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- PDB-2al7: Structure Of Human ADP-Ribosylation Factor-Like 10C -

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Basic information

Entry
Database: PDB / ID: 2al7
TitleStructure Of Human ADP-Ribosylation Factor-Like 10C
ComponentsADP-ribosylation factor-like 10C
KeywordsTRANSPORT PROTEIN / GDP-BINDING / MEMBRANE TRAFFICKING / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


antigen processing and presentation of polysaccharide antigen via MHC class II / antigen processing and presentation following phagocytosis / viral exocytosis / calcium ion regulated lysosome exocytosis / endosome to lysosome transport of low-density lipoprotein particle / protein localization to early endosome / phagosome-lysosome fusion / early endosome to Golgi transport / cytolytic granule membrane / late endosome to lysosome transport ...antigen processing and presentation of polysaccharide antigen via MHC class II / antigen processing and presentation following phagocytosis / viral exocytosis / calcium ion regulated lysosome exocytosis / endosome to lysosome transport of low-density lipoprotein particle / protein localization to early endosome / phagosome-lysosome fusion / early endosome to Golgi transport / cytolytic granule membrane / late endosome to lysosome transport / autophagosome-lysosome fusion / lysosome localization / plasma membrane repair / anterograde axonal transport / natural killer cell mediated cytotoxicity / beta-tubulin binding / alpha-tubulin binding / spindle midzone / axon cytoplasm / small monomeric GTPase / chromosome segregation / GDP binding / late endosome membrane / protein transport / G protein activity / midbody / early endosome membrane / lysosome / lysosomal membrane / cell division / GTPase activity / synapse / GTP binding / extracellular exosome / membrane / cytosol / 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 / Ras subfamily of RAS small GTPases / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...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 / Ras subfamily of RAS small GTPases / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor-like protein 8B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsIsmail, S. / Dimov, S. / Atanassova, A. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: GTP-like conformation of GDP-bound ARL10C GTPase
Authors: Ismail, S. / Dimov, S. / Atanassova, A. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium
History
DepositionAug 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns / Item: _reflns.percent_possible_obs
Revision 1.4Aug 23, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Assembly

Deposited unit
A: ADP-ribosylation factor-like 10C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6723
Polymers21,2041
Non-polymers4682
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.732, 62.393, 63.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADP-ribosylation factor-like 10C


Mass: 21204.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARL10C / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q9NVJ2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350 25%, Ammonium Acetate 100mM, 100mM HEPES (7.5), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 3, 2005
RadiationMonochromator: CONFOCAL MAXFLUX OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→44.59 Å / Num. all: 13639 / Num. obs: 13639 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rsym value: 0.032 / Net I/σ(I): 52
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 16.25 / Num. unique all: 1157 / Rsym value: 0.08 / % possible all: 79.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZD9

1zd9


Resolution: 1.85→44.59 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.905 / SU B: 2.918 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.161 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25062 747 5.2 %RANDOM
Rwork0.20068 ---
obs0.20318 13639 97.38 %-
all-14060 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.653 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---0.55 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1245 0 29 142 1416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221292
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9931744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5495153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.924.91559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5915251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.572159
X-RAY DIFFRACTIONr_chiral_restr0.0960.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02932
X-RAY DIFFRACTIONr_nbd_refined0.2260.2644
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2878
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2126
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.210
X-RAY DIFFRACTIONr_mcbond_it1.131.5795
X-RAY DIFFRACTIONr_mcangle_it1.75321243
X-RAY DIFFRACTIONr_scbond_it2.7063580
X-RAY DIFFRACTIONr_scangle_it4.4674.5501
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 44 -
Rwork0.217 795 -
obs--77.18 %

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