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- PDB-1s9d: ARF1[DELTA 1-17]-GDP-MG IN COMPLEX WITH BREFELDIN A AND A SEC7 DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1s9d
TitleARF1[DELTA 1-17]-GDP-MG IN COMPLEX WITH BREFELDIN A AND A SEC7 DOMAIN
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 / regulation of receptor internalization ...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 / regulation of receptor internalization / MHC class II antigen presentation / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / 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 / postsynaptic density / neuron projection / 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 / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-AFB / GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor 1 / Cytohesin-2
Similarity search - Component
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionFeb 4, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 10, 2004ID: 1R8R
Revision 1.0Feb 10, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / 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_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 / _struct_conn_type.id / _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)43,0855
Polymers42,3372
Non-polymers7483
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-27 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.462, 111.462, 74.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11E-393-

HOH

21E-395-

HOH

Detailsthe biological unit consists of a quaternary complex with 2 proteins (chain A and E) and is identical to the asymmetric unit.

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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 (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: 23514.754 Da / Num. of mol.: 1 / Fragment: Sec7 Domain (Residues 50-252) / Mutation: F190Y,A191S,S198D,P208M
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 , 4 types, 289 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Chemical ChemComp-AFB / 1,6,7,8,9,11A,12,13,14,14A-DECAHYDRO-1,13-DIHYDROXY-6-METHYL-4H-CYCLOPENT[F]OXACYCLOTRIDECIN-4-ONE / BREFELDIN A


Mass: 280.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24O4 / Comment: antivirus*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 29% PEG 3350, 40MM NH4CL, 40MM POTASSIUM FORMATE, 100MM TRIS, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 26, 2003 / Details: mirrors
RadiationMonochromator: double Si crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 43814 / Num. obs: 43814 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 22.76 Å2 / Rsym value: 0.05 / Net I/σ(I): 26.2
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 6.4 / Num. unique all: 3319 / Rsym value: 0.405 / % possible all: 97.1

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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 1RRG and coordinates of arf1[D1-17]/Gea2-Sec7 (Goldberg, J., (1998) Cell 95(2): 237-48)

1rrg


Resolution: 1.8→29.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.786 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.111 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22148 2225 5.1 %RANDOM
Rwork0.18193 ---
all0.184 43814 --
obs0.18397 41588 99.54 %-
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: 19.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å20 Å20 Å2
2---1.95 Å20 Å2
3---3.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 49 286 3165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0212942
X-RAY DIFFRACTIONr_bond_other_d0.0020.022646
X-RAY DIFFRACTIONr_angle_refined_deg1.941.9773974
X-RAY DIFFRACTIONr_angle_other_deg0.99936146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625345
X-RAY DIFFRACTIONr_chiral_restr0.1280.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023218
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02598
X-RAY DIFFRACTIONr_nbd_refined0.2260.2638
X-RAY DIFFRACTIONr_nbd_other0.2560.23246
X-RAY DIFFRACTIONr_nbtor_other0.090.21682
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.219
X-RAY DIFFRACTIONr_mcbond_it1.2331.51728
X-RAY DIFFRACTIONr_mcangle_it2.08122781
X-RAY DIFFRACTIONr_scbond_it3.24331214
X-RAY DIFFRACTIONr_scangle_it5.0654.51193
LS refinement shellResolution: 1.8→1.849 Å / Total num. of bins used: 19
RfactorNum. reflection
Rfree0.245 181
Rwork0.235 3171
obs-3171
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)
12.48260.29670.08921.1361-0.31121.0024-0.11390.08730.18980.0578-0.0812-0.1553-0.05530.04670.19510.10860.0016-0.00010.08920.01960.124439.758116.403632.9009
20.9489-0.30360.15462.28420.48551.13490.07740.1902-0.1816-0.1310.032-0.07720.21130.0849-0.10940.1718-0.01720.01240.1708-0.07450.087322.9252-5.556623.5297
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA18 - 1781 - 161
2X-RAY DIFFRACTION1AD - C401 - 4021
3X-RAY DIFFRACTION2EB57 - 2498 - 200

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