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- PDB-5j5c: Crystal structure of ARL1-GTP and DCB domain of BIG1 complex -

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Basic information

Entry
Database: PDB / ID: 5j5c
TitleCrystal structure of ARL1-GTP and DCB domain of BIG1 complex
Components
  • ADP-ribosylation factor-like protein 1
  • Brefeldin A-inhibited guanine nucleotide-exchange protein 1
KeywordsSIGNALING PROTEIN / small GTPase / effector / GEF
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
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 / SAD / Resolution: 3.4 Å
AuthorsWang, R. / Wang, Z. / Zhang, T. / Ding, J.
CitationJournal: J Mol Cell Biol / Year: 2016
Title: Structural basis for targeting BIG1 to Golgi apparatus through interaction of its DCB domain with Arl1
Authors: Wang, R. / Wang, Z. / Wang, K. / Zhang, T. / Ding, J.
History
DepositionApr 2, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,7676
Polymers44,0272
Non-polymers7404
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-59 kcal/mol
Surface area17510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.819, 107.819, 204.627
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein ADP-ribosylation factor-like protein 1


Mass: 19044.982 Da / Num. of mol.: 1 / Fragment: small GTPase, UNP residues 16-181 / Mutation: Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARL1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: P40616
#2: 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: 24981.939 Da / Num. of mol.: 1 / Fragment: DCB domain, UNP residues 1-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARFGEF1, ARFGEP1, BIG1 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q9Y6D6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: 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

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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: 3.9 Å3/Da / Density % sol: 68.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: 0.2M lithium sulfate, 0.1M sodium citrate tribasic, 0.1M Tris-HCl pH 9.1, and 27% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9777 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 8735 / % possible obs: 85 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.107 / Net I/av σ(I): 12.5 / Net I/σ(I): 3.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.4-3.525.80.488130
3.52-3.666.20.475145.3
3.66-3.836.40.53175.1
3.83-4.036.60.441100
4.03-4.286.50.2941100
4.28-4.616.10.173199.9
4.61-5.085.90.12199.1
5.08-5.816.50.118199.5
5.81-7.326.30.089199.1
7.32-505.60.049197

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
SOLVEphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 57.947 / SU ML: 0.411 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.54 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 429 4.9 %RANDOM
Rwork0.2249 ---
obs0.2267 8283 84.82 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 246.98 Å2 / Biso mean: 128.011 Å2 / Biso min: 76.34 Å2
Baniso -1Baniso -2Baniso -3
1-5.31 Å22.65 Å20 Å2
2--5.31 Å20 Å2
3----7.96 Å2
Refinement stepCycle: final / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 43 0 2717
Biso mean--111.12 --
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.022753
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9853751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7985356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95525.146103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91715453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7031512
X-RAY DIFFRACTIONr_chiral_restr0.0780.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211997
LS refinement shellResolution: 3.403→3.491 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 6 -
Rwork0.306 152 -
all-158 -
obs--22.8 %
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)
11.61480.0408-0.04312.5081-0.21822.18180.0433-0.1495-0.0078-0.0184-0.1014-0.0840.1950.18370.05810.15930.1026-0.010.3793-0.02280.0655-37.665631.4136-7.7601
23.21121.28670.29652.46570.04962.2166-0.21080.25830.5005-0.1056-0.03180.2879-0.1501-0.15690.24260.16020.1567-0.07490.31590.03010.1328-51.966746.3736-25.9557
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 181
2X-RAY DIFFRACTION2B14 - 221

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