[English] 日本語
Yorodumi
- PDB-3m0a: Crystal structure of TRAF2:cIAP2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m0a
TitleCrystal structure of TRAF2:cIAP2 complex
Components
  • Baculoviral IAP repeat-containing protein 3
  • TNF receptor-associated factor 2
KeywordsSIGNALING PROTEIN / TRAF2: cIAP2 and the TRAF1: TRAF2: cIAP2 complexes / Apoptosis / Metal-binding / Phosphoprotein
Function / homology
Function and homology information


TORC2 complex disassembly / CD40 receptor binding / TORC1 complex assembly / tumor necrosis factor receptor superfamily complex / sphingolipid binding / regulation of RIG-I signaling pathway / IRE1-TRAF2-ASK1 complex / TRAF2-GSTP1 complex / CD27 signaling pathway / Defective RIPK1-mediated regulated necrosis ...TORC2 complex disassembly / CD40 receptor binding / TORC1 complex assembly / tumor necrosis factor receptor superfamily complex / sphingolipid binding / regulation of RIG-I signaling pathway / IRE1-TRAF2-ASK1 complex / TRAF2-GSTP1 complex / CD27 signaling pathway / Defective RIPK1-mediated regulated necrosis / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / CD40 signaling pathway / tumor necrosis factor binding / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / negative regulation of glial cell apoptotic process / interleukin-17-mediated signaling pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / TNF signaling / programmed necrotic cell death / Caspase activation via Death Receptors in the presence of ligand / CD40 receptor complex / negative regulation of necroptotic process / thioesterase binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / regulation of immunoglobulin production / mRNA stabilization / regulation of JNK cascade / positive regulation of extrinsic apoptotic signaling pathway / non-canonical NF-kappaB signal transduction / vesicle membrane / mitogen-activated protein kinase kinase kinase binding / TNFR1-induced proapoptotic signaling / signal transduction involved in regulation of gene expression / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / regulation of toll-like receptor signaling pathway / regulation of innate immune response / positive regulation of JUN kinase activity / TRAF6 mediated NF-kB activation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / protein K63-linked ubiquitination / canonical NF-kappaB signal transduction / ubiquitin ligase complex / regulation of protein-containing complex assembly / protein autoubiquitination / tumor necrosis factor-mediated signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / positive regulation of protein ubiquitination / signaling adaptor activity / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of interleukin-2 production / cellular response to nitric oxide / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / T cell activation / response to endoplasmic reticulum stress / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / protein catabolic process / positive regulation of NF-kappaB transcription factor activity / positive regulation of T cell cytokine production / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / transferase activity / protein-containing complex assembly / regulation of inflammatory response / cell cortex / protein phosphatase binding / protein-macromolecule adaptor activity / spermatogenesis / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / Ub-specific processing proteases / regulation of cell cycle / membrane raft / innate immune response / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / protein-containing complex binding / enzyme binding / signal transduction / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / : / TRAF/meprin, MATH domain ...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 / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / Caspase recruitment domain / BIR repeat. / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / TRAF-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Zinc finger, C3HC4 type (RING finger) / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Death-like domain superfamily / Ring finger / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TNF receptor-associated factor 2 / Baculoviral IAP repeat-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.61 Å
AuthorsKabaleeswaran, V. / Wu, H.
CitationJournal: Mol.Cell / Year: 2010
Title: Crystal structures of the TRAF2: cIAP2 and the TRAF1: TRAF2: cIAP2 complexes: affinity, specificity, and regulation.
Authors: Zheng, C. / Kabaleeswaran, V. / Wang, Y. / Cheng, G. / Wu, H.
History
DepositionMar 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2015Group: Structure summary
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TNF receptor-associated factor 2
B: TNF receptor-associated factor 2
C: TNF receptor-associated factor 2
D: Baculoviral IAP repeat-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3655
Polymers31,3004
Non-polymers651
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-88 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.123, 92.123, 85.971
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein TNF receptor-associated factor 2 / Tumor necrosis factor type 2 receptor-associated protein 3


Mass: 7572.612 Da / Num. of mol.: 3 / Fragment: Residues 266-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF2 / Plasmid: pET26B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL / References: UniProt: Q12933
#2: Protein Baculoviral IAP repeat-containing protein 3 / Inhibitor of apoptosis protein 1 / IAP-1 / hIAP-1 / hIAP1 / C-IAP2 / TNFR2-TRAF-signaling complex ...Inhibitor of apoptosis protein 1 / IAP-1 / hIAP-1 / hIAP1 / C-IAP2 / TNFR2-TRAF-signaling complex protein 1 / IAP homolog C / Apoptosis inhibitor 2 / API2 / RING finger protein 49


Mass: 8581.972 Da / Num. of mol.: 1 / Fragment: Residues 26-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC3, API2, IAP1, MIHC, RNF49 / Plasmid: pET26B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL / References: UniProt: Q13489
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.79 % / Mosaicity: 0.525 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 8% PEG 3350, 6% Tacsimate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.2822,1.2832,1.2664
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2009
RadiationMonochromator: Si-111 double cryst / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28221
21.28321
31.26641
ReflectionResolution: 2.6→50 Å / Num. obs: 11032 / % possible obs: 88.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.049 / Χ2: 1.51 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.692.50.39310021.08146.4
2.69-2.830.30914761.062168.7
2.8-2.933.20.22917321.133180.9
2.93-3.083.50.17820911.217196.4
3.08-3.283.80.12921561.2781100
3.28-3.533.80.08421671.4741100
3.53-3.883.80.05621581.5391100
3.88-4.453.80.0421261.7421100
4.45-5.63.80.03921392.028199
5.6-503.60.02820581.905195.3

-
Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.61→32.6 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 25.24 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.66 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.268 459 4.7 %RANDOM
Rwork0.227 9230 --
obs-9689 87.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.253 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å20 Å20 Å2
2---2.67 Å20 Å2
3---5.34 Å2
Refinement stepCycle: LAST / Resolution: 2.61→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 1 36 1926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211910
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.9692588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52823.57170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.51415312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0651514
X-RAY DIFFRACTIONr_chiral_restr0.1160.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021401
X-RAY DIFFRACTIONr_mcbond_it0.751.51298
X-RAY DIFFRACTIONr_mcangle_it1.45422047
X-RAY DIFFRACTIONr_scbond_it2.4923612
X-RAY DIFFRACTIONr_scangle_it4.1414.5541
LS refinement shellResolution: 2.61→2.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.525 12 -
Rwork0.419 312 -
all-324 -
obs--40.1 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.20820.94570.07952.03990.67880.4717-0.0748-0.14340.04290.38930.33230.0086-0.0228-0.2601-00.7974-0.0781-0.06540.40740.08440.6726.1772-0.585672.7212
20.29360.24950.30710.87320.29670.68650.03440.0179-0.02110.61640.0069-0.02010.07210.1433-00.76810.0025-0.0910.38290.01960.6429.383-0.901468.8999
30.2589-1.1566-0.08391.931-0.46050.6871-0.20230.187-0.0376-0.0740.42390.92050.1264-0.070.00220.7183-0.041-0.03430.3896-0.03030.550424.1122-0.740968.1228
42.13810.6026-1.13262.3286-0.83554.1531-0.10610.0931-0.3008-0.20360.0046-0.3090.6955-0.137600.5763-0.01220.03250.4935-0.05330.523232.16268.860950.0993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A267 - 328
2X-RAY DIFFRACTION2B267 - 328
3X-RAY DIFFRACTION3C267 - 328
4X-RAY DIFFRACTION4D25 - 99

+
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