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- PDB-1re0: Structure of ARF1-GDP bound to Sec7 domain complexed with Brefeldin A -

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Basic information

Entry
Database: PDB / ID: 1re0
TitleStructure of ARF1-GDP bound to Sec7 domain complexed with Brefeldin A
Components
  • ADP-ribosylation factor 1ARF1
  • ARF guanine-nucleotide exchange factor 1
KeywordsPROTEIN TRANSPORT / all-helical / alph-beta
Function / homology
Function and homology information


guanyl-nucleotide exchange factor activity => GO:0005085 / Synthesis of PIPs at the Golgi membrane / synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / Synthesis of PIPs at the plasma membrane / Golgi to transport vesicle transport / phospholipase D activator activity / Intra-Golgi traffic ...guanyl-nucleotide exchange factor activity => GO:0005085 / Synthesis of PIPs at the Golgi membrane / synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / Synthesis of PIPs at the plasma membrane / Golgi to transport vesicle transport / phospholipase D activator activity / Intra-Golgi traffic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / cellular bud / Golgi cis cisterna / trans-Golgi Network Vesicle Budding / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / positive regulation of ER to Golgi vesicle-mediated transport / regulation of ARF protein signal transduction / Lysosome Vesicle Biogenesis / regulation of receptor internalization / very-low-density lipoprotein particle assembly / regulation of Arp2/3 complex-mediated actin nucleation / Golgi Associated Vesicle Biogenesis / Intra-Golgi traffic / MHC class II antigen presentation / positive regulation of calcium ion-dependent exocytosis / postsynaptic actin cytoskeleton organization / Synthesis of PIPs at the Golgi membrane / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / positive regulation of dendritic spine development / Lysosome Vesicle Biogenesis / extrinsic component of membrane / positive regulation of sodium ion transmembrane transport / Golgi Associated Vesicle Biogenesis / positive regulation of endocytosis / cell leading edge / Synthesis of PIPs at the plasma membrane / intracellular copper ion homeostasis / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / 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 / small monomeric GTPase / actin filament organization / positive regulation of protein secretion / macroautophagy / intracellular protein transport / cellular response to virus / GDP binding / late endosome / actin cytoskeleton organization / postsynaptic density / neuron projection / protein domain specific binding / Golgi membrane / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mon2/Sec7/BIG1-like, HUS domain / Mon2/Sec7/BIG1-like, HUS domain / 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. ...Mon2/Sec7/BIG1-like, HUS domain / Mon2/Sec7/BIG1-like, HUS domain / 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 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-AFB / CITRIC ACID / GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor 1 / ARF guanine-nucleotide exchange factor 1 / ADP-ribosylation factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGoldberg, J. / Mossessova, E.
CitationJournal: Mol.Cell / Year: 2003
Title: Crystal structure of ARF1*Sec7 complexed with Brefeldin A and its implications for the guanine nucleotide exchange mechanism.
Authors: Mossessova, E. / Corpina, R.A. / Goldberg, J.
History
DepositionNov 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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_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 1
B: ARF guanine-nucleotide exchange factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1816
Polymers44,2412
Non-polymers9404
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-24 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.725, 72.294, 119.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ADP-ribosylation factor 1 / ARF1


Mass: 18822.455 Da / Num. of mol.: 1 / Fragment: Truncated form of ARF1 (residues 17-180)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P32889, UniProt: P84077*PLUS
#2: Protein ARF guanine-nucleotide exchange factor 1


Mass: 25418.918 Da / Num. of mol.: 1 / Fragment: Core Sec7 domain of Gea1 (residues 540-754)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Gea1 / Production host: Escherichia coli (E. coli) / References: UniProt: P47102

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Non-polymers , 5 types, 117 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 / Guanosine 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 / Brefeldin A


Mass: 280.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24O4 / Comment: antivirus*YM
#6: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 400, sodium citrate, Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMsodium citrate1reservoir
219 %(w/v)PEG4001reservoir
3100 mMTris-HCl1reservoirpH8.5
420 mMHEPES1drop
5150 mM1dropNaCl
64 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 22531 / Num. obs: 22531 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.4→2.49 Å / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 136824
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 2221 / Num. measured obs: 13339 / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 6.3

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1201695.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1106 5 %RANDOM
Rwork0.209 ---
all0.214 22531 --
obs0.209 22049 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.7622 Å2 / ksol: 0.348137 e/Å3
Displacement parametersBiso mean: 42.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.18 Å20 Å20 Å2
2--0.83 Å20 Å2
3---4.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2887 0 62 113 3062
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 193 5.5 %
Rwork0.242 3312 -
obs--95.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM.IONION.TOP
X-RAY DIFFRACTION4GDP.PARAMGDP.TOPOL
X-RAY DIFFRACTION5BRE+CITRATE.PARBRE+CITRATE.TOP
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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