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- PDB-1om9: Structure of the GGA1-appendage in complex with the p56 binding p... -

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Basic information

Entry
Database: PDB / ID: 1om9
TitleStructure of the GGA1-appendage in complex with the p56 binding peptide
Components
  • 15-mer peptide fragment of p56
  • ADP-ribosylation factor binding protein GGA1
KeywordsPROTEIN TRANSPORT / SIGNALING PROTEIN / beta sandwich / beta augmentation / GGA / adaptin / clathrin adaptor
Function / homology
Function and homology information


protein localization to ciliary membrane / Golgi to lysosome transport / 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 localization to ciliary membrane / Golgi to lysosome transport / 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 / trans-Golgi network / protein catabolic process / small GTPase binding / positive regulation of protein catabolic process / protein localization / protein transport / 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
Coiled-coil domain-containing protein 91 / 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 ...Coiled-coil domain-containing protein 91 / 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
Coiled-coil domain-containing protein 91 / ADP-ribosylation factor-binding protein GGA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCollins, B.M. / Praefcke, G.J.K. / Robinson, M.S. / Owen, D.J.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structural basis for binding of accessory proteins by the appendage domain of GGAs
Authors: Collins, B.M. / Praefcke, G.J.K. / Robinson, M.S. / Owen, D.J.
History
DepositionFeb 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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
P: 15-mer peptide fragment of p56
B: ADP-ribosylation factor binding protein GGA1
Q: 15-mer peptide fragment of p56


Theoretical massNumber of molelcules
Total (without water)37,9474
Polymers37,9474
Non-polymers00
Water1,18966
1
A: ADP-ribosylation factor binding protein GGA1
P: 15-mer peptide fragment of p56


Theoretical massNumber of molelcules
Total (without water)18,9742
Polymers18,9742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-9 kcal/mol
Surface area8820 Å2
MethodPISA
2
B: ADP-ribosylation factor binding protein GGA1
Q: 15-mer peptide fragment of p56


Theoretical massNumber of molelcules
Total (without water)18,9742
Polymers18,9742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-10 kcal/mol
Surface area8760 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-39 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.414, 61.414, 145.008
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12P
22Q

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEUAA498 - 63913 - 154
21ALAALALEULEUBC498 - 63913 - 154
12ASPASPTHRTHRPB4 - 134 - 13
22ASPASPTHRTHRQD4 - 134 - 13

NCS ensembles :
ID
1
2
DetailsProtein chain A is paired with peptide chain P / Protein chain B is paired with peptide chain Q

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Components

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


Mass: 17323.117 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) / Gene: GGA1 / Plasmid: pMWH6172 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: Q9UJY5
#2: Protein/peptide 15-mer peptide fragment of p56


Mass: 1650.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: sequence occurs naturally in Homo sapiens / References: UniProt: Q7Z6B0*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.31 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM sodium citrate, 100 mM MgCl2 and 35% PEG 400, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMsodium citrate1reservoirpH5.5
2100 mM1reservoirMgCl2
335 %(w/v)PEG4001reservoir
45 mMHEPES1droppH7.5
5100 mM1dropNaCl

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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: Jan 5, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 11523 / Num. obs: 11512 / % possible obs: 99.9 % / Observed criterion σ(I): 3.1 / Redundancy: 4.9 % / Biso Wilson estimate: 55.4 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1NA8 chain A

1na8


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.434 / SU ML: 0.231 / Cross valid method: THROUGHOUT / σ(F): 1.55 / σ(I): 3.1 / ESU R: 0.784 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26203 553 4.8 %RANDOM
Rwork0.21338 ---
obs0.21569 10957 99.84 %-
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: 42.167 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 0 66 2446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222444
X-RAY DIFFRACTIONr_bond_other_d0.0020.022258
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9723337
X-RAY DIFFRACTIONr_angle_other_deg0.94135284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5875301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022659
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02451
X-RAY DIFFRACTIONr_nbd_refined0.1940.2362
X-RAY DIFFRACTIONr_nbd_other0.2380.22411
X-RAY DIFFRACTIONr_nbtor_other0.0950.21569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0660.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0221.51541
X-RAY DIFFRACTIONr_mcangle_it1.91922534
X-RAY DIFFRACTIONr_scbond_it2.373903
X-RAY DIFFRACTIONr_scangle_it4.194.5803
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A828tight positional0.040.05
22B57tight positional0.040.05
11A1357medium positional0.470.5
22B71medium positional0.220.5
11A828tight thermal0.080.5
22B57tight thermal0.120.5
11A1357medium thermal0.382
22B71medium thermal0.422
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 49
Rwork0.285 775
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.82
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.56 Å

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