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- PDB-1r8s: ARF1[DELTA1-17]-GDP IN COMPLEX WITH A SEC7 DOMAIN CARRYING THE MU... -

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Basic information

Entry
Database: PDB / ID: 1r8s
TitleARF1[DELTA1-17]-GDP IN COMPLEX WITH A SEC7 DOMAIN CARRYING THE MUTATION OF THE CATALYTIC GLUTAMATE TO LYSINE
Components
  • ADP-ribosylation factor 1
  • Arno
KeywordsPROTEIN TRANSPORT/EXCHANGE FACTOR / PROTEIN TRANSPORT-EXCHANGE FACTOR complex
Function / homology
Function and homology information


Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / Intra-Golgi traffic / Glycosphingolipid transport / Synthesis of PIPs at the plasma membrane / Golgi Associated Vesicle Biogenesis / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Lysosome Vesicle Biogenesis / MHC class II antigen presentation ...Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / Intra-Golgi traffic / Glycosphingolipid transport / Synthesis of PIPs at the plasma membrane / Golgi Associated Vesicle Biogenesis / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Lysosome Vesicle Biogenesis / MHC class II antigen presentation / regulation of receptor internalization / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / dendritic spine organization / long-term synaptic depression / bicellular tight junction / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / small monomeric GTPase / adherens junction / intracellular protein transport / endocytosis / growth cone / actin cytoskeleton organization / neuron projection / postsynaptic density / Golgi membrane / GTPase activity / lipid binding / GTP binding / Golgi apparatus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / ADP-ribosylation factor 1-5 ...Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / ADP-ribosylation factor 1-5 / 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 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / 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
BETA-MERCAPTOETHANOL / FORMIC ACID / GUANOSINE-5'-DIPHOSPHATE / SULFITE ION / ADP-ribosylation factor 1 / Cytohesin-2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsRenault, L. / Guibert, B. / Cherfils, J.
CitationJournal: Nature / Year: 2003
Title: Structural snapshots of the mechanism and inhibition of a guanine nucleotide exchange factor
Authors: Renault, L. / Guibert, B. / Cherfils, J.
History
DepositionOct 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE The engineered mutations in the Arno structure (F190Y, A191S, S198D, P208M) are Brefeldin ...SEQUENCE The engineered mutations in the Arno structure (F190Y, A191S, S198D, P208M) are Brefeldin A- sensitizing mutations.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosylation factor 1
E: Arno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0979
Polymers42,2612
Non-polymers8367
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-40 kcal/mol
Surface area16130 Å2
MethodPISA
2
A: ADP-ribosylation factor 1
E: Arno
hetero molecules

A: ADP-ribosylation factor 1
E: Arno
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,19318
Polymers84,5224
Non-polymers1,67114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area12390 Å2
ΔGint-90 kcal/mol
Surface area29630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.018, 104.018, 69.277
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AE

#1: Protein ADP-ribosylation factor 1


Mass: 18822.455 Da / Num. of mol.: 1 / Fragment: Residues 18-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ARF1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P84080
#2: Protein Arno / ARF nucleotide-binding site opener / cytohesin 2 / ARF exchange factor


Mass: 23438.703 Da / Num. of mol.: 1 / Fragment: Sec7 domain (Residues 50-252) / Mutation: F190Y/A191S/S198D/P208M/E156K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSCD2, ARNO / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q99418

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Non-polymers , 6 types, 357 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.88M Ammonium Sulfate, 100mM MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.88 Mammonium sulfate1reservoir
2100 %MES1reservoirpH6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.46→30 Å / Num. obs: 75051 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16 % / Biso Wilson estimate: 18.35 Å2 / Rsym value: 0.059 / Net I/σ(I): 26.6
Reflection shellResolution: 1.46→1.47 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 5.9 / Rsym value: 0.462 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R8R and crystal structure of the Arf1[D1-17]/Gea2-Sec7 complex (Goldberg, J., (1998) Cell 95(2):237-48)

1r8r
PDB Unreleased entry


Resolution: 1.46→28.87 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.804 / SU ML: 0.032 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1698 3744 5 %RANDOM
Rwork0.15885 ---
obs0.15941 71299 99.91 %-
all-75051 --
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: 12.525 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.46→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 50 350 3206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212933
X-RAY DIFFRACTIONr_bond_other_d0.0180.022649
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.973964
X-RAY DIFFRACTIONr_angle_other_deg0.8736163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1535345
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_restr0.0860.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023205
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02587
X-RAY DIFFRACTIONr_nbd_refined0.2180.2640
X-RAY DIFFRACTIONr_nbd_other0.2460.23089
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.21525
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.560.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8811.51736
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6822797
X-RAY DIFFRACTIONr_scbond_it2.52931197
X-RAY DIFFRACTIONr_scangle_it4.084.51167
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.46→1.47 Å / Total num. of bins used: 76 /
RfactorNum. reflection
Rfree0.208 70
Rwork0.214 1428
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)
10.6202-0.0866-0.1481.1428-0.30240.60.04660.11560.0337-0.0487-0.0395-0.03620.0313-0.03-0.00710.04670.04810.01220.09730.020.042330.985933.9145-20.6461
20.7195-0.2528-0.04020.5470.14560.5843-0.05830.0116-0.00430.02670.00550.02950.0787-0.00780.05280.07440.03250.00290.03260.00940.066535.121717.6432-0.7583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA18 - 1771 - 160
2X-RAY DIFFRACTION1AE401
3X-RAY DIFFRACTION2EB62 - 24813 - 199
4X-RAY DIFFRACTION2EC501
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.173 / Rfactor Rwork: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS

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