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- PDB-1ku1: Crystal Structure of the Sec7 Domain of Yeast GEA2 -

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Basic information

Entry
Database: PDB / ID: 1ku1
TitleCrystal Structure of the Sec7 Domain of Yeast GEA2
ComponentsARF guanine-nucleotide exchange factor 2
KeywordsENDOCYTOSIS/EXOCYTOSIS / Sec7 domain / Guanine Nucleotide Exchange Factor (GEF) / ARF small GTP-binding proteins / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


secretory granule organization / VxPx cargo-targeting to cilium / Golgi cis cisterna / trans-Golgi Network Vesicle Budding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / intra-Golgi vesicle-mediated transport / regulation of ARF protein signal transduction / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport ...secretory granule organization / VxPx cargo-targeting to cilium / Golgi cis cisterna / trans-Golgi Network Vesicle Budding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / intra-Golgi vesicle-mediated transport / regulation of ARF protein signal transduction / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / guanyl-nucleotide exchange factor activity / macroautophagy / actin cytoskeleton organization / Golgi membrane / cytosol
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 / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ARF guanine-nucleotide exchange factor 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsRenault, L. / Christova, P. / Guibert, B. / Pasqualato, S. / Cherfils, J.
CitationJournal: Biochemistry / Year: 2002
Title: Mechanism of domain closure of Sec7 domains and role in BFA sensitivity.
Authors: Renault, L. / Christova, P. / Guibert, B. / Pasqualato, S. / Cherfils, J.
History
DepositionJan 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999sequence the coordinate numbering is not sequential. The cloning artifacts are numbered -9 to -1 ...sequence the coordinate numbering is not sequential. The cloning artifacts are numbered -9 to -1 and the Sec7 domain is numbered 558-759.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARF guanine-nucleotide exchange factor 2
B: ARF guanine-nucleotide exchange factor 2


Theoretical massNumber of molelcules
Total (without water)53,0962
Polymers53,0962
Non-polymers00
Water3,909217
1
A: ARF guanine-nucleotide exchange factor 2


Theoretical massNumber of molelcules
Total (without water)26,5481
Polymers26,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ARF guanine-nucleotide exchange factor 2


Theoretical massNumber of molelcules
Total (without water)26,5481
Polymers26,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.052, 75.881, 76.199
Angle α, β, γ (deg.)90.00, 105.37, 90.00
Int Tables number5
Space group name H-MC121
DetailsSec7 domains are known to be active as monomer. The crystal asymetric unit is composed of two copies of the protein.

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Components

#1: Protein ARF guanine-nucleotide exchange factor 2


Mass: 26547.891 Da / Num. of mol.: 2 / Fragment: Sec7 domain (residues 570-714) / Mutation: I747V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold / References: UniProt: P39993
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.4M Ammonium Sulfate, 0.1M Sodium Acetate or Sodium Citrate at pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Details: used microseeding / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130-40 mg/mlprotein1drop
220 mMHEPES1droppH7.5
3150 mM1dropKCl
41-4 mMdithiothreitol1drop
51.4 Mammonium sulfate1reservoir
60.1 Msodium acetate1reservoiror sodium citrate, pH5.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONLURE DW3210.948
SYNCHROTRONMPG/DESY, HAMBURG BW621.05
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEMar 1, 2001
MARRESEARCH2CCDMar 24, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1monocrystal Si 111SINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9481
21.051
ReflectionResolution: 1.93→24.04 Å / Num. obs: 52653 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.6
Reflection shellResolution: 1.93→1.97 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2543 / % possible all: 94.4
Reflection
*PLUS
Lowest resolution: 25 Å / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 94.4 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→24.04 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 156814001.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3709 7.4 %RANDOM
Rwork0.214 ---
obs0.22 50288 97.2 %-
all-52656 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.7862 Å2 / ksol: 0.375713 e/Å3
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å22.42 Å2
2--3.68 Å20 Å2
3----4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.93→24.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 0 217 3629
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it2.61.5
X-RAY DIFFRACTIONc_mcangle_it4.392
X-RAY DIFFRACTIONc_scbond_it4.252
X-RAY DIFFRACTIONc_scangle_it6.912.5
LS refinement shellResolution: 1.93→1.97 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.298 189 7.4 %
Rwork0.276 2352 -
obs-2900 94.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 7 % / Rfactor all: 0.22 / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01
LS refinement shell
*PLUS
Rfactor obs: 0.276

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