[English] 日本語
Yorodumi
- PDB-7ypc: Notothenia coriiceps TRAF4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ypc
TitleNotothenia coriiceps TRAF4
ComponentsTNF receptor-associated factor
KeywordsIMMUNE SYSTEM / TRAF / Tumor Necrosis Factor Receptor Association Factor / Notothenia coriiceps TRAF4 / PROTEIN BINDING
Function / homology
Function and homology information


activation of NF-kappaB-inducing kinase activity / tumor necrosis factor receptor binding / positive regulation of JNK cascade / regulation of apoptotic process / apoptotic process / zinc ion binding / cytoplasm
Similarity search - Function
TNF receptor-associated factor 4, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like ...TNF receptor-associated factor 4, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
TNF receptor-associated factor
Similarity search - Component
Biological speciesNotothenia coriiceps (black rockcod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsPark, H.H. / Kim, C.M. / Jang, H.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Fish Shellfish Immunol. / Year: 2023
Title: Structure of fish TRAF4 and its implication in TRAF4-mediated immune cell and platelet signaling.
Authors: Kim, C.M. / Jang, H. / Hong, E. / Lee, J.H. / Park, H.H.
History
DepositionAug 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TNF receptor-associated factor
B: TNF receptor-associated factor
C: TNF receptor-associated factor


Theoretical massNumber of molelcules
Total (without water)66,4383
Polymers66,4383
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-17 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.859, 112.208, 112.036
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

-
Components

#1: Protein TNF receptor-associated factor


Mass: 22145.984 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Notothenia coriiceps (black rockcod) / Gene: traf4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I9N9S6

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.29 Å3/Da / Density % sol: 76.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.5, 10% w/v PEG-8000, 8% v/v Ethylene glycol

-
Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→45.773 Å / Num. obs: 40583 / % possible obs: 98.4 % / Redundancy: 13.2 % / Biso Wilson estimate: 32.89 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.2
Reflection shellResolution: 2.66→2.755 Å / Num. unique obs: 3392 / CC1/2: 0.926

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K8U

4k8u


Resolution: 2.66→45.77 Å / SU ML: 0.3376 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9124
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2279 2070 5.11 %
Rwork0.2068 38453 -
obs0.2079 40523 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.46 Å2
Refinement stepCycle: LAST / Resolution: 2.66→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 0 0 4054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01024177
X-RAY DIFFRACTIONf_angle_d1.14385647
X-RAY DIFFRACTIONf_chiral_restr0.074573
X-RAY DIFFRACTIONf_plane_restr0.0071729
X-RAY DIFFRACTIONf_dihedral_angle_d30.02231552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.720.3449970.30161967X-RAY DIFFRACTION76.16
2.72-2.790.32461950.27822501X-RAY DIFFRACTION100
2.79-2.870.36871360.25342557X-RAY DIFFRACTION100
2.87-2.950.32131600.25412599X-RAY DIFFRACTION100
2.95-3.040.35951140.25682560X-RAY DIFFRACTION100
3.04-3.150.1963910.19632609X-RAY DIFFRACTION100
3.15-3.280.3189850.24662645X-RAY DIFFRACTION100
3.28-3.430.25211410.23552591X-RAY DIFFRACTION100
3.43-3.610.21631820.21242574X-RAY DIFFRACTION100
3.61-3.840.21641700.19372519X-RAY DIFFRACTION100
3.84-4.130.19031420.17462615X-RAY DIFFRACTION100
4.13-4.550.15761140.15762645X-RAY DIFFRACTION100
4.55-5.20.14841320.14842634X-RAY DIFFRACTION100
5.2-6.550.20871390.18292684X-RAY DIFFRACTION100
6.55-45.770.21581720.20042753X-RAY DIFFRACTION99.97

+
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