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- PDB-1d0j: STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M... -

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Basic information

Entry
Database: PDB / ID: 1d0j
TitleSTRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE
Components
  • 4-1BB LIGAND RECEPTOR
  • TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
KeywordsAPOPTOSIS / B-SANDWICH / PROTEIN-PEPTIDE COMPLEX
Function / homology
Function and homology information


TORC2 complex disassembly / CD40 receptor binding / TORC1 complex assembly / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily complex / 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 / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily complex / 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 / regulation of immature T cell proliferation in thymus / 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 / positive regulation of extrinsic apoptotic signaling pathway / mitogen-activated protein kinase kinase kinase binding / regulation of JNK cascade / signal transduction involved in regulation of gene expression / TNFR1-induced proapoptotic signaling / TRAF6 mediated IRF7 activation / RIPK1-mediated regulated necrosis / positive regulation of JUN kinase activity / TRAF6 mediated NF-kB activation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / 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 / protein catabolic process / Regulation of TNFR1 signaling / : / 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 / signaling receptor activity / protein-containing complex assembly / cell cortex / protein phosphatase binding / regulation of apoptotic process / protein-macromolecule adaptor activity / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / membrane raft / negative regulation of cell population proliferation / innate immune response / external side of plasma membrane / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / protein-containing complex binding / enzyme binding / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / 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 / Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa ...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 / Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / 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 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 9 / TNF receptor-associated factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 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 10, 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 1.4Nov 6, 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_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_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: 4-1BB LIGAND RECEPTOR
H: 4-1BB LIGAND RECEPTOR
I: 4-1BB LIGAND RECEPTOR
J: 4-1BB LIGAND RECEPTOR
K: 4-1BB LIGAND RECEPTOR


Theoretical massNumber of molelcules
Total (without water)117,19011
Polymers117,19011
Non-polymers00
Water4,306239
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: 4-1BB LIGAND RECEPTOR
H: 4-1BB LIGAND RECEPTOR


Theoretical massNumber of molelcules
Total (without water)58,2805
Polymers58,2805
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-29 kcal/mol
Surface area22790 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
I: 4-1BB LIGAND RECEPTOR
J: 4-1BB LIGAND RECEPTOR
K: 4-1BB LIGAND RECEPTOR


Theoretical massNumber of molelcules
Total (without water)58,9106
Polymers58,9106
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-29 kcal/mol
Surface area23060 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: 4-1BB LIGAND RECEPTOR
H: 4-1BB LIGAND RECEPTOR

D: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
E: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
F: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
I: 4-1BB LIGAND RECEPTOR
J: 4-1BB LIGAND RECEPTOR
K: 4-1BB LIGAND RECEPTOR


Theoretical massNumber of molelcules
Total (without water)117,19011
Polymers117,19011
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
identity operation1_555x,y,z1
Buried area11610 Å2
ΔGint-60 kcal/mol
Surface area44790 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: 4-1BB LIGAND RECEPTOR
H: 4-1BB LIGAND RECEPTOR

D: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
E: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
F: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
I: 4-1BB LIGAND RECEPTOR
J: 4-1BB LIGAND RECEPTOR
K: 4-1BB LIGAND RECEPTOR


Theoretical massNumber of molelcules
Total (without water)117,19011
Polymers117,19011
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
identity operation1_555x,y,z1
Buried area11160 Å2
ΔGint-60 kcal/mol
Surface area45240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.9, 85.6, 124.1
Angle α, β, γ (deg.)90, 119.1, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2


Mass: 19006.916 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
4-1BB LIGAND RECEPTOR


Mass: 629.617 Da / Num. of mol.: 5 / Fragment: TRAF2-BINDING SEQUENCE / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN MOUSE (MUS MUSCULUS)
References: UniProt: P20334
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE DEPOSITED TRAF2-RECEPTOR PEPTIDE COMPLEX CONTAINS 6 TRAF2 PER ASYMMETRIC UNIT, ONE OF WHICH ...THE DEPOSITED TRAF2-RECEPTOR PEPTIDE COMPLEX CONTAINS 6 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: 2.69 Å3/Da / Density % sol: 54.27 %
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: NSLS / Beamline: X4A / Wavelength: 0.937
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.937 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / % possible obs: 90.2 % / Rmerge(I) obs: 0.061
Reflection shellHighest resolution: 2.5 Å / Rmerge(I) obs: 0.296 / % possible all: 85.2
Reflection shell
*PLUS
% possible obs: 85.2 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→20 Å / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.227 / Rfactor obs: 0.227
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7873 0 0 239 8112
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS

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