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- PDB-1qsc: CRYSTAL STRUCTURE OF THE TRAF DOMAIN OF TRAF2 IN A COMPLEX WITH A... -

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Basic information

Entry
Database: PDB / ID: 1qsc
TitleCRYSTAL STRUCTURE OF THE TRAF DOMAIN OF TRAF2 IN A COMPLEX WITH A PEPTIDE FROM THE CD40 RECEPTOR
Components
  • CD40 RECEPTOR
  • TNF RECEPTOR ASSOCIATED FACTOR 2
KeywordsSIGNALING PROTEIN / TNF SIGNALING / TRAF / CD40 RECEPTOR / ADAPTER PROTEIN / CELL SURVIVAL / COILED COIL
Function / homology
Function and homology information


TORC2 complex disassembly / CD40 receptor binding / TORC1 complex assembly / tumor necrosis factor receptor superfamily complex / sphingolipid binding / IRE1-TRAF2-ASK1 complex / TRAF2-GSTP1 complex / Defective RIPK1-mediated regulated necrosis / CD27 signaling pathway / CD40 signaling pathway ...TORC2 complex disassembly / CD40 receptor binding / TORC1 complex assembly / tumor necrosis factor receptor superfamily complex / sphingolipid binding / IRE1-TRAF2-ASK1 complex / TRAF2-GSTP1 complex / Defective RIPK1-mediated regulated necrosis / CD27 signaling pathway / CD40 signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / tumor necrosis factor binding / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / negative regulation of glial cell apoptotic process / interleukin-17-mediated signaling pathway / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / programmed necrotic cell death / CD40 receptor complex / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / mRNA stabilization / regulation of immunoglobulin production / regulation of JNK cascade / positive regulation of extrinsic apoptotic signaling pathway / signal transduction involved in regulation of gene expression / non-canonical NF-kappaB signal transduction / vesicle membrane / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / TRAF6 mediated NF-kB activation / positive regulation of JUN kinase activity / 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 / tumor necrosis factor-mediated signaling pathway / signaling adaptor activity / positive regulation of interleukin-2 production / cellular response to nitric oxide / response to endoplasmic reticulum stress / T cell activation / positive regulation of DNA-binding transcription factor activity / 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 / RING-type E3 ubiquitin transferase / positive regulation of T cell cytokine production / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / positive regulation of NF-kappaB transcription factor activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / cell cortex / protein-containing complex assembly / protein phosphatase binding / protein-macromolecule adaptor activity / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / membrane raft / innate immune response / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase 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 / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain ...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
TNF receptor-associated factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsMcWhirter, S.M. / Pullen, S.S. / Holton, J.M. / Crute, J.J. / Kehry, M.R. / Alber, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystallographic analysis of CD40 recognition and signaling by human TRAF2.
Authors: McWhirter, S.M. / Pullen, S.S. / Holton, J.M. / Crute, J.J. / Kehry, M.R. / Alber, T.
History
DepositionJun 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: TNF RECEPTOR ASSOCIATED FACTOR 2
B: TNF RECEPTOR ASSOCIATED FACTOR 2
C: TNF RECEPTOR ASSOCIATED FACTOR 2
D: CD40 RECEPTOR
E: CD40 RECEPTOR
F: CD40 RECEPTOR


Theoretical massNumber of molelcules
Total (without water)68,0886
Polymers68,0886
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-48 kcal/mol
Surface area25390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.110, 90.090, 92.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TNF RECEPTOR ASSOCIATED FACTOR 2 / TRAF2


Mass: 21920.156 Da / Num. of mol.: 3 / Fragment: TRAF DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12933
#2: Protein/peptide CD40 RECEPTOR


Mass: 775.846 Da / Num. of mol.: 3 / Fragment: TRAF BINDING PEPTIDE / Mutation: V251I / Source method: obtained synthetically / Details: SEQUENCE DERIVED FROM HUMAN CD40
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MME-PEG 2000, MAGNESIUM CHLORIDE, BISTRIS PROPANE, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298.00K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 %PEGMME20001reservoir
30.1 MBis-Tris-propane1reservoir
40.2 M1reservoirMgCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONALS 5.0.210.9694
SYNCHROTRONSSRL BL1-521.006
Detector
TypeIDDetector
NULL1CCD
2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.96941
21.0061
ReflectionResolution: 2.4→40 Å / Num. obs: 28075 / % possible obs: 98.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 58.3 Å2 / Rsym value: 0.048 / Net I/σ(I): 9.1
Reflection shellResolution: 2.4→2.51 Å / Redundancy: 6.8 % / Rsym value: 0.317 / % possible all: 94.6
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 40 Å / % possible obs: 98.7 % / Rmerge(I) obs: 0.048

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.4refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.4→25 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1274615.47 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1476 5.1 %RANDOM
Rwork0.215 ---
obs0.215 28791 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.4 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 58.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---5.5 Å20 Å2
3---5.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-25 Å
Luzzati sigma a0.37 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 0 273 4589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTR
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
Num. reflection% reflection
Rfree235 5.1 %
Rwork4402 -
obs-97.2 %
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 58.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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