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- PDB-1ca9: STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A P... -

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Basic information

Entry
Database: PDB / ID: 1ca9
TitleSTRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A PEPTIDE FROM TNF-R2
Components
  • PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
  • PROTEIN (TNF-R2)
KeywordsTNF SIGNALING / TRAF / ADAPTER PROTEIN / CELL SURVIVAL
Function / homology
Function and homology information


glial cell-neuron signaling / regulation of cytokine production involved in immune response / TORC2 complex disassembly / CD40 receptor binding / TORC1 complex assembly / tumor necrosis factor receptor superfamily complex / pulmonary valve development / RNA destabilization / sphingolipid binding / aortic valve development ...glial cell-neuron signaling / regulation of cytokine production involved in immune response / TORC2 complex disassembly / CD40 receptor binding / TORC1 complex assembly / tumor necrosis factor receptor superfamily complex / pulmonary valve development / RNA destabilization / sphingolipid binding / aortic valve development / tumor necrosis factor receptor activity / negative regulation of extracellular matrix constituent secretion / positive regulation of apoptotic process involved in morphogenesis / IRE1-TRAF2-ASK1 complex / TRAF2-GSTP1 complex / CD27 signaling pathway / regulation of T cell cytokine production / Defective RIPK1-mediated regulated necrosis / negative regulation of neuroinflammatory response / TNFs bind their physiological receptors / 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 / negative regulation of cardiac muscle hypertrophy / negative regulation of glial cell apoptotic process / interleukin-17-mediated signaling pathway / positive regulation of myelination / TNF signaling / programmed necrotic cell death / Caspase activation via Death Receptors in the presence of ligand / CD40 receptor complex / regulation of neuroinflammatory response / thioesterase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / regulation of immunoglobulin production / mRNA stabilization / positive regulation of membrane protein ectodomain proteolysis / regulation of JNK cascade / non-canonical NF-kappaB signal transduction / positive regulation of extrinsic apoptotic signaling pathway / vesicle membrane / mitogen-activated protein kinase kinase kinase binding / TNFR1-induced proapoptotic signaling / signal transduction involved in regulation of gene expression / regulation of myelination / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / Interleukin-10 signaling / positive regulation of JUN kinase activity / TRAF6 mediated NF-kB activation / regulation of T cell proliferation / positive regulation of oligodendrocyte differentiation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / protein K63-linked ubiquitination / ubiquitin ligase complex / regulation of protein-containing complex assembly / specific granule membrane / protein autoubiquitination / extrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / signaling adaptor activity / cellular response to nitric oxide / positive regulation of interleukin-2 production / T cell activation / response to endoplasmic reticulum stress / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / cellular response to lipopolysaccharide / protein-containing complex assembly / cell cortex / protein-macromolecule adaptor activity / protein phosphatase binding / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / inflammatory response / membrane raft / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / protein kinase binding / enzyme binding / signal transduction
Similarity search - Function
Tumour necrosis factor receptor 1B / Tumor necrosis factor receptor 1B, 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 1B / Tumor necrosis factor receptor 1B, 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 1B / TNF receptor-associated factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPark, Y.C. / Burkitt, V. / Villa, A.R. / Tong, L. / Wu, H.
CitationJournal: 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
DepositionFeb 25, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
B: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
C: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
D: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
E: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
F: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
G: PROTEIN (TNF-R2)
H: PROTEIN (TNF-R2)


Theoretical massNumber of molelcules
Total (without water)132,4908
Polymers132,4908
Non-polymers00
Water16,394910
1
A: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
B: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
C: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
G: PROTEIN (TNF-R2)
H: PROTEIN (TNF-R2)


Theoretical massNumber of molelcules
Total (without water)67,3695
Polymers67,3695
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-47 kcal/mol
Surface area28240 Å2
MethodPISA
2
D: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
E: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
F: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)


Theoretical massNumber of molelcules
Total (without water)65,1213
Polymers65,1213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-36 kcal/mol
Surface area26830 Å2
MethodPISA
3
D: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
E: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
F: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)

A: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
B: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
C: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
G: PROTEIN (TNF-R2)
H: PROTEIN (TNF-R2)


Theoretical massNumber of molelcules
Total (without water)132,4908
Polymers132,4908
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation2_645-x+1,y-1/2,-z1
identity operation1_555x,y,z1
Buried area14310 Å2
ΔGint-96 kcal/mol
Surface area51610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.000, 84.400, 100.700
Angle α, β, γ (deg.)90.00, 108.70, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein
PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2) / TRAF2


Mass: 21706.980 Da / Num. of mol.: 6 / Fragment: TRAF DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET24D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q12933
#2: Protein/peptide PROTEIN (TNF-R2)


Mass: 1124.243 Da / Num. of mol.: 2 / Fragment: TRAF-BINDING SITE / Source method: obtained synthetically
Details: SEQUENCE FROM HUMAN TNF-R2, SWISS PROT ACCESSION P20333
References: UniProt: P20333
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 910 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 %PEG400011
20.1 MMES11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.987
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 59650 / Num. obs: 59650 / % possible obs: 99 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.048
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.279

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Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CA4

1ca4


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.289 3112 5.3 %RANDOM
Rwork0.234 ---
obs-51071 87.2 %-
Displacement parametersBiso mean: 47.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8644 0 0 910 9554
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.465
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.89
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.717
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.89
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.717
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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