[English] 日本語
Yorodumi
- PDB-2k6s: Structure of Rab11-FIP2 C-terminal Coiled-coil Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k6s
TitleStructure of Rab11-FIP2 C-terminal Coiled-coil Domain
ComponentsRab11fip2 protein
KeywordsPROTEIN TRANSPORT / Rab11-FIP2 / Coiled-coil Domain / Solution Structure
Function / homology
Function and homology information


TRAM-dependent toll-like receptor 4 signaling pathway / regulated exocytosis / insulin secretion involved in cellular response to glucose stimulus / establishment of cell polarity / phagocytic cup / phagocytosis / positive regulation of protein localization to plasma membrane / positive regulation of GTPase activity / cell projection / cytoplasmic vesicle membrane ...TRAM-dependent toll-like receptor 4 signaling pathway / regulated exocytosis / insulin secretion involved in cellular response to glucose stimulus / establishment of cell polarity / phagocytic cup / phagocytosis / positive regulation of protein localization to plasma membrane / positive regulation of GTPase activity / cell projection / cytoplasmic vesicle membrane / small GTPase binding / Vasopressin regulates renal water homeostasis via Aquaporins / recycling endosome membrane / endosome / intracellular membrane-bounded organelle / protein kinase binding / protein homodimerization activity / nucleoplasm / identical protein binding
Similarity search - Function
Rab11-family interacting protein class I / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2440 / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / FIP domain / FIP-RBD domain profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. ...Rab11-family interacting protein class I / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2440 / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / FIP domain / FIP-RBD domain profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Rab11 family-interacting protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWei, J. / Liu, Y. / Baleja, J.D.
CitationJournal: Biochemistry / Year: 2009
Title: Disorder and structure in the Rab11 binding domain of Rab11 family interacting protein 2.
Authors: Wei, J. / Liu, Y. / Bose, K. / Henry, G.D. / Baleja, J.D.
History
DepositionJul 18, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 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 1.4May 8, 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: Rab11fip2 protein
B: Rab11fip2 protein


Theoretical massNumber of molelcules
Total (without water)10,0102
Polymers10,0102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 30all calculated structures submitted
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Rab11fip2 protein


Mass: 5004.783 Da / Num. of mol.: 2
Fragment: C-terminal Coiled-coil Domain (UNP residues 450-489)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Rab11fip2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7L804

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H COSY
1312D 1H-1H NOESY
1433D HNCO
1533D HNCA
1633D HN(CA)CB
1733D HN(CO)CA
1833D (H)CCH-TOCSY
1933D CBCA(CO)NH
11022D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM protein, 20 uM DSS, 20 mM sodium phosphate, 100% D2O100% D2O
21.5 mM [U-100% 15N] protein, 20 uM DSS, 20 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM [U-100% 13C; U-100% 15N] protein, 20 uM DSS, 20 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity1
20 uMDSS1
20 mMsodium phosphate1
1.5 mMentity[U-100% 15N]2
20 uMDSS2
20 mMsodium phosphate2
0.8 mMentity[U-100% 13C; U-100% 15N]3
20 uMDSS3
20 mMsodium phosphate3
Sample conditionsIonic strength: 0.08 / pH: 7.2 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
TopSpin1.3Bruker Biospincollection
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 30 / Conformers submitted total number: 30

+
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://pdbjlvh1.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