[English] 日本語
Yorodumi
- PDB-1ca9: STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ca9
TitleSTRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A PEPTIDE FROM TNF-R2
Components
  • PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
  • PROTEIN (TNF-R2)
KeywordsTNF SIGNALING / TRAF / ADAPTER PROTEIN / CELL SURVIVAL
Function / homology
Function and homology information


glial cell-neuron signaling / regulation of cytokine production involved in immune response / CD40 receptor binding / tumor necrosis factor receptor superfamily complex / pulmonary valve development / RNA destabilization / sphingolipid binding / aortic valve development / tumor necrosis factor receptor activity / negative regulation of extracellular matrix constituent secretion ...glial cell-neuron signaling / regulation of cytokine production involved in immune response / CD40 receptor binding / tumor necrosis factor receptor superfamily complex / pulmonary valve development / RNA destabilization / sphingolipid binding / aortic valve development / tumor necrosis factor receptor activity / negative regulation of extracellular matrix constituent secretion / positive regulation of apoptotic process involved in morphogenesis / IRE1-TRAF2-ASK1 complex / Defective RIPK1-mediated regulated necrosis / varicosity / regulation of T cell cytokine production / TRAF2-GSTP1 complex / negative regulation of neuroinflammatory response / negative regulation of glial cell apoptotic process / TNFs bind their physiological receptors / negative regulation of cardiac muscle hypertrophy / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / tumor necrosis factor binding / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / interleukin-17-mediated signaling pathway / programmed necrotic cell death / positive regulation of myelination / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / CD40 receptor complex / regulation of neuroinflammatory response / signal transduction involved in regulation of gene expression / activation of NF-kappaB-inducing kinase activity / mRNA stabilization / vesicle membrane / mitogen-activated protein kinase kinase kinase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / thioesterase binding / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / regulation of immunoglobulin production / positive regulation of membrane protein ectodomain proteolysis / TNFR1-induced proapoptotic signaling / regulation of myelination / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / positive regulation of oligodendrocyte differentiation / regulation of T cell proliferation / non-canonical NF-kappaB signal transduction / protein K63-linked ubiquitination / Interleukin-10 signaling / TRAF6 mediated NF-kB activation / regulation of JNK cascade / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / regulation of protein-containing complex assembly / protein autoubiquitination / specific granule membrane / signaling adaptor activity / extrinsic apoptotic signaling pathway / ubiquitin ligase complex / positive regulation of JUN kinase activity / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-2 production / response to endoplasmic reticulum stress / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / protein catabolic process / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / positive regulation of T cell cytokine production / cellular response to growth factor stimulus / positive regulation of DNA-binding transcription factor activity / ubiquitin-protein transferase activity / intrinsic apoptotic signaling pathway in response to DNA damage / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / cell cortex / regulation of apoptotic process / protein phosphatase binding / protein-containing complex assembly / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / molecular adaptor activity / Ub-specific processing proteases / inflammatory response / immune response / membrane raft / innate immune response / neuronal cell body / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 1B / Tumor necrosis factor receptor 1B, N-terminal / TNF receptor-associated factor 2 / TNF receptor-associated factor 2, MATH domain / : / TRAF2, second zinc finger / TNF receptor-associated factor, BIRC3 binding domain / TNF receptor-associated factor BIRC3 binding domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa ...Tumour necrosis factor receptor 1B / Tumor necrosis factor receptor 1B, N-terminal / TNF receptor-associated factor 2 / TNF receptor-associated factor 2, MATH domain / : / TRAF2, second zinc finger / TNF receptor-associated factor, BIRC3 binding domain / TNF receptor-associated factor BIRC3 binding domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : / TRAF/meprin, MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 1B / TNF receptor-associated factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPark, Y.C. / Burkitt, V. / Villa, A.R. / Tong, L. / Wu, H.
CitationJournal: Nature / Year: 1999
Title: Structural basis for self-association and receptor recognition of human TRAF2.
Authors: Park, Y.C. / Burkitt, V. / Villa, A.R. / Tong, L. / Wu, H.
History
DepositionFeb 25, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
B: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
C: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
D: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
E: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
F: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
G: PROTEIN (TNF-R2)
H: PROTEIN (TNF-R2)


Theoretical massNumber of molelcules
Total (without water)132,4908
Polymers132,4908
Non-polymers00
Water16,394910
1
A: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
B: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
C: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
G: PROTEIN (TNF-R2)
H: PROTEIN (TNF-R2)


Theoretical massNumber of molelcules
Total (without water)67,3695
Polymers67,3695
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-47 kcal/mol
Surface area28240 Å2
MethodPISA
2
D: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
E: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
F: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)


Theoretical massNumber of molelcules
Total (without water)65,1213
Polymers65,1213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-36 kcal/mol
Surface area26830 Å2
MethodPISA
3
D: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
E: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
F: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)

A: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
B: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
C: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
G: PROTEIN (TNF-R2)
H: PROTEIN (TNF-R2)


Theoretical massNumber of molelcules
Total (without water)132,4908
Polymers132,4908
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation2_645-x+1,y-1/2,-z1
identity operation1_555x,y,z1
Buried area14310 Å2
ΔGint-96 kcal/mol
Surface area51610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.000, 84.400, 100.700
Angle α, β, γ (deg.)90.00, 108.70, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

-
Components

#1: Protein
PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2) / TRAF2


Mass: 21706.980 Da / Num. of mol.: 6 / Fragment: TRAF DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET24D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q12933
#2: Protein/peptide PROTEIN (TNF-R2)


Mass: 1124.243 Da / Num. of mol.: 2 / Fragment: TRAF-BINDING SITE / Source method: obtained synthetically
Details: SEQUENCE FROM HUMAN TNF-R2, SWISS PROT ACCESSION P20333
References: UniProt: P20333
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 910 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 %PEG400011
20.1 MMES11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.987
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 59650 / Num. obs: 59650 / % possible obs: 99 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.048
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.279

-
Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CA4

1ca4


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.289 3112 5.3 %RANDOM
Rwork0.234 ---
obs-51071 87.2 %-
Displacement parametersBiso mean: 47.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8644 0 0 910 9554
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.465
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.89
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.717
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.89
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.717
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

+
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