin filament binding / tertiary granule lumen / presynapse / lamellipodium / actin binding / cell cortex / secretory granule lumen / perikaryon / ficolin-1-rich granule lumen / adaptive immune response / early endosome / postsynaptic density / cadherin binding / Golgi membrane / protein domain specific binding / intracellular membrane-bounded organelle / dendrite / Neutrophil degranulation / glutamatergic synapse / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Drebrin-like protein, SH3 domain / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / Variant SH3 domain / ADF-H/Gelsolin-like domain superfamily / Src homology 3 domains ...Drebrin-like protein, SH3 domain / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / Variant SH3 domain / ADF-H/Gelsolin-like domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Drebrin-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGoroncy, A.K. / Kigawa, T. / Koshiba, S. / Sato, M. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2009
Title: NMR solution structures of actin depolymerizing factor homology domains.
Authors: Goroncy, A.K. / Koshiba, S. / Tochio, N. / Tomizawa, T. / Sato, M. / Inoue, M. / Watanabe, S. / Hayashizaki, Y. / Tanaka, A. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Drebrin-like protein


Theoretical massNumber of molelcules
Total (without water)15,4031
Polymers15,4031
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 least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein Drebrin-like protein / SH3 domain-containing protein 7 / Drebrin F / Cervical SH3P7 / HPK1-interacting protein of 55 kDa / ...SH3 domain-containing protein 7 / Drebrin F / Cervical SH3P7 / HPK1-interacting protein of 55 kDa / HIP-55 / Cervical mucin-associated protein / PP5423


Mass: 15403.144 Da / Num. of mol.: 1 / Fragment: cofilin homology domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: DBNL / Plasmid: P041129-01 / References: UniProt: Q9UJU6

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

-
Sample preparation

DetailsContents: 1.33mM COFILIN HOMOLOGY DOMAIN, 20mM TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5BRUKERcollection
NMRPipe20020425FRANK DELAGLIOprocessing
NMRView5.0.4BRUCE A. JOHNSONdata analysis
KUJIRA0.899aNAOHIRO KOBAYASHdata analysis
CYANA2PETER GUNTERTrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
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