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- PDB-3gj3: Crystal structure of human RanGDP-Nup153ZnF2 complex -

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Basic information

Entry
Database: PDB / ID: 3gj3
TitleCrystal structure of human RanGDP-Nup153ZnF2 complex
Components
  • GTP-binding nuclear protein Ran
  • Nuclear pore complex protein Nup153
KeywordsTRANSPORT PROTEIN / G protein / GDP / RAN / Nuclear Pore / Nup153 / Zinc Finger / Acetylation / Cytoplasm / GTP-binding / Host-virus interaction / Isopeptide bond / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism / Protein transport / Transport / Ubl conjugation / DNA-binding / Metal-binding / mRNA transport / Nuclear pore complex / Translocation / Zinc / Zinc-finger
Function / homology
Function and homology information


nucleoplasmic side of nuclear pore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins ...nucleoplasmic side of nuclear pore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / Transcriptional regulation by small RNAs / Regulation of Glucokinase by Glucokinase Regulatory Protein / SUMOylation of DNA damage response and repair proteins / negative regulation of RNA export from nucleus / Regulation of HSF1-mediated heat shock response / annulate lamellae / nuclear pore complex assembly / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / manchette / cellular response to mineralocorticoid stimulus / nuclear inclusion body / nuclear pore nuclear basket / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / nuclear localization sequence binding / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / dynein intermediate chain binding / mitotic sister chromatid segregation / viral process / spermatid development / ribosomal large subunit export from nucleus / positive regulation of protein binding / mRNA transport / sperm flagellum / nuclear pore / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / protein-membrane adaptor activity / centriole / nuclear periphery / protein export from nucleus / mitotic spindle organization / male germ cell nucleus / hippocampus development / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / recycling endosome / positive regulation of protein import into nucleus / small GTPase binding / protein import into nucleus / GDP binding / melanosome / nuclear envelope / mitotic cell cycle / G protein activity / actin cytoskeleton organization / double-stranded DNA binding / midbody / nuclear membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / amyloid fibril formation / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / GTP binding / protein-containing complex binding / nucleolus / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Ran GTPase / Small GTPase Ran-type domain profile. / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. ...Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Ran GTPase / Small GTPase Ran-type domain profile. / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Nuclear pore complex protein Nup153 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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: GTP-binding nuclear protein Ran
B: Nuclear pore complex protein Nup153
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8475
Polymers28,3142
Non-polymers5333
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.709, 80.236, 57.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-277-

HOH

21A-320-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): BL21(DE3)-RIL / References: UniProt: P62826
#2: Protein/peptide Nuclear pore complex protein Nup153 / Nucleoporin Nup153 / 153 kDa nucleoporin


Mass: 3407.889 Da / Num. of mol.: 1
Fragment: Nup153 - Zinc finger module 2: UNP residues 723-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nup153 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21(DE3)-RIL / References: UniProt: P49791

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Non-polymers , 4 types, 253 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
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: 1.79→50 Å / Num. all: 26894 / Num. obs: 26894 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 25.51 Å2 / Rsym value: 0.08 / Net I/σ(I): 30.2
Reflection shellResolution: 1.79→1.86 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 2.92 / Rsym value: 0.4 / % possible all: 99.4

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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: 1.79→33.3 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 17.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.1941 1349 5.02 %
Rwork0.1612 --
obs0.1629 26860 98.99 %
all-26894 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.887 Å2 / ksol: 0.321 e/Å3
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.79→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 30 250 2104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071899
X-RAY DIFFRACTIONf_angle_d1.1172583
X-RAY DIFFRACTIONf_dihedral_angle_d15.36694
X-RAY DIFFRACTIONf_chiral_restr0.066285
X-RAY DIFFRACTIONf_plane_restr0.004326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.84920.23511250.20722365X-RAY DIFFRACTION93
1.8492-1.92320.22861400.18132520X-RAY DIFFRACTION99
1.9232-2.01070.22881230.17612522X-RAY DIFFRACTION99
2.0107-2.11670.21441310.16412529X-RAY DIFFRACTION100
2.1167-2.24930.18631310.15622563X-RAY DIFFRACTION100
2.2493-2.42290.1761230.15512563X-RAY DIFFRACTION100
2.4229-2.66660.19561410.15942559X-RAY DIFFRACTION100
2.6666-3.05230.20621570.16122558X-RAY DIFFRACTION100
3.0523-3.84460.16921520.15232598X-RAY DIFFRACTION100
3.8446-33.30540.18041260.15292734X-RAY DIFFRACTION99
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)
1refined1.55620.21190.21581.47250.23031.14860.027-0.0856-0.15550.15970.0638-0.13440.1244-0.0025-0.08810.0730.014-0.02180.04540.00940.08824.696725.461-14.7855
21.1028-0.23371.5321.52140.0086-3.8376-0.28311.35030.0654-0.5921-0.0869-0.04690.09380.64150.21510.323-0.07280.00380.6630.03130.1234
Refinement TLS groupSelection details: Chain B

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