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- PDB-3g2w: VHS Domain of human GGA1 complexed with a DXXLL hinge peptide -

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Basic information

Entry
Database: PDB / ID: 3g2w
TitleVHS Domain of human GGA1 complexed with a DXXLL hinge peptide
Components
  • ADP-ribosylation factor-binding protein GGA1
  • Internal peptide of the Hinge domain of ADP-ribosylation factor-binding protein GGA1
KeywordsPROTEIN TRANSPORT / ADP-ribosylation factor binding protein GGA1 / VHS / acidic-cluster dileucine signal / Hinge domain / autoinhibition
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 / 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. ...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. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCramer, J.F. / Behrens, M.A. / Gustafsen, C. / Oliveira, C.L.P. / Pedersen, J.S. / Madsen, P. / Petersen, C.M. / Thirup, S.S.
CitationJournal: Traffic / Year: 2010
Title: GGA autoinhibition revisited
Authors: Cramer, J.F. / Gustafsen, C. / Behrens, M.A. / Oliveira, C.L.P. / Pedersen, J.S. / Madsen, P. / Petersen, C.M. / Thirup, S.S.
History
DepositionFeb 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Nov 1, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosylation factor-binding protein GGA1
B: ADP-ribosylation factor-binding protein GGA1
C: Internal peptide of the Hinge domain of ADP-ribosylation factor-binding protein GGA1
D: Internal peptide of the Hinge domain of ADP-ribosylation factor-binding protein GGA1


Theoretical massNumber of molelcules
Total (without water)37,0364
Polymers37,0364
Non-polymers00
Water55831
1
A: ADP-ribosylation factor-binding protein GGA1
C: Internal peptide of the Hinge domain of ADP-ribosylation factor-binding protein GGA1


Theoretical massNumber of molelcules
Total (without water)18,5182
Polymers18,5182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-5 kcal/mol
Surface area8050 Å2
MethodPISA
2
B: ADP-ribosylation factor-binding protein GGA1
D: Internal peptide of the Hinge domain of ADP-ribosylation factor-binding protein GGA1


Theoretical massNumber of molelcules
Total (without water)18,5182
Polymers18,5182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-5 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.800, 72.900, 103.500
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: 16958.564 Da / Num. of mol.: 2 / Fragment: VHS Domain (N-terminal domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus-RIL / References: UniProt: Q9UJY5
#2: Protein/peptide Internal peptide of the Hinge domain of ADP-ribosylation factor-binding protein GGA1


Mass: 1559.630 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: UniProt: Q9UJY5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.044 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2008
RadiationMonochromator: SLS X06 mono / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 14717 / Num. obs: 14702 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.09 % / Biso Wilson estimate: 41.66 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.8
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 10.55 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1661 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JWF

1jwf


Resolution: 2.4→37.289 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.812 / SU B: 19.864 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / ESU R: 0.377 / ESU R Free: 0.261 / Phase error: 25.46 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 736 5.01 %RANDOM
Rwork0.215 13965 --
obs0.217 14701 99.85 %-
all-14717 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.35 Å2 / ksol: 0.288 e/Å3
Displacement parametersBiso max: 167.27 Å2 / Biso mean: 63.918 Å2 / Biso min: 28.21 Å2
Baniso -1Baniso -2Baniso -3
1-3.209 Å2-0 Å2-0 Å2
2---19.032 Å2-0 Å2
3----10.077 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 0 31 2393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122405
X-RAY DIFFRACTIONf_angle_d1.4313238
X-RAY DIFFRACTIONf_chiral_restr0.124367
X-RAY DIFFRACTIONf_plane_restr0.013410
X-RAY DIFFRACTIONf_dihedral_angle_d24.074915
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.5850.3031440.24627202864
2.585-2.8450.3331450.24227662911
2.845-3.2570.31450.23527552900
3.257-4.1030.2331480.20128022950
4.103-37.2930.2341540.20229223076
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.31550.8342-1.6923.7497-1.19617.12610.2224-0.1435-0.0346-0.0499-0.39110.0232-0.45070.130400.1891-0.0129-0.05030.39670.02030.21548.0665-8.8765-4.2192
23.56330.46290.493.6516-1.00956.5053-0.31340.3489-0.1945-0.32550.26770.3494-0.04780.058200.3713-0.03610.08380.37240.13690.44116.9852-1.2851-28.7715
30.270.5595-0.02070.382-0.59650.4660.07090.33540.8252-0.16580.4425-0.0896-1.0547-0.04790.04330.4645-0.0483-0.02381.0217-0.09890.4924-6.6502-14.9106-8.9647
40.02980.00690.039-0.0236-0.00480.02220.2322-0.5841-0.20210.21110.4171-0.61690.4733-0.582700.8286-0.13460.10331.0574-0.02441.12912.0064-17.4-30.0789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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