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- PDB-1na8: Crystal structure of ADP-ribosylation factor binding protein GGA1 -

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Basic information

Entry
Database: PDB / ID: 1na8
TitleCrystal structure of ADP-ribosylation factor binding protein GGA1
ComponentsADP-ribosylation factor binding protein GGA1
KeywordsSIGNALING PROTEIN / MEMBRANE PROTEIN / clathrin-adaptor / GGA / appendage / beta-sandwich
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 / 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 / TBC/RABGAPs / protein localization to cell surface / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / protein catabolic process / trans-Golgi network / small GTPase binding / positive regulation of protein catabolic process / intracellular protein localization / 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 / Clathrin adaptor, appendage, Ig-like subdomain superfamily / ENTH/VHS / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLui, W.W. / Collins, B.M. / Hirst, J. / Motley, A. / Millar, C. / Schu, P. / Owen, D.J. / Robinson, M.S.
CitationJournal: Mol.Cell.Biol. / Year: 2003
Title: Binding partners for the COOH-terminal appendage domains of the GGAs and gamma-adaptin
Authors: Lui, W.W. / Collins, B.M. / Hirst, J. / Motley, A. / Millar, C. / Schu, P. / Owen, D.J. / Robinson, M.S.
History
DepositionNov 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Aug 16, 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


Theoretical massNumber of molelcules
Total (without water)34,7062
Polymers34,7062
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-17 kcal/mol
Surface area14800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.426, 65.426, 142.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221
DetailsThe assymetric unit contains a dimer of two identical chains but this dimer is not observed in solution

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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: 17353.209 Da / Num. of mol.: 2 / Fragment: appendage domain, Residues 494-639 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) / References: UniProt: Q9UJY5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.52 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: sodium citrate, ammonium sulphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
137 mg/mlprotein1drop
2100 mMsodium citrate1reservoirpH5.6
31.7 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→57 Å / Num. obs: 16193 / % possible obs: 99 % / Observed criterion σ(F): 5.9 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 23.7
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 5.9 / % possible all: 99
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 57 Å / % possible obs: 99 %
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1GYU

1gyu


Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement used / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27923 813 5 %RANDOM
Rwork0.21571 ---
all0.21869 ---
obs0.21869 15310 98.93 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.119 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20.96 Å20 Å2
2--1.92 Å20 Å2
3----2.88 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 0 172 2499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222393
X-RAY DIFFRACTIONr_bond_other_d0.0010.022241
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9723270
X-RAY DIFFRACTIONr_angle_other_deg0.80235244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6893294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.16715442
X-RAY DIFFRACTIONr_chiral_restr0.0910.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022574
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02432
X-RAY DIFFRACTIONr_nbd_refined0.2390.3472
X-RAY DIFFRACTIONr_nbd_other0.2360.32218
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.5212
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1060.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.349
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5630.58
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8031.51500
X-RAY DIFFRACTIONr_mcangle_it1.48322478
X-RAY DIFFRACTIONr_scbond_it2.313893
X-RAY DIFFRACTIONr_scangle_it3.9924.5792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 66
Rwork0.253 1105
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)
12.5684-0.58980.32442.00370.60086.41860.1190.00320.2046-0.17820.0859-0.3355-0.18951.0623-0.2050.004-0.0287-0.00850.2564-0.01660.134533.673834.76442.3842
22.416-0.03970.64062.22180.42294.2627-0.0624-0.33040.3710.2196-0.07750.1162-0.3454-0.31970.13990.0398-0.0471-0.03120.2694-0.01350.100431.888432.67133.651
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA489 - 6394 - 154
2X-RAY DIFFRACTION2BB495 - 63910 - 154
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 15 Å / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.72
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.36 Å

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