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- PDB-3o47: Crystal structure of ARFGAP1-ARF1 fusion protein -

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Basic information

Entry
Database: PDB / ID: 3o47
TitleCrystal structure of ARFGAP1-ARF1 fusion protein
ComponentsADP-ribosylation factor GTPase-activating protein 1, ADP-ribosylation factor 1
KeywordsHYDROLASE / HYDROLASE ACTIVATOR / structural genomics consortium / GTPase activation / fusion protein / chimera protein / SGC
Function / homology
Function and homology information


mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Glycosphingolipid transport / regulation of receptor internalization / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the Golgi membrane / XBP1(S) activates chaperone genes / regulation of ARF protein signal transduction / Nef Mediated CD4 Down-regulation ...mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Glycosphingolipid transport / regulation of receptor internalization / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the Golgi membrane / XBP1(S) activates chaperone genes / regulation of ARF protein signal transduction / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / cell leading edge / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / intracellular copper ion homeostasis / COPI-mediated anterograde transport / vesicle-mediated transport / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / sarcomere / GTPase activator activity / small monomeric GTPase / intracellular protein transport / cellular response to virus / protein transport / Clathrin-mediated endocytosis / postsynaptic density / neuron projection / protein domain specific binding / Golgi membrane / focal adhesion / GTPase activity / synapse / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Arf GTPase activating protein / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / Annexin V; domain 1 ...Arf GTPase activating protein / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / Annexin V; domain 1 / small GTPase Arf family 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'-DIPHOSPHATE / ADP-ribosylation factor 1 / ADP-ribosylation factor GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsWang, H. / Tong, Y. / Nedyalkova, L. / Tempel, W. / Guan, X. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Wang, H. / Tong, Y. / Nedyalkova, L. / Tempel, W. / Guan, X. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of ARFGAP1-ARF1 fusion protein
Authors: Wang, H. / Tong, Y. / Nedyalkova, L. / Tempel, W. / Guan, X. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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 GTPase-activating protein 1, ADP-ribosylation factor 1
B: ADP-ribosylation factor GTPase-activating protein 1, ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9076
Polymers75,8902
Non-polymers1,0174
Water00
1
A: ADP-ribosylation factor GTPase-activating protein 1, ADP-ribosylation factor 1
hetero molecules

A: ADP-ribosylation factor GTPase-activating protein 1, ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9076
Polymers75,8902
Non-polymers1,0174
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1/2,z1
Buried area3280 Å2
ΔGint-22 kcal/mol
Surface area26100 Å2
MethodPISA
2
B: ADP-ribosylation factor GTPase-activating protein 1, ADP-ribosylation factor 1
hetero molecules

B: ADP-ribosylation factor GTPase-activating protein 1, ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9076
Polymers75,8902
Non-polymers1,0174
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_456-x-1/2,y,-z+11
Buried area3540 Å2
ΔGint-24 kcal/mol
Surface area26050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.298, 129.161, 157.685
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein ADP-ribosylation factor GTPase-activating protein 1, ADP-ribosylation factor 1 / ARF GAP 1 / ADP-ribosylation factor 1 GTPase-activating protein / ARF1 GAP / ARF1-directed GTPase- ...ARF GAP 1 / ADP-ribosylation factor 1 GTPase-activating protein / ARF1 GAP / ARF1-directed GTPase-activating protein


Mass: 37945.070 Da / Num. of mol.: 2
Fragment: ARF1GAP, UNP residues 1-140, ARF1, UNP residues 11-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARFGAP1, ARF1GAP, ARF1 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q8N6T3, UniProt: P84077
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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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: 2.66 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 20% PEG-3350, 0.2M trilithium sulfate, pH not applicable, vapor diffusion, temperature 291K
PH range: not applicable

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 20250 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.116 / Χ2: 1.627 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.94.90.9919711.53899.8
2.9-3.024.90.73119841.538100
3.02-3.154.90.54720131.577100
3.15-3.324.90.33820081.551100
3.32-3.534.90.22620051.599100
3.53-3.84.90.14220131.558100
3.8-4.184.90.11420191.962100
4.18-4.794.90.07720251.802100
4.79-6.034.90.06220701.513100
6.03-404.70.03821421.62799.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1HUR, 3DWD

1hur

3dwd


Resolution: 2.8→39.65 Å / Cor.coef. Fo:Fc: 0.9166 / Cor.coef. Fo:Fc free: 0.8932 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
Details: Programs COOT and PHENIX and the MOLPROBITY server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 823 4.07 %thin shells (sftools)
Rwork0.2056 ---
obs0.2072 20246 --
Displacement parametersBiso max: 132.76 Å2 / Biso mean: 65.1668 Å2 / Biso min: 34.63 Å2
Baniso -1Baniso -2Baniso -3
1-17.3953 Å20 Å20 Å2
2---17.4482 Å20 Å2
3---0.0529 Å2
Refine analyzeLuzzati coordinate error obs: 0.387 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4446 0 58 0 4504
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d15482
X-RAY DIFFRACTIONt_trig_c_planes1092
X-RAY DIFFRACTIONt_gen_planes6645
X-RAY DIFFRACTIONt_it459720
X-RAY DIFFRACTIONt_nbd15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion5925
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact52224
X-RAY DIFFRACTIONt_bond_d459720.009
X-RAY DIFFRACTIONt_angle_deg625321.08
X-RAY DIFFRACTIONt_omega_torsion2.75
X-RAY DIFFRACTIONt_other_torsion19.71
LS refinement shellResolution: 2.8→2.95 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2895 86 3.03 %
Rwork0.2436 2752 -
all0.245 2838 -

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