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- PDB-1czz: STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 1... -

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Basic information

Entry
Database: PDB / ID: 1czz
TitleSTRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 17-RESIDUE CD40 PEPTIDE
Components
  • CD 40 PEPTIDE
  • TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
KeywordsAPOPTOSIS / B-SANDWICH / PROTEIN-PEPTIDE COMPLEX
Function / homology
Function and homology information


positive regulation of protein kinase C signaling / TORC2 complex disassembly / cellular response to erythropoietin / CD40 receptor binding / TORC1 complex assembly / tumor necrosis factor receptor superfamily complex / varicosity / sphingolipid binding / B cell mediated immunity / positive regulation of interleukin-4-mediated signaling pathway ...positive regulation of protein kinase C signaling / TORC2 complex disassembly / cellular response to erythropoietin / CD40 receptor binding / TORC1 complex assembly / tumor necrosis factor receptor superfamily complex / varicosity / sphingolipid binding / B cell mediated immunity / positive regulation of interleukin-4-mediated signaling pathway / immune response-regulating cell surface receptor signaling pathway / IRE1-TRAF2-ASK1 complex / TRAF2-GSTP1 complex / Defective RIPK1-mediated regulated necrosis / CD27 signaling pathway / CD40 signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB 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 / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / programmed necrotic cell death / CD40 receptor complex / positive regulation of isotype switching to IgG isotypes / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / mRNA stabilization / regulation of immunoglobulin production / regulation of JNK cascade / positive regulation of extrinsic apoptotic signaling pathway / signal transduction involved in regulation of gene expression / non-canonical NF-kappaB signal transduction / vesicle membrane / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / defense response to protozoan / response to cobalamin / B cell activation / TRAF6 mediated NF-kB activation / B cell proliferation / cellular response to interleukin-1 / positive regulation of JUN kinase activity / response to type II interferon / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of endothelial cell apoptotic process / protein K63-linked ubiquitination / cell surface receptor signaling pathway via JAK-STAT / positive regulation of blood vessel endothelial cell migration / ubiquitin ligase complex / regulation of protein-containing complex assembly / antigen binding / protein autoubiquitination / tumor necrosis factor-mediated signaling pathway / signaling adaptor activity / positive regulation of B cell proliferation / positive regulation of interleukin-12 production / positive regulation of interleukin-2 production / cellular response to nitric oxide / response to endoplasmic reticulum stress / T cell activation / positive regulation of DNA-binding transcription factor activity / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of TNFR1 signaling / protein catabolic process / RING-type E3 ubiquitin transferase / positive regulation of T cell cytokine production / platelet activation / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / intracellular calcium ion homeostasis / cellular response to mechanical stimulus / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of NF-kappaB transcription factor activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / cellular response to tumor necrosis factor / signaling receptor activity / cellular response to lipopolysaccharide / cell cortex / protein-containing complex assembly / protein phosphatase binding / protein-macromolecule adaptor activity / regulation of apoptotic process / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / Ub-specific processing proteases / inflammatory response / protein domain specific binding
Similarity search - Function
Tumour necrosis factor receptor 5 / Tumour necrosis factor receptor 5, 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 ...Tumour necrosis factor receptor 5 / Tumour necrosis factor receptor 5, 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 / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / 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 5 / TNF receptor-associated factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsYe, H. / Park, Y.C. / Kreishman, M. / Kieff, E. / Wu, H.
Citation
Journal: Mol.Cell / Year: 1999
Title: The structural basis for the recognition of diverse receptor sequences by TRAF2.
Authors: Ye, H. / Park, Y.C. / Kreishman, M. / Kieff, E. / Wu, H.
#1: Journal: 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
DepositionSep 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
B: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
C: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
D: CD 40 PEPTIDE
E: CD 40 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)65,4175
Polymers65,4175
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-48 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.400, 81.100, 77.200
Angle α, β, γ (deg.)90.00, 96.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2 / TRAF2


Mass: 21132.373 Da / Num. of mol.: 3 / Fragment: TRAF DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET24D / Production host: Escherichia coli (E. coli) / References: UniProt: Q12933
#2: Protein/peptide CD 40 PEPTIDE / CD40


Mass: 1010.144 Da / Num. of mol.: 2 / Fragment: TRAF2-BINDING REGION / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN HUMANS (HOMO SAPIENS).
References: UniProt: P25942
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE DEPOSITED TRAF2-RECEPTOR PEPTIDE COMPLEX CONTAINS 3 TRAF2 PER ASYMMETRIC UNIT, ONE OF WHICH ...THE DEPOSITED TRAF2-RECEPTOR PEPTIDE COMPLEX CONTAINS 3 TRAF2 PER ASYMMETRIC UNIT, ONE OF WHICH DOES NOT HAVE THE PEPTIDE BOUND DUE TO CONFLICT WITH CRYSTAL PACKING.
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: PEG4K, MES, PH 5.6, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 %PEG400011
20.2 Mammonium acetate11
30.1 Mcitrate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.937
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.937 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 2.7 Å / % possible obs: 98.6 % / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 99.4 % / Rmerge(I) obs: 0.255

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 2.7→20 Å / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.221 / Rfactor obs: 0.221 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 0 104 4444

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