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- PDB-1d0a: STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 1d0a
TitleSTRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE
Components
  • OX40L RECEPTOR PEPTIDE
  • TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
KeywordsAPOPTOSIS / B-SANDWICH / PROTEIN-PEPTIDE COMPLEX
Function / homology
Function and homology information


CD40 receptor binding / tumor necrosis factor receptor superfamily complex / sphingolipid binding / tumor necrosis factor receptor activity / IRE1-TRAF2-ASK1 complex / TRAF2-GSTP1 complex / Defective RIPK1-mediated regulated necrosis / CD40 signaling pathway / TNFs bind their physiological receptors / interleukin-17-mediated signaling pathway ...CD40 receptor binding / tumor necrosis factor receptor superfamily complex / sphingolipid binding / tumor necrosis factor receptor activity / IRE1-TRAF2-ASK1 complex / TRAF2-GSTP1 complex / Defective RIPK1-mediated regulated necrosis / CD40 signaling pathway / TNFs bind their physiological receptors / interleukin-17-mediated signaling pathway / tumor necrosis factor binding / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / negative regulation of glial cell apoptotic process / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNF signaling / programmed necrotic cell death / Caspase activation via Death Receptors in the presence of ligand / CD40 receptor complex / regulation of immunoglobulin production / signal transduction involved in regulation of gene expression / positive regulation of tumor necrosis factor-mediated signaling pathway / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / tumor necrosis factor receptor binding / mRNA stabilization / positive regulation of extrinsic apoptotic signaling pathway / vesicle membrane / TNFR1-induced proapoptotic signaling / non-canonical NF-kappaB signal transduction / TRAF6 mediated IRF7 activation / positive regulation of immunoglobulin production / RIPK1-mediated regulated necrosis / TRAF6 mediated NF-kB activation / protein K63-linked ubiquitination / regulation of JNK cascade / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / regulation of protein-containing complex assembly / cellular response to nitric oxide / protein autoubiquitination / signaling adaptor activity / ubiquitin ligase complex / T cell proliferation / positive regulation of B cell proliferation / positive regulation of JUN kinase activity / tumor necrosis factor-mediated signaling pathway / response to endoplasmic reticulum stress / positive regulation of interleukin-2 production / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / positive regulation of DNA-binding transcription factor activity / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / protein catabolic process / negative regulation of DNA-binding transcription factor activity / Regulation of necroptotic cell death / positive regulation of T cell cytokine production / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / virus receptor activity / cell cortex / protein-macromolecule adaptor activity / protein-containing complex assembly / protein phosphatase binding / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / inflammatory response / immune response / membrane raft / external side of plasma membrane / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / enzyme binding / cell surface / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 4 / Tumour necrosis factor receptor 4, 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 ...Tumour necrosis factor receptor 4 / Tumour necrosis factor receptor 4, 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 / Putative ephrin-receptor 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 4 / 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 9, 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 16, 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 / _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: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
E: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
F: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
G: OX40L RECEPTOR PEPTIDE
H: OX40L RECEPTOR PEPTIDE
I: OX40L RECEPTOR PEPTIDE
J: OX40L RECEPTOR PEPTIDE
K: OX40L RECEPTOR PEPTIDE
L: OX40L RECEPTOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)118,04212
Polymers118,04212
Non-polymers00
Water12,881715
1
A: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
B: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
C: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
G: OX40L RECEPTOR PEPTIDE
H: OX40L RECEPTOR PEPTIDE
I: OX40L RECEPTOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)59,0216
Polymers59,0216
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-35 kcal/mol
Surface area23040 Å2
MethodPISA
2
D: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
E: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
F: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
J: OX40L RECEPTOR PEPTIDE
K: OX40L RECEPTOR PEPTIDE
L: OX40L RECEPTOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)59,0216
Polymers59,0216
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-34 kcal/mol
Surface area23010 Å2
MethodPISA
3
A: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
B: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
C: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
G: OX40L RECEPTOR PEPTIDE
H: OX40L RECEPTOR PEPTIDE
I: OX40L RECEPTOR PEPTIDE

D: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
E: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
F: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
J: OX40L RECEPTOR PEPTIDE
K: OX40L RECEPTOR PEPTIDE
L: OX40L RECEPTOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)118,04212
Polymers118,04212
Non-polymers00
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area14170 Å2
ΔGint-72 kcal/mol
Surface area44840 Å2
MethodPISA
4
A: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
B: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
C: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
G: OX40L RECEPTOR PEPTIDE
H: OX40L RECEPTOR PEPTIDE
I: OX40L RECEPTOR PEPTIDE

D: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
E: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
F: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
J: OX40L RECEPTOR PEPTIDE
K: OX40L RECEPTOR PEPTIDE
L: OX40L RECEPTOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)118,04212
Polymers118,04212
Non-polymers00
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area13650 Å2
ΔGint-71 kcal/mol
Surface area45360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.400, 85.600, 125.400
Angle α, β, γ (deg.)90.00, 118.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2


Mass: 19032.953 Da / Num. of mol.: 6 / 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
OX40L RECEPTOR PEPTIDE


Mass: 640.682 Da / Num. of mol.: 6 / Fragment: TRAF-BINDING SEQUENCE / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN HUMANS (HOMO SAPIENS)
References: UniProt: P43489
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 293K
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: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.937
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.937 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.038
Reflection shellHighest resolution: 2 Å / Rmerge(I) obs: 0.127 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 2→20 Å / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.225 / Rfactor obs: 0.225
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7968 0 0 715 8683

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