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- PDB-3m0a: Crystal structure of TRAF2:cIAP2 complex -

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Basic information

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


CD40 receptor binding / tumor necrosis factor receptor superfamily complex / regulation of cysteine-type endopeptidase activity / sphingolipid binding / regulation of RIG-I signaling pathway / Defective RIPK1-mediated regulated necrosis / IRE1-TRAF2-ASK1 complex / TRAF2-GSTP1 complex / negative regulation of glial cell apoptotic process / tumor necrosis factor binding ...CD40 receptor binding / tumor necrosis factor receptor superfamily complex / regulation of cysteine-type endopeptidase activity / sphingolipid binding / regulation of RIG-I signaling pathway / Defective RIPK1-mediated regulated necrosis / IRE1-TRAF2-ASK1 complex / TRAF2-GSTP1 complex / negative regulation of glial cell apoptotic process / tumor necrosis factor binding / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / interleukin-17-mediated signaling pathway / programmed necrotic cell death / TNF signaling / regulation of necroptotic process / Caspase activation via Death Receptors in the presence of ligand / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / CD40 receptor complex / signal transduction involved in regulation of gene expression / activation of NF-kappaB-inducing kinase activity / vesicle membrane / mRNA stabilization / negative regulation of necroptotic process / positive regulation of tumor necrosis factor-mediated signaling pathway / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / tumor necrosis factor receptor binding / regulation of immunoglobulin production / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / regulation of innate immune response / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / regulation of toll-like receptor signaling pathway / protein K63-linked ubiquitination / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / regulation of JNK cascade / regulation of protein-containing complex assembly / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / canonical NF-kappaB signal transduction / protein autoubiquitination / ubiquitin ligase complex / signaling adaptor activity / positive regulation of JUN kinase activity / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-2 production / response to endoplasmic reticulum stress / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / protein catabolic process / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / cytoplasmic side of plasma membrane / Regulation of necroptotic cell death / positive regulation of T cell cytokine production / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of DNA-binding transcription factor activity / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / cell cortex / regulation of inflammatory response / transferase activity / spermatogenesis / protein-containing complex assembly / protein phosphatase binding / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / molecular adaptor activity / regulation of cell cycle / Ub-specific processing proteases / membrane raft / innate immune response / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / enzyme binding / signal transduction / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / metal ion 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 / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. ...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 / : / 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 / TRAF-like / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / 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 RING-type / Zinc finger, C3HC4 type (RING finger) / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

#1: Protein TNF receptor-associated factor 2 / TRAF2 / 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 / Water


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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

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