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- PDB-1d00: STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 5... -

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Basic information

Entry
Database: PDB / ID: 1d00
TitleSTRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 5-RESIDUE CD40 PEPTIDE
Components
  • B-CELL SURFACE ANTIGEN CD40
  • TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
KeywordsAPOPTOSIS / B-SANDWICH / PROTEIN-PEPTIDE COMPLEX
Function / homology
Function and homology information


cellular response to erythropoietin / CD40 receptor binding / tumor necrosis factor receptor superfamily complex / B cell mediated immunity / sphingolipid binding / immune response-regulating cell surface receptor signaling pathway / response to peptide / positive regulation of protein kinase C signaling / IRE1-TRAF2-ASK1 complex / Defective RIPK1-mediated regulated necrosis ...cellular response to erythropoietin / CD40 receptor binding / tumor necrosis factor receptor superfamily complex / B cell mediated immunity / sphingolipid binding / immune response-regulating cell surface receptor signaling pathway / response to peptide / positive regulation of protein kinase C signaling / IRE1-TRAF2-ASK1 complex / Defective RIPK1-mediated regulated necrosis / varicosity / TRAF2-GSTP1 complex / CD40 signaling pathway / negative regulation of glial cell apoptotic process / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / tumor necrosis factor binding / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / interleukin-17-mediated signaling pathway / programmed necrotic cell death / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / positive regulation of isotype switching to IgG isotypes / CD40 receptor complex / signal transduction involved in regulation of gene expression / positive regulation of endothelial cell apoptotic process / mitogen-activated protein kinase kinase kinase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / thioesterase binding / tumor necrosis factor receptor binding / mRNA stabilization / positive regulation of extrinsic apoptotic signaling pathway / regulation of immunoglobulin production / vesicle membrane / TNFR1-induced proapoptotic signaling / non-canonical NF-kappaB signal transduction / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / B cell activation / response to cobalamin / B cell proliferation / defense response to protozoan / response to type II interferon / TRAF6 mediated NF-kB activation / protein K63-linked ubiquitination / regulation of JNK cascade / cellular response to interleukin-1 / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / regulation of protein-containing complex assembly / positive regulation of blood vessel endothelial cell migration / protein autoubiquitination / signaling adaptor activity / ubiquitin ligase complex / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of JUN kinase activity / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-12 production / positive regulation of interleukin-2 production / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to endoplasmic reticulum stress / positive regulation of GTPase activity / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / antigen binding / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / positive regulation of MAP kinase activity / RING-type E3 ubiquitin transferase / protein catabolic process / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / positive regulation of T cell cytokine production / platelet activation / positive regulation of DNA-binding transcription factor activity / intracellular calcium ion homeostasis / cellular response to mechanical stimulus / positive regulation of angiogenesis / ubiquitin-protein transferase activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cellular response to tumor necrosis factor / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / protein-macromolecule adaptor activity / cell cortex / protein-containing complex assembly / cellular response to lipopolysaccharide / protein phosphatase binding / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / molecular adaptor activity / Ub-specific processing proteases / inflammatory response / positive regulation of protein phosphorylation / membrane raft / protein domain specific binding / external side of plasma membrane
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 / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : / TRAF/meprin, MATH domain / 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 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 29, 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

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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: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
E: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
F: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
G: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
H: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
I: B-CELL SURFACE ANTIGEN CD40
J: B-CELL SURFACE ANTIGEN CD40
K: B-CELL SURFACE ANTIGEN CD40
L: B-CELL SURFACE ANTIGEN CD40
M: B-CELL SURFACE ANTIGEN CD40
N: B-CELL SURFACE ANTIGEN CD40
O: B-CELL SURFACE ANTIGEN CD40
P: B-CELL SURFACE ANTIGEN CD40


Theoretical massNumber of molelcules
Total (without water)156,82916
Polymers156,82916
Non-polymers00
Water1,26170
1
A: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
I: B-CELL SURFACE ANTIGEN CD40

A: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
I: B-CELL SURFACE ANTIGEN CD40

A: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
I: B-CELL SURFACE ANTIGEN CD40


Theoretical massNumber of molelcules
Total (without water)58,8116
Polymers58,8116
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555z,x,y1
crystal symmetry operation3_555y,z,x1
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
K: B-CELL SURFACE ANTIGEN CD40
L: B-CELL SURFACE ANTIGEN CD40
M: B-CELL SURFACE ANTIGEN CD40


Theoretical massNumber of molelcules
Total (without water)58,8116
Polymers58,8116
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-34 kcal/mol
Surface area22840 Å2
MethodPISA
3
F: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
G: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
H: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
N: B-CELL SURFACE ANTIGEN CD40
O: B-CELL SURFACE ANTIGEN CD40
P: B-CELL SURFACE ANTIGEN CD40


Theoretical massNumber of molelcules
Total (without water)58,8116
Polymers58,8116
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-35 kcal/mol
Surface area23210 Å2
MethodPISA
4
B: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
J: B-CELL SURFACE ANTIGEN CD40

B: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
J: B-CELL SURFACE ANTIGEN CD40

B: TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2
J: B-CELL SURFACE ANTIGEN CD40


Theoretical massNumber of molelcules
Total (without water)58,8116
Polymers58,8116
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654z+1,x,y-11
crystal symmetry operation3_564y,z+1,x-11
Unit cell
Length a, b, c (Å)111.4, 111.4, 111.4
Angle α, β, γ (deg.)103.7, 103.7, 103.7
Int Tables number146
Space group name H-MR3

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Components

#1: Protein
TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2


Mass: 19006.916 Da / Num. of mol.: 8 / 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: GenBank: 1363002, UniProt: Q12933*PLUS
#2: Protein/peptide
B-CELL SURFACE ANTIGEN CD40


Mass: 596.653 Da / Num. of mol.: 8 / Fragment: ACETYLATED 5-RESIDUE PEPTIDE / 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.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: PEG4K, MES, Ph6.0, VAPOR DIFFUSION, temperature 20K
Crystal grow
*PLUS
pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-15 %PEG40001reservoir
20.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.937
DetectorType: ADSC / Detector: CCD / Date: Dec 1, 1998
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: 100 % / Rmerge(I) obs: 0.055
Reflection shellHighest resolution: 2 Å / Rmerge(I) obs: 0.18 / % possible all: 99
Reflection
*PLUS
% possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.18

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
RefinementResolution: 2→20 Å / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.219 / σ(F): 2 / σ(I): 0
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10600 0 0 70 10670

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