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- PDB-5ee5: Structure of human ARL1 in complex with the DCB domain of BIG1 -

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Basic information

Entry
Database: PDB / ID: 5ee5
TitleStructure of human ARL1 in complex with the DCB domain of BIG1
Components
  • ADP-ribosylation factor-like protein 1
  • Brefeldin A-inhibited guanine nucleotide-exchange protein 1
KeywordsTRANSCRIPTION / ARF1-GEF ARL1-effector Trans-golgi DCB domain
Function / homology
Function and homology information


endomembrane system organization / phospholipase D activator activity / toxin metabolic process / Retrograde transport at the Trans-Golgi-Network / protein localization to Golgi apparatus / negative regulation of actin filament polymerization / regulation of ARF protein signal transduction / small nuclear ribonucleoprotein complex / retrograde transport, endosome to Golgi / regulation of establishment of cell polarity ...endomembrane system organization / phospholipase D activator activity / toxin metabolic process / Retrograde transport at the Trans-Golgi-Network / protein localization to Golgi apparatus / negative regulation of actin filament polymerization / regulation of ARF protein signal transduction / small nuclear ribonucleoprotein complex / retrograde transport, endosome to Golgi / regulation of establishment of cell polarity / negative regulation of GTPase activity / positive regulation of wound healing / myosin binding / protein glycosylation / exocytosis / protein kinase A regulatory subunit binding / Golgi organization / vesicle-mediated transport / enzyme activator activity / guanyl-nucleotide exchange factor activity / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / nuclear matrix / protein transport / protein domain specific binding / Golgi membrane / GTPase activity / nucleolus / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Sec7/BIG1-like, C-terminal domain / BIG2 C-terminal domain / Mon2/Sec7/BIG1-like, HDS / Mon2/Sec7/BIG1-like, HDS / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, HUS domain / Mon2/Sec7/BIG1-like, HUS domain / Sec7 domain / Sec7, C-terminal domain superfamily ...Sec7/BIG1-like, C-terminal domain / BIG2 C-terminal domain / Mon2/Sec7/BIG1-like, HDS / Mon2/Sec7/BIG1-like, HDS / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, HUS domain / Mon2/Sec7/BIG1-like, HUS domain / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / 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 / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GUANOSINE-5'-TRIPHOSPHATE / ADP-ribosylation factor-like protein 1 / Brefeldin A-inhibited guanine nucleotide-exchange protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.279 Å
AuthorsGalindo, A. / Soler, N. / Munro, S.
CitationJournal: Cell Rep / Year: 2016
Title: Structural Insights into Arl1-Mediated Targeting of the Arf-GEF BIG1 to the trans-Golgi.
Authors: Galindo, A. / Soler, N. / McLaughlin, S.H. / Yu, M. / Williams, R.L. / Munro, S.
History
DepositionOct 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Brefeldin A-inhibited guanine nucleotide-exchange protein 1
B: ADP-ribosylation factor-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,97831
Polymers43,5442
Non-polymers1,43429
Water73941
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-187 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.166, 50.727, 103.837
Angle α, β, γ (deg.)90.00, 111.98, 90.00
Int Tables number5
Space group name H-MI121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Brefeldin A-inhibited guanine nucleotide-exchange protein 1 / Brefeldin A-inhibited GEP 1 / ADP-ribosylation factor guanine nucleotide-exchange factor 1 / p200 ...Brefeldin A-inhibited GEP 1 / ADP-ribosylation factor guanine nucleotide-exchange factor 1 / p200 ARF guanine nucleotide exchange factor / p200 ARF-GEP1


Mass: 24172.963 Da / Num. of mol.: 1 / Mutation: delta-52-70
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARFGEF1, ARFGEP1, BIG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y6D6
#2: Protein ADP-ribosylation factor-like protein 1


Mass: 19371.314 Da / Num. of mol.: 1 / Mutation: delta N14, Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40616

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Non-polymers , 7 types, 70 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 8K/PEG 1k 10% Sodium Acetate 0.1-0.2mM Tris pH8.5 glacial acetic 0.100mM
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.279→29.069 Å / Num. obs: 18726 / % possible obs: 97.3 % / Observed criterion σ(I): 1.7 / Redundancy: 3.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.4
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 1.7 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1810)refinement
Aimlessdata reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.279→29.069 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1750 4.95 %Random selection
Rwork0.2172 ---
obs0.2193 35351 97.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.279→29.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 73 41 3009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012981
X-RAY DIFFRACTIONf_angle_d1.1584020
X-RAY DIFFRACTIONf_dihedral_angle_d17.9941132
X-RAY DIFFRACTIONf_chiral_restr0.064469
X-RAY DIFFRACTIONf_plane_restr0.005499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2786-2.34020.39861270.35982511X-RAY DIFFRACTION94
2.3402-2.4090.39351400.34272639X-RAY DIFFRACTION99
2.409-2.48670.391520.32862571X-RAY DIFFRACTION98
2.4867-2.57550.36731480.30222637X-RAY DIFFRACTION99
2.5755-2.67860.3071170.29522553X-RAY DIFFRACTION95
2.6786-2.80040.28181600.25732621X-RAY DIFFRACTION99
2.8004-2.94790.30811180.24982652X-RAY DIFFRACTION100
2.9479-3.13240.30431420.24712645X-RAY DIFFRACTION100
3.1324-3.37390.29451450.25222612X-RAY DIFFRACTION99
3.3739-3.71280.25131350.20972446X-RAY DIFFRACTION92
3.7128-4.24860.22281180.18662529X-RAY DIFFRACTION95
4.2486-5.34740.18571280.17232591X-RAY DIFFRACTION98
5.3474-29.07170.22511200.17572594X-RAY DIFFRACTION97

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