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- PDB-5yc1: TRAF4_GPIb complex -

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Basic information

Entry
Database: PDB / ID: 5yc1
TitleTRAF4_GPIb complex
Components
  • GPIb peptide
  • TNF receptor-associated factor 4
KeywordsSIGNALING PROTEIN/PEPTIDE / Complex / Platelet receptor / TRAF4 / interaction / SIGNALING PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


respiratory tube development / WW domain binding / respiratory gaseous exchange by respiratory system / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / bicellular tight junction / positive regulation of protein kinase activity / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase ...respiratory tube development / WW domain binding / respiratory gaseous exchange by respiratory system / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / bicellular tight junction / positive regulation of protein kinase activity / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / fibrillar center / transferase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / cytoskeleton / innate immune response / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
TNF receptor-associated factor 4, MATH 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 / MATH/TRAF domain ...TNF receptor-associated factor 4, MATH 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 / 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.506 Å
AuthorsPark, H.H. / Kim, C.M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Molecular basis for unique specificity of human TRAF4 for platelets GPIb beta and GPVI
Authors: Kim, C.M. / Son, Y.J. / Kim, S. / Kim, S.Y. / Park, H.H.
History
DepositionSep 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: TNF receptor-associated factor 4
B: TNF receptor-associated factor 4
C: TNF receptor-associated factor 4
D: TNF receptor-associated factor 4
E: TNF receptor-associated factor 4
F: TNF receptor-associated factor 4
G: GPIb peptide
I: GPIb peptide
K: GPIb peptide


Theoretical massNumber of molelcules
Total (without water)126,2969
Polymers126,2969
Non-polymers00
Water52229
1
A: TNF receptor-associated factor 4
B: TNF receptor-associated factor 4
C: TNF receptor-associated factor 4
I: GPIb peptide


Theoretical massNumber of molelcules
Total (without water)62,8114
Polymers62,8114
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: TNF receptor-associated factor 4
E: TNF receptor-associated factor 4
F: TNF receptor-associated factor 4
G: GPIb peptide
K: GPIb peptide


Theoretical massNumber of molelcules
Total (without water)63,4855
Polymers63,4855
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.716, 88.594, 120.757
Angle α, β, γ (deg.)90.00, 93.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TNF receptor-associated factor 4 / Cysteine-rich domain associated with RING and Traf domains protein 1 / Metastatic lymph node gene ...Cysteine-rich domain associated with RING and Traf domains protein 1 / Metastatic lymph node gene 62 protein / MLN 62 / RING finger protein 83


Mass: 20712.406 Da / Num. of mol.: 6 / Fragment: UNP residues 290-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF4, CART1, MLN62, RNF83 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BUZ4
#2: Protein/peptide GPIb peptide


Mass: 673.832 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: magnesium formate dehydrate, polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 42567 / % possible obs: 95 % / Redundancy: 3.1 % / Net I/σ(I): 21.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.506→33.781 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.39
RfactorNum. reflection% reflection
Rfree0.2649 1994 5.14 %
Rwork0.2114 --
obs0.2141 38763 94.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.506→33.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7805 0 0 29 7834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018026
X-RAY DIFFRACTIONf_angle_d1.3910849
X-RAY DIFFRACTIONf_dihedral_angle_d12.6822959
X-RAY DIFFRACTIONf_chiral_restr0.0591112
X-RAY DIFFRACTIONf_plane_restr0.0081412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.506-2.56860.35311300.27142352X-RAY DIFFRACTION84
2.5686-2.63810.35971390.27082588X-RAY DIFFRACTION95
2.6381-2.71570.34371460.26392631X-RAY DIFFRACTION94
2.7157-2.80330.33361370.25842585X-RAY DIFFRACTION94
2.8033-2.90340.31651440.25652590X-RAY DIFFRACTION94
2.9034-3.01960.34831420.25532593X-RAY DIFFRACTION92
3.0196-3.15690.30611340.25192592X-RAY DIFFRACTION93
3.1569-3.32320.26361420.23092566X-RAY DIFFRACTION93
3.3232-3.53120.30871400.23012578X-RAY DIFFRACTION93
3.5312-3.80350.23861410.21092616X-RAY DIFFRACTION94
3.8035-4.18570.22031450.18912680X-RAY DIFFRACTION96
4.1857-4.78990.21581530.16912767X-RAY DIFFRACTION98
4.7899-6.02910.23311460.182785X-RAY DIFFRACTION100
6.0291-33.78420.26291550.20962846X-RAY DIFFRACTION99

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