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- PDB-3qye: Crystal Structure of Human TBC1D1 RabGAP domain -

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Basic information

Entry
Database: PDB / ID: 3qye
TitleCrystal Structure of Human TBC1D1 RabGAP domain
ComponentsTBC1 domain family member 1
KeywordsHYDROLASE ACTIVATOR / TBC / RabGAP / Rab / Myocytes
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / membrane organization / activation of GTPase activity / GTPase activator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / regulation of protein localization / nucleus / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 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 1
B: TBC1 domain family member 1


Theoretical massNumber of molelcules
Total (without water)76,9272
Polymers76,9272
Non-polymers00
Water7,170398
1
A: TBC1 domain family member 1


Theoretical massNumber of molelcules
Total (without water)38,4641
Polymers38,4641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TBC1 domain family member 1


Theoretical massNumber of molelcules
Total (without water)38,4641
Polymers38,4641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.360, 117.360, 141.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein TBC1 domain family member 1


Mass: 38463.547 Da / Num. of mol.: 2 / Fragment: Rab-GAP Domain, UNP residues 750-1076
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D1, KIAA1108 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q86TI0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 2.0-3.2 M ammonium formate, 0.1 HEPES pH 7.5 and 20-25% ethylene glycol, VAPOR DIFFUSION, temperature 298 KK

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.0809
SYNCHROTRONNSLS X12C21.1394,1.1399,1.0876
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDNov 12, 2008
ADSC QUANTUM 3152CCDNov 12, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.08091
21.13941
31.13991
41.08761
ReflectionResolution: 2.2→50 Å / Num. obs: 50676
Reflection shellResolution: 2.2→2.28 Å / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→50 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.239 -10 %
Rwork0.199 --
obs-50676 -
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5211 0 0 398 5609
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.0106
X-RAY DIFFRACTIONc_angle_deg1.606

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