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- PDB-3qyb: X-ray Crystal Structure of Human TBC1D4 (AS160) RabGAP domain -

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Basic information

Entry
Database: PDB / ID: 3qyb
TitleX-ray Crystal Structure of Human TBC1D4 (AS160) RabGAP domain
ComponentsTBC1 domain family member 4
KeywordsHYDROLASE ACTIVATOR / RabGAP / Rab / Adipocyte
Function / homology
Function and homology information


negative regulation of vesicle fusion / vesicle-mediated transport / GTPase activator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to insulin stimulus / vesicle / cytosol
Similarity search - Function
Arc Repressor Mutant, subunit A - #2750 / Domain of unknown function DUF3350 / Domain of unknown function (DUF3350) / putative rabgap domain of human tbc1 domain family member 14 like domains / Ypt/Rab-GAP domain of gyp1p, domain 3 / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. ...Arc Repressor Mutant, subunit A - #2750 / Domain of unknown function DUF3350 / Domain of unknown function (DUF3350) / putative rabgap domain of human tbc1 domain family member 14 like domains / Ypt/Rab-GAP domain of gyp1p, domain 3 / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Cyclin A; domain 1 / Helicase, Ruva Protein; domain 3 / PH-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TBC1 domain family member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsPark, S.Y. / Shoelson, S.E.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structures of human TBC1D1 and TBC1D4 (AS160) RabGTPase-activating protein (RabGAP) domains reveal critical elements for GLUT4 translocation.
Authors: Park, S.Y. / Jin, W. / Woo, J.R. / Shoelson, S.E.
History
DepositionMar 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TBC1 domain family member 4


Theoretical massNumber of molelcules
Total (without water)35,1621
Polymers35,1621
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.214, 151.214, 53.155
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TBC1 domain family member 4 / Akt substrate of 160 kDa / AS160


Mass: 35161.824 Da / Num. of mol.: 1 / Fragment: Rab-GAP Domain, UNP residues 874-1170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D4, AS160, KIAA0603 / Production host: Escherichia coli (E. coli) / References: UniProt: O60343
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.99 Å3/Da / Density % sol: 75.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 5-8% PEG 8K, 0.1 TRIS pH 8.5 and 35% glycerol, VAPOR DIFFUSION, temperature 298KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 8683
Reflection shellResolution: 3.5→3.63 Å / % possible all: 99.7

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→50 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.3 -10 %
Rwork0.246 --
obs-8683 -
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 0 9 2453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0133
X-RAY DIFFRACTIONc_angle_deg1.572

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