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- PDB-1x79: Crystal structure of human GGA1 GAT domain complexed with the GAT... -

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Basic information

Entry
Database: PDB / ID: 1x79
TitleCrystal structure of human GGA1 GAT domain complexed with the GAT-binding domain of Rabaptin5
Components
  • ADP-ribosylation factor binding protein GGA1
  • Rab GTPase binding effector protein 1
KeywordsPROTEIN TRANSPORT / Rabaptin5 / GGA protein / GAT domain / intracellular trafficking
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 / TBC/RABGAPs / protein localization to cell surface / regulation of postsynaptic neurotransmitter receptor internalization / endocytic vesicle / vesicle-mediated transport / phosphatidylinositol binding ...protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / TBC/RABGAPs / protein localization to cell surface / regulation of postsynaptic neurotransmitter receptor internalization / endocytic vesicle / vesicle-mediated transport / phosphatidylinositol binding / GTPase activator activity / ubiquitin binding / intracellular protein transport / growth factor activity / trans-Golgi network / protein catabolic process / recycling endosome / small GTPase binding / endocytosis / positive regulation of protein catabolic process / intracellular protein localization / protein transport / early endosome membrane / membrane fusion / early endosome / endosome membrane / endosome / Amyloid fiber formation / protein domain specific binding / intracellular membrane-bounded organelle / apoptotic process / glutamatergic synapse / Golgi apparatus / protein homodimerization activity / protein-containing complex / nucleoplasm / membrane / cytosol
Similarity search - Function
Rabaptin / Rabaptin, GTPase-Rab5 binding domain / Rabaptin coiled-coil domain / Rabaptin / Rabaptin-like protein / 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 ...Rabaptin / Rabaptin, GTPase-Rab5 binding domain / Rabaptin coiled-coil domain / Rabaptin / Rabaptin-like protein / 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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / 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 / Clathrin adaptor, appendage, Ig-like subdomain superfamily / ENTH/VHS / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Rab GTPase-binding effector protein 1 / ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.41 Å
AuthorsZhu, G. / Zhang, X.C.
CitationJournal: EMBO J. / Year: 2004
Title: Crystal structure of human GGA1 GAT domain complexed with the GAT-binding domain of Rabaptin5.
Authors: Zhu, G. / Zhai, P. / He, X. / Wakeham, N. / Rodgers, K. / Li, G. / Tang, J. / Zhang, X.C.
History
DepositionAug 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: ADP-ribosylation factor binding protein GGA1
B: Rab GTPase binding effector protein 1
C: Rab GTPase binding effector protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2627
Polymers36,7613
Non-polymers5014
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.222, 155.222, 53.052
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 ADP-ribosylation factor binding protein GGA1 / Golgi-localized / gamma ear-containing / ARF-binding protein 1 / Gamma-adaptin related protein 1


Mass: 10920.255 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGA1 / Plasmid: PGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UJY5
#2: Protein Rab GTPase binding effector protein 1 / Rabaptin-5 / Rabaptin-5alpha / Rabaptin-4


Mass: 12920.548 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABEP1, RABPT5, RABPT5A / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15276
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 5.4 Å3/Da / Density % sol: 77 %
Description: The phase was solved by a Se-Met derivative crystal at three wavelengths (with 0.95667, 0.97938, 0.97952A respectively) to 2.8 A resolution at CHESS F2 beamline
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: AMMONIUM SULFATE, TRIS, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418,0.95667,0.97938,0.97952
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 15, 2003
RadiationMonochromator: OSMIC OPTICS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.956671
30.979381
40.979521
ReflectionResolution: 2.4→51 Å / Num. all: 28214 / Num. obs: 28214 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 30.1
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2217 / % possible all: 77.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MAD / Resolution: 2.41→50.81 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 911335.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 910 3.8 %RANDOM
Rwork0.233 ---
all0.233 28214 --
obs0.233 23653 82.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.9799 Å2 / ksol: 0.341796 e/Å3
Displacement parametersBiso mean: 59.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å210.7 Å20 Å2
2--3.9 Å20 Å2
3----7.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.39 Å
Luzzati d res low-4 Å
Luzzati sigma a0.7 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.41→50.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 26 117 2243
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.891.5
X-RAY DIFFRACTIONc_mcangle_it4.552
X-RAY DIFFRACTIONc_scbond_it5.292
X-RAY DIFFRACTIONc_scangle_it7.682.5
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.066 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.438 44 3.6 %
Rwork0.398 1162 -
obs--41.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DTT.PARDTT.TOP

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