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- PDB-1r4a: Crystal Structure of GTP-bound ADP-ribosylation Factor Like Prote... -

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Basic information

Entry
Database: PDB / ID: 1r4a
TitleCrystal Structure of GTP-bound ADP-ribosylation Factor Like Protein 1 (Arl1) and GRIP Domain of Golgin245 COMPLEX
Components
  • ADP-ribosylation factor-like protein 1
  • Golgi autoantigen, golgin subfamily A member 4
KeywordsPROTEIN TRANSPORT / Ras-like G Protein structure / Three-helix GRIP domain
Function / homology
Function and homology information


phospholipase D activator activity / Retrograde transport at the Trans-Golgi-Network / toxin metabolic process / Retrograde transport at the Trans-Golgi-Network / Golgi vesicle transport / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / protein localization to Golgi apparatus / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / Golgi organization ...phospholipase D activator activity / Retrograde transport at the Trans-Golgi-Network / toxin metabolic process / Retrograde transport at the Trans-Golgi-Network / Golgi vesicle transport / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / protein localization to Golgi apparatus / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / Golgi organization / positive regulation of axon extension / vesicle-mediated transport / enzyme activator activity / intracellular protein transport / trans-Golgi network / small GTPase binding / GTPase binding / protein domain specific binding / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GRIP domain / GRIP domain / GRIP domain / GRIP domain profile. / golgin-97, RanBP2alpha,Imh1p and p230/golgin-245 / Small GTPase superfamily, ARF type / small GTPase Arf family profile. / Annexin V; domain 1 / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type ...GRIP domain / GRIP domain / GRIP domain / GRIP domain profile. / golgin-97, RanBP2alpha,Imh1p and p230/golgin-245 / Small GTPase superfamily, ARF type / small GTPase Arf family profile. / Annexin V; domain 1 / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / ADP-ribosylation factor-like protein 1 / Golgin subfamily A member 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWu, M. / Lu, L. / Hong, W. / Song, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural basis for recruitment of GRIP domain golgin-245 by small GTPase Arl1.
Authors: Wu, M. / Lu, L. / Hong, W. / Song, H.
History
DepositionOct 4, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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-like protein 1
E: Golgi autoantigen, golgin subfamily A member 4
B: ADP-ribosylation factor-like protein 1
F: Golgi autoantigen, golgin subfamily A member 4
C: ADP-ribosylation factor-like protein 1
G: Golgi autoantigen, golgin subfamily A member 4
D: ADP-ribosylation factor-like protein 1
H: Golgi autoantigen, golgin subfamily A member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,93016
Polymers99,7448
Non-polymers2,1868
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.083, 86.924, 86.246
Angle α, β, γ (deg.)118.11, 99.65, 95.47
Int Tables number1
Space group name H-MP1
DetailsFour molecules are generated by two 2-fold symmetry operations. / Tetramer is generated by two 2-fold symmetry operations.

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Components

#1: Protein
ADP-ribosylation factor-like protein 1 / Arl1


Mass: 18737.615 Da / Num. of mol.: 4 / Fragment: Arl1 (Residue 16-180)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: ARL1 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: P61212
#2: Protein
Golgi autoantigen, golgin subfamily A member 4 / Trans-Golgi p230 / 256 kDa golgin / Golgin-245 / 72.1 protein


Mass: 6198.274 Da / Num. of mol.: 4 / Fragment: GRIP Domain (Residue 2172-2222)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOLGIN-245 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: Q13439
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.6 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3350, potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
17.5 mg/mlprotein1drop
217-18 %(w/v)PEG33501reservoir
3200 mM1reservoirKSCN
420 mMTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.972 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.1→99.9 Å / Num. all: 55269 / Num. obs: 55268 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.88 / Rsym value: 0.479 / % possible all: 56.5
Reflection
*PLUS
Lowest resolution: 39 Å / % possible obs: 97.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KSG

1ksg


Resolution: 2.3→20 Å / Cross valid method: free R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: The structure was refined also with CNS(BRUNGER)
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 2137 5 %RANDOM
Rwork0.24626 ---
obs0.2508 42731 97.3 %-
all-55269 --
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6980 0 132 268 7380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227228
X-RAY DIFFRACTIONr_bond_other_d00.026712
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9929772
X-RAY DIFFRACTIONr_angle_other_deg3.502315600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.4385856
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_restr0.1080.21116
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027700
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021428
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.39 Å / Total num. of bins used: 20 /
Num. reflection% reflection
obs42731 97.1 %
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.26 / Rfactor Rwork: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.7

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