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- PDB-2dwx: Co-crystal Structure Analysis of GGA1-GAE with the WNSF motif -

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Basic information

Entry
Database: PDB / ID: 2dwx
TitleCo-crystal Structure Analysis of GGA1-GAE with the WNSF motif
Components
  • ADP-ribosylation factor-binding protein GGA1
  • hinge peptide from ADP-ribosylation factor binding protein GGA1
KeywordsPROTEIN TRANSPORT / IG FOLD / ADAPTIN
Function / homology
Function and homology information


protein localization to ciliary membrane / Golgi to plasma membrane protein transport / Golgi to plasma membrane transport / protein localization to cell surface / retrograde transport, endosome to Golgi / TBC/RABGAPs / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / protein catabolic process ...protein localization to ciliary membrane / Golgi to plasma membrane protein transport / Golgi to plasma membrane transport / protein localization to cell surface / retrograde transport, endosome to Golgi / 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
ADP-ribosylation factor-binding protein GGA3 / Gamma-adaptin ear (GAE) domain / 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 ...ADP-ribosylation factor-binding protein GGA3 / Gamma-adaptin ear (GAE) domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsInoue, M. / Shiba, T. / Yamada, Y. / Ihara, K. / Kawasaki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S.
CitationJournal: Traffic / Year: 2007
Title: Molecular Basis for Autoregulatory Interaction Between GAE Domain and Hinge Region of GGA1
Authors: Inoue, M. / Shiba, T. / Ihara, K. / Yamada, Y. / Hirano, S. / Kamikubo, H. / Kataoka, M. / Kawasaki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S.
History
DepositionAug 21, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: ADP-ribosylation factor-binding protein GGA1
B: ADP-ribosylation factor-binding protein GGA1
C: ADP-ribosylation factor-binding protein GGA1
D: ADP-ribosylation factor-binding protein GGA1
P: hinge peptide from ADP-ribosylation factor binding protein GGA1
Q: hinge peptide from ADP-ribosylation factor binding protein GGA1


Theoretical massNumber of molelcules
Total (without water)62,3366
Polymers62,3366
Non-polymers00
Water2,198122
1
A: ADP-ribosylation factor-binding protein GGA1
P: hinge peptide from ADP-ribosylation factor binding protein GGA1


Theoretical massNumber of molelcules
Total (without water)16,2772
Polymers16,2772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-5 kcal/mol
Surface area7580 Å2
MethodPISA
2
B: ADP-ribosylation factor-binding protein GGA1


Theoretical massNumber of molelcules
Total (without water)14,8911
Polymers14,8911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ADP-ribosylation factor-binding protein GGA1
Q: hinge peptide from ADP-ribosylation factor binding protein GGA1


Theoretical massNumber of molelcules
Total (without water)16,2772
Polymers16,2772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-7 kcal/mol
Surface area7640 Å2
MethodPISA
4
D: ADP-ribosylation factor-binding protein GGA1


Theoretical massNumber of molelcules
Total (without water)14,8911
Polymers14,8911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.220, 69.620, 184.967
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 14891.319 Da / Num. of mol.: 4 / Fragment: GAE DOMAIN, RESIDUES 507-639
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UJY5
#2: Protein/peptide hinge peptide from ADP-ribosylation factor binding protein GGA1


Mass: 1385.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE / References: UniProt: Q9UJY5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.64 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.978
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2003
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 20904 / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.1
Reflection shellResolution: 2.55→2.64 Å / Rmerge(I) obs: 0.345 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBENTRY 1IU1

1iu1


Resolution: 2.55→38.63 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.877 / SU B: 13.306 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.85 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1041 5.1 %RANDOM
Rwork0.238 ---
obs0.241 19211 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.55→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 0 122 4235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224223
X-RAY DIFFRACTIONr_bond_other_d0.0020.023891
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.9645769
X-RAY DIFFRACTIONr_angle_other_deg0.93939093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1635511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024565
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02796
X-RAY DIFFRACTIONr_nbd_refined0.2320.2814
X-RAY DIFFRACTIONr_nbd_other0.2470.24590
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.22613
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.050.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0461.52624
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92924322
X-RAY DIFFRACTIONr_scbond_it1.81131599
X-RAY DIFFRACTIONr_scangle_it3.124.51447
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.422 77
Rwork0.342 1230

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