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- PDB-4ile: Structure of human ADP-ribosylation factor-like 8A binding to GDP -

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Basic information

Entry
Database: PDB / ID: 4ile
TitleStructure of human ADP-ribosylation factor-like 8A binding to GDP
ComponentsADP-ribosylation factor-like protein 8A
KeywordsTRANSPORT PROTEIN / GTPase / MEMBRANE TRAFFICKING
Function / homology
Function and homology information


anterograde axonal transport / azurophil granule membrane / beta-tubulin binding / alpha-tubulin binding / ficolin-1-rich granule membrane / spindle midzone / axon cytoplasm / chromosome segregation / protein transport / late endosome membrane ...anterograde axonal transport / azurophil granule membrane / beta-tubulin binding / alpha-tubulin binding / ficolin-1-rich granule membrane / spindle midzone / axon cytoplasm / chromosome segregation / protein transport / late endosome membrane / midbody / cell division / lysosomal membrane / GTPase activity / synapse / Neutrophil degranulation / GTP binding / extracellular exosome / membrane / plasma membrane / cytoplasm
Similarity search - Function
ADP-ribosylation factor-like protein 8A/8B / 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 / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...ADP-ribosylation factor-like protein 8A/8B / 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 / Small GTP-binding protein domain / 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'-DIPHOSPHATE / ADP-ribosylation factor-like protein 8A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.676 Å
AuthorsXie, Y. / Ren, J. / Cheng, Z. / Qian, H.
CitationJournal: To be Published
Title: Structure of human ADP-ribosylation factor-like 8A binding to GDP
Authors: Xie, Y. / Ren, J. / Cheng, Z. / Qian, H.
History
DepositionDec 31, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosylation factor-like protein 8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8982
Polymers21,4551
Non-polymers4431
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.032, 37.374, 39.315
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ADP-ribosylation factor-like protein 8A / ADP-ribosylation factor-like protein 10B / Novel small G protein indispensable for equal chromosome ...ADP-ribosylation factor-like protein 10B / Novel small G protein indispensable for equal chromosome segregation 2


Mass: 21454.768 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARL8A, ARL10B, GIE2 / Plasmid: pGEX-4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q96BM9
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 16% PEG 4000, 200mM NaCl, 100mM Tris-HCL (pH7.4), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9724 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.676→39.315 Å / Num. obs: 5242 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 18.78 Å2 / Rmerge(I) obs: 0.049
Reflection shellResolution: 2.68→2.74 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 1.98 / Num. unique all: 631 / % possible all: 87.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H18

2h18


Resolution: 2.676→39.3 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7864 / SU ML: 0.33 / σ(F): 1.38 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2703 238 4.54 %RANDOM
Rwork0.1814 ---
obs0.1854 5242 98.79 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 7.85 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso max: 85.98 Å2 / Biso mean: 14.8499 Å2 / Biso min: 2.41 Å2
Baniso -1Baniso -2Baniso -3
1-3.4706 Å2-0 Å20 Å2
2---2.537 Å2-0 Å2
3----0.9337 Å2
Refinement stepCycle: LAST / Resolution: 2.676→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1421 0 28 55 1504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091477
X-RAY DIFFRACTIONf_angle_d1.2851997
X-RAY DIFFRACTIONf_chiral_restr0.086220
X-RAY DIFFRACTIONf_plane_restr0.004248
X-RAY DIFFRACTIONf_dihedral_angle_d18.171561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6759-3.37110.32791180.20052404252298
3.3711-39.31920.23691200.1726002720100

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