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- PDB-3m0d: Crystal structure of the TRAF1:TRAF2:cIAP2 complex -

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Basic information

Entry
Database: PDB / ID: 3m0d
TitleCrystal structure of the TRAF1:TRAF2:cIAP2 complex
Components
  • Baculoviral IAP repeat-containing protein 3
  • TNF receptor-associated factor 1
  • TNF receptor-associated factor 2TRAF2
KeywordsSIGNALING PROTEIN / trimeric helix coiled coiled / acetylation / alternative splicing / apoptosis / coiled coil / cytoplasm / metal-binding / ubl conjugation / polymorphism / chromosomal rearrangement
Function / homology
Function and homology information


CD40 receptor binding / regulation of extrinsic apoptotic signaling pathway / 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 ...CD40 receptor binding / regulation of extrinsic apoptotic signaling pathway / 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 / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / regulation of innate immune response / regulation of toll-like receptor signaling pathway / non-canonical NF-kappaB signal transduction / protein K63-linked ubiquitination / 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 / protein autoubiquitination / canonical NF-kappaB signal transduction / 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 / positive regulation of canonical NF-kappaB signal transduction / regulation of apoptotic process / 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
Similarity search - Function
TNF receptor-associated factor 1, 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 / Zinc finger, TRAF-type ...TNF receptor-associated factor 1, 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 / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / : / 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 / TNF receptor-associated factor 1 / Baculoviral IAP repeat-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1
D: Baculoviral IAP repeat-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2615
Polymers31,1964
Non-polymers651
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-85 kcal/mol
Surface area14710 Å2
MethodPISA
2
D: Baculoviral IAP repeat-containing protein 3
hetero molecules

A: TNF receptor-associated factor 2
B: TNF receptor-associated factor 2
C: TNF receptor-associated factor 1


Theoretical massNumber of molelcules
Total (without water)31,2615
Polymers31,1964
Non-polymers651
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation8_555y,-x+1/2,z+1/41
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-83 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.867, 91.867, 88.702
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.: 2 / 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 TNF receptor-associated factor 1 / Epstein-Barr virus-induced protein 6


Mass: 7468.690 Da / Num. of mol.: 1 / Fragment: Residues 266-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF1, EBI6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13077
#3: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13489
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.99 % / Mosaicity: 0.486 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.15M AmSO4, 0.1M MES, 15% PEG 4000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9137 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.097 / Rsym value: 0.062 / Χ2: 1.35 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.94.40.4788990.871197.8
2.9-3.026.20.3649040.8741100
3.02-3.156.40.2919110.8841100
3.15-3.326.40.21689511100
3.32-3.536.40.1619201.0911100
3.53-3.86.40.1159091.2261100
3.8-4.186.40.0829241.4651100
4.18-4.796.30.0669061.7211100
4.79-6.036.20.089281.9841100
6.03-5060.0449412.271199.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3M0A (TRAF2:ciap2)

3m0a


Resolution: 2.8→32.5 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.937 / SU B: 27.453 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.432 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 436 4.8 %RANDOM
Rwork0.197 8753 --
obs0.204 8753 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.197 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å20 Å2
2---1.83 Å20 Å2
3---3.66 Å2
Refinement stepCycle: LAST / Resolution: 2.8→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 1 42 2089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222066
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9752780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74924.39691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.97715392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4461516
X-RAY DIFFRACTIONr_chiral_restr0.1210.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021500
X-RAY DIFFRACTIONr_mcbond_it0.641.51313
X-RAY DIFFRACTIONr_mcangle_it1.28822100
X-RAY DIFFRACTIONr_scbond_it2.5173753
X-RAY DIFFRACTIONr_scangle_it4.4614.5680
LS refinement shellResolution: 2.8→2.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 28 -
Rwork0.297 603 -
all-631 -
obs--93.9 %
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)
10.48620.30880.136512.47720.84250.5842-0.0326-0.12360.15010.36140.2125-0.43410.0936-0.0503-0.17980.3096-0.03010.06870.1373-0.00210.227526.6863-1.517932.6451
20.29471.569-0.068924.32670.19050.5824-0.26850.03840.0559-0.17660.53780.09090.05250.1436-0.26930.34390.02170.00040.12750.0190.199229.9562-1.695128.1585
30.85591.4841-0.65923.0927-4.00511.37970.01130.08280.12890.68190.25751.01280.0002-0.0886-0.26880.2254-0.00020.01620.1380.00390.108524.6142-1.141527.7754
43.67770.6461-3.29014.4132.11458.2418-0.17840.374-0.5075-0.46280.00820.10911.07790.01280.17020.45740.0925-0.11350.1696-0.01580.324233.3889.11019.106
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A267 - 329
2X-RAY DIFFRACTION2B267 - 329
3X-RAY DIFFRACTION3C266 - 328
4X-RAY DIFFRACTION4D25 - 99

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