[English] 日本語
Yorodumi
- PDB-8kcq: Solution structures of the N-terminal divergent caplonin homology... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8kcq
TitleSolution structures of the N-terminal divergent caplonin homology (NN-CH) domains of human intraflagellar transport protein 54
ComponentsTRAF3-interacting protein 1
KeywordsTRANSPORT PROTEIN / NN-CH domain / Intraflagellar transport (IFT) machinery / IFT54 / ciliopathy / Structural Genomics / PSI-2 / Protein Structure Initiative / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


intraciliary anterograde transport / intraciliary transport particle B / neural tube patterning / negative regulation of defense response to virus / embryonic camera-type eye development / intraciliary transport / ciliary transition zone / ciliary tip / Intraflagellar transport / post-anal tail morphogenesis ...intraciliary anterograde transport / intraciliary transport particle B / neural tube patterning / negative regulation of defense response to virus / embryonic camera-type eye development / intraciliary transport / ciliary transition zone / ciliary tip / Intraflagellar transport / post-anal tail morphogenesis / morphogenesis of a polarized epithelium / negative regulation of interferon-beta production / embryonic heart tube development / embryonic digit morphogenesis / negative regulation of type I interferon production / ciliary base / negative regulation of protein phosphorylation / axoneme / cilium assembly / negative regulation of protein-containing complex assembly / regulation of microtubule cytoskeleton organization / negative regulation of smoothened signaling pathway / kidney development / fibrillar center / defense response to virus / microtubule binding / nuclear body / cilium / ciliary basal body / centrosome / nucleoplasm
Similarity search - Function
TRAF3-interacting protein 1, N-terminal / TRAF3-interacting protein 1, C-terminal domain / TRAF3-interacting protein 1, N-terminal domain superfamily / Microtubule-binding protein MIP-T3 CH-like domain / Microtubule-binding protein MIP-T3 C-terminal region / TRAF3-interacting protein 1
Similarity search - Domain/homology
TRAF3-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / sumilated annealing
AuthorsDang, W. / Kuwasako, K. / He, F. / Takahashi, M. / Tsuda, K. / Nagata, T. / Tanaka, A. / Kobayashi, N. / Kigawa, T. / Guentert, P. ...Dang, W. / Kuwasako, K. / He, F. / Takahashi, M. / Tsuda, K. / Nagata, T. / Tanaka, A. / Kobayashi, N. / Kigawa, T. / Guentert, P. / Shirouzu, M. / Yokoyama, S. / Muto, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomol.Nmr Assign. / Year: 2024
Title: 1 H, 13 C, and 15 N resonance assignments and solution structure of the N-terminal divergent calponin homology (NN-CH) domain of human intraflagellar transport protein 54.
Authors: Kuwasako, K. / Dang, W. / He, F. / Takahashi, M. / Tsuda, K. / Nagata, T. / Tanaka, A. / Kobayashi, N. / Kigawa, T. / Guntert, P. / Shirouzu, M. / Yokoyama, S. / Muto, Y.
History
DepositionAug 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRAF3-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)15,4011
Polymers15,4011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with favorable non-bond energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein TRAF3-interacting protein 1


Mass: 15401.022 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF3IP1 / Details (production host): CELL-Free Protein Synthesis
Production host: Cell-free gateway cloning vector N-term 8xHis mcherry pCellFree_G05 (others)
References: UniProt: Q8TDR0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 13C,15N-SEPARATED NOESY SPECTRA
121isotropic23D CBCA(CO)NH
131isotropic23D HN(CA)CB
141isotropic23D (H)CCH-COSY
151isotropic23D (H)CCH-TOCSY

-
Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-99% 13C; U-99% 15N] NN-CH domain of human IFT54, 100 mM None NaCl, 1 mM [U-99% 2H] d-DTT, 20 mM [U-99% 2H] d-Tris HCl, 0.02 % None NaN3, 90% H2O/10% D2O
Details: 1mM D-DTT;0.02% NaN3 were used to keep the protein condition
Label: 13C,15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMNN-CH domain of human IFT54[U-99% 13C; U-99% 15N]1
100 mMNaClNone1
1 mMd-DTT[U-99% 2H]1
20 mMd-Tris HCl[U-99% 2H]1
0.02 %NaN3None1
Sample conditionsDetails: 20mM D-Tris-HCL (PH7.0); 100mM NaCl; 1mM D-DTT;0.02% NaN3
Ionic strength: 100 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE80013D_13C,15N-SEPARATED_NOESY
Bruker AVANCEBrukerAVANCE6002Assignments (CBCACONH et al.)

-
Processing

NMR software
NameVersionDeveloperClassification
KUJIRA0.863N. Kobayashi, T. Kigawa, S. Yokoyamachemical shift assignment
CYANA2.2Guntert, Mumenthaler and Wuthrichstructure calculation
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
MagRO-NMRView1.2.38N. Kobayashipeak picking
TALOSCornilescu, Delaglio and Baxgeometry optimization
TopSpinBruker Biospinprocessing
RefinementMethod: sumilated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 400 / 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