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- PDB-3gj0: Crystal structure of human RanGDP -

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Basic information

Entry
Database: PDB / ID: 3gj0
TitleCrystal structure of human RanGDP
ComponentsGTP-binding nuclear protein Ran
KeywordsTRANSPORT PROTEIN / G Protein / GDP / Acetylation / Cytoplasm / GTP-binding / Host-virus interaction / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism / Protein transport / Transport
Function / homology
Function and homology information


RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein ...RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / dynein intermediate chain binding / DNA metabolic process / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / nuclear pore / centriole / protein export from nucleus / viral process / mitotic spindle organization / G protein activity / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / recycling endosome / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
small GTPase Ran family profile. / Ran GTPase / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...small GTPase Ran family profile. / Ran GTPase / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / 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 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsPartridge, J.R. / Schwartz, T.U.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystallographic and Biochemical Analysis of the Ran-binding Zinc Finger Domain.
Authors: Partridge, J.R. / Schwartz, T.U.
History
DepositionMar 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: GTP-binding nuclear protein Ran
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7486
Polymers49,8132
Non-polymers9354
Water8,611478
1
A: GTP-binding nuclear protein Ran
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3743
Polymers24,9071
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTP-binding nuclear protein Ran
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3743
Polymers24,9071
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.544, 81.544, 130.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-494-

HOH

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Components

#1: Protein GTP-binding nuclear protein Ran / GTPase Ran / Ras-related nuclear protein / Ras-like protein TC4 / Androgen receptor-associated protein 24


Mass: 24906.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARA24, OK/SW-cl.81, RAN / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P62826
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 43.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 18-20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. all: 70774 / Num. obs: 70774 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 19.6 Å2 / Rsym value: 0.07 / Net I/σ(I): 32.6
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.6 / % possible all: 93

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BYU

1byu


Resolution: 1.48→43.217 Å / SU ML: 0.48 / σ(F): 1.33 / Phase error: 19.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.203 3552 5.04 %
Rwork0.1804 --
obs0.1816 70432 95.18 %
all-70774 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.539 Å2 / ksol: 0.331 e/Å3
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 1.48→43.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 58 478 3742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083345
X-RAY DIFFRACTIONf_angle_d1.2444547
X-RAY DIFFRACTIONf_dihedral_angle_d15.8991216
X-RAY DIFFRACTIONf_chiral_restr0.081500
X-RAY DIFFRACTIONf_plane_restr0.005571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.49970.25651270.25072498X-RAY DIFFRACTION91
1.4997-1.52110.26251100.23312607X-RAY DIFFRACTION93
1.5211-1.54380.22221400.21822617X-RAY DIFFRACTION95
1.5438-1.56790.24941390.20272658X-RAY DIFFRACTION95
1.5679-1.59360.24361380.20052621X-RAY DIFFRACTION95
1.5936-1.62110.2261360.19182655X-RAY DIFFRACTION95
1.6211-1.65060.21661330.17662656X-RAY DIFFRACTION96
1.6506-1.68240.23161480.17762652X-RAY DIFFRACTION96
1.6824-1.71670.21191300.17562681X-RAY DIFFRACTION96
1.7167-1.7540.2251440.17122682X-RAY DIFFRACTION96
1.754-1.79480.2181370.17622684X-RAY DIFFRACTION96
1.7948-1.83970.19351410.17712699X-RAY DIFFRACTION97
1.8397-1.88950.2341300.20662659X-RAY DIFFRACTION95
1.8895-1.94510.19981500.17792685X-RAY DIFFRACTION97
1.9451-2.00780.20071620.17882667X-RAY DIFFRACTION96
2.0078-2.07960.16881360.16492729X-RAY DIFFRACTION97
2.0796-2.16290.18591640.1662675X-RAY DIFFRACTION97
2.1629-2.26130.20231320.18522732X-RAY DIFFRACTION96
2.2613-2.38050.22381520.17142671X-RAY DIFFRACTION96
2.3805-2.52960.21171670.17952713X-RAY DIFFRACTION96
2.5296-2.72490.19211450.17722737X-RAY DIFFRACTION96
2.7249-2.99910.20721500.18072704X-RAY DIFFRACTION96
2.9991-3.43290.18721660.16272703X-RAY DIFFRACTION94
3.4329-4.32450.15831400.15062727X-RAY DIFFRACTION93
4.3245-43.23550.18261350.1782768X-RAY DIFFRACTION90
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.07290.23830.09510.8808-0.02010.7160.02550.0049-0.05720.0163-0.03920.0617-0.0448-0.02550.00560.1109-0.00520.00030.0926-0.01820.107114.00338.6393-14.2278
21.0874-0.1960.00411.1712-0.02670.7020.00710.02380.11110.1480.0152-0.17810.0510.1138-0.01640.10510.0293-0.03930.1194-0.02760.1162
Refinement TLS groupSelection details: Chain B

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