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- PDB-1naf: Crystal structure of the human GGA1 GAT domain -

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Basic information

Entry
Database: PDB / ID: 1naf
TitleCrystal structure of the human GGA1 GAT domain
ComponentsADP-ribosylation factor binding protein GGA1
KeywordsSIGNALING PROTEIN / MEMBRANE PROTEIN / clathrin-adaptor / GGA / GAT domain / helical paper-clip / three-helix bundle
Function / homology
Function and homology information


protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / protein localization to cell surface / TBC/RABGAPs / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / protein catabolic process ...protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / protein localization to cell surface / TBC/RABGAPs / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / protein catabolic process / trans-Golgi network / protein localization / small GTPase binding / positive regulation of protein catabolic process / early endosome membrane / early endosome / endosome membrane / Amyloid fiber formation / intracellular membrane-bounded organelle / Golgi apparatus / protein-containing complex / nucleoplasm / membrane / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #160 / ADP-ribosylation factor-binding protein GGA3 / N-terminal extension of GAT domain / N-terminal extension of GAT domain / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #160 / ADP-ribosylation factor-binding protein GGA3 / N-terminal extension of GAT domain / N-terminal extension of GAT domain / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / ENTH/VHS / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsCollins, B.M. / Watson, P.J. / Owen, D.J.
CitationJournal: Dev.Cell / Year: 2003
Title: The Structure of the GGA1-GAT Domain Reveals the Molecular Basis for ARF Binding and Membrane Association of GGAs
Authors: Collins, B.M. / Watson, P.J. / Owen, D.J.
History
DepositionNov 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Structure summary / Category: exptl_crystal_grow / struct
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosylation factor binding protein GGA1


Theoretical massNumber of molelcules
Total (without water)18,4121
Polymers18,4121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.700, 82.700, 69.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Cell settinghexagonal
Space group name H-MP63

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Components

#1: Protein ADP-ribosylation factor binding protein GGA1 / GGA1 appendage domain / Golgi-localized / gamma ear-containing / ARF-binding protein 1 / Gamma- ...GGA1 appendage domain / Golgi-localized / gamma ear-containing / ARF-binding protein 1 / Gamma-adaptin related protein 1


Mass: 18412.449 Da / Num. of mol.: 1 / Fragment: GAT domain, Residues 165-314 of SWS Q9UJY5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: Q9UJY5

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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: 4.9 Å3/Da / Density % sol: 74.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: sodium acetate, lithium sulphate, NaH2PO4/K2HPO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mMdithiothreitol1drop
210-15 mg/mlprotein1drop
30.1 Msodium acetate1reservoirpH4.5
40.3 Msodium phosphate1reservoir
50.45 Mpotassium phosphate1reservoir
60.2 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9796, 0.9798, 0.9393
DetectorDetector: CCD / Date: Jun 15, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97981
30.93931
ReflectionResolution: 2.8→70 Å / Num. obs: 6684 / % possible obs: 99.7 % / Observed criterion σ(F): 2.6 / Redundancy: 3.7 % / Biso Wilson estimate: 105 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2.6 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2833 294 random
Rwork0.2483 --
all0.2485 6768 -
obs0.2484 5495 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.609 Å2-29.295 Å20 Å2
2---11.609 Å20 Å2
3---23.219 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1006 0 0 0 1006
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.18

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