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- PDB-1czy: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE TRAF DOMAIN OF HUMAN... -

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Basic information

Entry
Database: PDB / ID: 1czy
TitleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE TRAF DOMAIN OF HUMAN TRAF2 AND AN LMP1 BINDING PEPTIDE
Components
  • LATENT MEMBRANE PROTEIN 1
  • TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
KeywordsAPOPTOSIS / BETA SANDWICH / PROTEIN-PEPTIDE COMPLEX / SIGNALING PROTEIN
Function / homology
Function and homology information


TORC2 complex disassembly / CD40 receptor binding / TORC1 complex assembly / tumor necrosis factor receptor superfamily complex / symbiont-mediated activation of host NF-kappaB cascade / sphingolipid binding / TRAF2-GSTP1 complex / IRE1-TRAF2-ASK1 complex / CD27 signaling pathway / Defective RIPK1-mediated regulated necrosis ...TORC2 complex disassembly / CD40 receptor binding / TORC1 complex assembly / tumor necrosis factor receptor superfamily complex / symbiont-mediated activation of host NF-kappaB cascade / sphingolipid binding / TRAF2-GSTP1 complex / IRE1-TRAF2-ASK1 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 / interleukin-17-mediated signaling pathway / negative regulation of glial cell apoptotic process / TNF signaling / CD40 receptor complex / programmed necrotic cell death / Caspase activation via Death Receptors in the presence of ligand / thioesterase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / mRNA stabilization / regulation of immunoglobulin production / non-canonical NF-kappaB signal transduction / vesicle membrane / regulation of JNK cascade / positive regulation of extrinsic apoptotic signaling pathway / mitogen-activated protein kinase kinase kinase binding / signal transduction involved in regulation of gene expression / TNFR1-induced proapoptotic signaling / TRAF6 mediated IRF7 activation / RIPK1-mediated regulated necrosis / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / positive regulation of JUN kinase activity / TRAF6 mediated NF-kB activation / host cell membrane / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / protein K63-linked ubiquitination / ubiquitin ligase complex / regulation of protein-containing complex assembly / protein autoubiquitination / signaling adaptor activity / positive regulation of interleukin-2 production / cellular response to nitric oxide / response to endoplasmic reticulum stress / T cell activation / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / protein catabolic process / positive regulation of NF-kappaB transcription factor activity / positive regulation of T cell cytokine production / RING-type E3 ubiquitin transferase / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein-containing complex assembly / cell cortex / protein phosphatase binding / protein-macromolecule adaptor activity / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / membrane raft / innate immune response / ubiquitin protein ligase binding / protein kinase binding / protein-containing complex binding / host cell plasma membrane / enzyme binding / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Herpesvirus latent membrane 1 / Herpesvirus latent membrane protein 1 (LMP1) / 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 ...Herpesvirus latent membrane 1 / Herpesvirus latent membrane protein 1 (LMP1) / 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 / 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
Latent membrane protein 1 / TNF receptor-associated factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Oct 9, 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 / struct_site
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 / _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: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
B: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
C: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
D: LATENT MEMBRANE PROTEIN 1
E: LATENT MEMBRANE PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)58,6985
Polymers58,6985
Non-polymers00
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-29 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.200, 76.800, 66.900
Angle α, β, γ (deg.)90.00, 93.20, 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: 19032.953 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 LATENT MEMBRANE PROTEIN 1 / LMP1


Mass: 799.783 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: P03230
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: PEG4K, MES BUFFER, pH 6.00, VAPOR DIFFUSION, temperature 20K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-15 %PEG400011
20.1 MMES11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.018
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.018 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.15

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 2→20 Å
RfactorSelection details
Rfree0.245 6%
Rwork0.206 -
obs0.206 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3957 0 0 391 4348

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