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- PDB-1upt: Structure of a complex of the golgin-245 GRIP domain with Arl1 -

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Basic information

Entry
Database: PDB / ID: 1upt
TitleStructure of a complex of the golgin-245 GRIP domain with Arl1
Components
  • ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1
  • GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4
KeywordsHYDROLASE/PROTEIN-BINDING / COMPLEX (GTPASE-GOLGIN) / GOLGIN-245 / GRIP / ARL1 / GOLGIN / GTPASE / G-PROTEIN / GOLGI / GRIP DIMER / PROTEIN SORTING / VESICLE TRAFFICKING / HYDROLASE-PROTEIN-BINDING complex
Function / homology
Function and homology information


phospholipase D activator activity / 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 ...phospholipase D activator activity / 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 / trans-Golgi network membrane / intracellular protein transport / enzyme activator activity / trans-Golgi network / small GTPase binding / GTPase binding / Golgi membrane / protein domain specific binding / GTPase activity / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / metal ion binding / plasma membrane / cytoplasm / cytosol
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 / Annexin V; domain 1 / Small GTPase Arf domain profile. / 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 / Annexin V; domain 1 / Small GTPase Arf domain profile. / 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
GUANOSINE-5'-TRIPHOSPHATE / ADP-ribosylation factor-like protein 1 / Golgin subfamily A member 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.7 Å
AuthorsPanic, B. / Perisic, O. / Veprintsev, D.B. / Williams, R.L. / Munro, S.
CitationJournal: Mol.Cell / Year: 2003
Title: Structural Basis for Arl1-Dependent Targeting of Homodimeric Grip Domains to the Golgi Apparatus
Authors: Panic, B. / Perisic, O. / Veprintsev, D.B. / Williams, R.L. / Munro, S.
History
DepositionOct 12, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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
B: GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4
C: ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1
D: GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4
E: ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1
F: GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4
G: ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1
H: GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,61916
Polymers108,4308
Non-polymers2,1908
Water4,864270
1
A: ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1
B: GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4
C: ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1
D: GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3108
Polymers54,2154
Non-polymers1,0954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1
F: GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4
G: ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1
H: GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3108
Polymers54,2154
Non-polymers1,0954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.497, 89.711, 72.534
Angle α, β, γ (deg.)90.00, 110.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.902, -0.1265, -0.4127), (-0.1473, -0.9889, -0.0189), (-0.4058, 0.0779, -0.9107)14.2154, 25.8952, 57.5195
2given(-0.9973, 0.0689, 0.0255), (0.0686, 0.9976, -0.0123), (-0.0263, -0.0105, -0.9996)-43.4342, -34.3617, 101.9896
3given(-0.9475, -0.0493, 0.3161), (0.0499, -0.9987, -0.0061), (0.316, 0.01, 0.9487)-55.6258, 65.9947, -22.7331
4given(0.9218, -0.103, -0.3737), (-0.0995, -0.9946, 0.0285), (-0.3747, 0.011, -0.9271)12.743, 25.6434, 60.5804
5given(-0.9969, 0.0617, 0.0481), (0.0644, 0.9964, 0.0553), (-0.0446, 0.0582, -0.9973)-44.7179, -38.6304, 98.7056
6given(-0.9204, -0.0579, 0.3866), (0.03, -0.9965, -0.0778), (0.3897, -0.0601, 0.919)-44.7179, -38.6304, 98.7056
DetailsTHE GRIP DOMAIN FOMES A DIMER IN SOLUTION . THERE ARE TWOGRIP DOMAIN DIMERS IN THE ASYMMETRIC UNIT. THESE DIMERS ARECHAINS B/D AND CHAINS F/H. SINCE EACH OF THESE DIMERS ISIN COMPLEX WITH ARL1, THE ENTRY IS GIVEN AS TETRAMERIC.

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Components

#1: Protein
ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1 / ARL1


Mass: 19699.580 Da / Num. of mol.: 4 / Fragment: RESIDUES 15-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPCG / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P40616
#2: Protein
GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4 / TRANS-GOLGI P230 / GOLGIN-245 / 72.1 PROTEIN / 256 KDA GOLGIN


Mass: 7407.808 Da / Num. of mol.: 4 / Fragment: GRIP DOMAIN RESIDUES 2170-2228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPCG / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q13439
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMOL_ID 1 MAY PLAY A ROLE IN VESICULAR TRANSPORT FROM THE TRANS- GOLGI. MOL_ID 2 BELONGS TO THE ...MOL_ID 1 MAY PLAY A ROLE IN VESICULAR TRANSPORT FROM THE TRANS- GOLGI. MOL_ID 2 BELONGS TO THE SMALL GTPASE SUPERFAMILY.
Has protein modificationY
Sequence detailsTHE SEQUENCE OF CHAINS B, D, F AND H ARE ANNOTATED AS A SPLICE ISOFORM OF GOA4_HUMAN, WHICH HAS A ...THE SEQUENCE OF CHAINS B, D, F AND H ARE ANNOTATED AS A SPLICE ISOFORM OF GOA4_HUMAN, WHICH HAS A MODIFIED AT THE C-TERMINUS (FTSPRSGIF -> SWLRSSS). THE ID OF THIS VARIABLE ISOFORM IS ANNOTATED AS VSP_004275 IN THE SWISS-PROT ENTRY FOR THIS PROTEIN. 12OCT,2003.

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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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growpH: 8.5
Details: GROWTH IN 20% PEG 3350, 0.2M TRIS-HCL PH 8.5. RESERVOIR EXCHANGED FOR 31% PEG 3350, 31% PEG 3350, 0.2M TRIS-HCL PH 8.5, FROZEN IN 31% PEG 3350, 0.2M TRIS-HCL PH 8.5.
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.5
2100 mM1dropNaCl
31 mM1dropMgCl2
45 mMdithiothreitol1drop
510000 nMGTP1drop
611 mg/mlprotein1drop
720 %PEG33501reservoir
80.2 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97925,0.97942,0.93928
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2003 / Details: TORROIDAL MIRROR
RadiationMonochromator: SI111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.979421
30.939281
ReflectionResolution: 1.7→67 Å / Num. obs: 94192 / % possible obs: 98.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1 / % possible all: 92.3
Reflection
*PLUS
Highest resolution: 1.7 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 92.3 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SHARPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1.7→67.42 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.388 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.126
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3198 3.4 %RANDOM
Rwork0.221 ---
obs0.222 90538 98.3 %-
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: 29.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20.91 Å2
2---0.39 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.7→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7140 0 132 270 7542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227387
X-RAY DIFFRACTIONr_bond_other_d0.0020.026842
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.999988
X-RAY DIFFRACTIONr_angle_other_deg0.83315907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775879
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_restr0.080.21145
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027860
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021451
X-RAY DIFFRACTIONr_nbd_refined0.2110.21378
X-RAY DIFFRACTIONr_nbd_other0.2290.27654
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.24543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3290.2135
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9061.54396
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70227130
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4132991
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9334.52858
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.392 182
Rwork0.349 5526
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 67 Å / % reflection Rfree: 3.4 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg6

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