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- PDB-3gj8: Crystal structure of human RanGDP-Nup153ZnF34 complex -

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Basic information

Entry
Database: PDB / ID: 3gj8
TitleCrystal structure of human RanGDP-Nup153ZnF34 complex
Components
  • GTP-binding nuclear protein Ran
  • Nuclear pore complex protein Nup153
KeywordsTRANSPORT PROTEIN / G protein / GDP / Ran / Nup153 / Nuclear Pore / 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 / annulate lamellae / Regulation of HSF1-mediated heat shock response / 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 / structural constituent of nuclear pore / nuclear localization sequence binding / Rev-mediated nuclear export of HIV RNA / protein localization to nucleolus / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / dynein intermediate chain binding / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / spermatid development / viral process / mRNA transport / positive regulation of protein binding / 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 / Transcriptional regulation by small RNAs / molecular condensate scaffold activity / 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 / cytoplasm / cytosol
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: 1.82 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 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Nuclear pore complex protein Nup153
C: GTP-binding nuclear protein Ran
D: Nuclear pore complex protein Nup153
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,59712
Polymers68,4824
Non-polymers1,1148
Water9,872548
1
A: GTP-binding nuclear protein Ran
B: Nuclear pore complex protein Nup153
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7986
Polymers34,2412
Non-polymers5574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: GTP-binding nuclear protein Ran
D: Nuclear pore complex protein Nup153
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7986
Polymers34,2412
Non-polymers5574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.257, 61.713, 70.635
Angle α, β, γ (deg.)90.00, 112.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 24846.479 Da / Num. of mol.: 2 / Mutation: F35S
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 Nuclear pore complex protein Nup153 / Nucleoporin Nup153 / 153 kDa nucleoporin


Mass: 9394.635 Da / Num. of mol.: 2
Fragment: Nup153 - Zinc finger module 34: UNP residues 790-876
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, 556 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
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: 1.82→50 Å / Num. all: 52824 / Num. obs: 52824 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 24.31 Å2 / Rsym value: 0.063 / Net I/σ(I): 19.3
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.97 / Rsym value: 0.56 / % possible all: 99.1

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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 entru 3GJ3

3gj3


Resolution: 1.82→33.754 Å / SU ML: 0.49 / Phase error: 20.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.2026 2688 5.09 %
Rwork0.1702 --
obs0.1718 52792 99.2 %
all-52824 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.192 Å2 / ksol: 0.337 e/Å3
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: LAST / Resolution: 1.82→33.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 62 548 4262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053796
X-RAY DIFFRACTIONf_angle_d0.9435157
X-RAY DIFFRACTIONf_dihedral_angle_d14.7141385
X-RAY DIFFRACTIONf_chiral_restr0.062572
X-RAY DIFFRACTIONf_plane_restr0.003649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.85210.26951390.24772529X-RAY DIFFRACTION96
1.8521-1.88780.25541500.22792617X-RAY DIFFRACTION100
1.8878-1.92630.2091410.20232639X-RAY DIFFRACTION100
1.9263-1.96820.23651490.19432641X-RAY DIFFRACTION100
1.9682-2.01390.24991290.17792646X-RAY DIFFRACTION100
2.0139-2.06430.20611300.17532662X-RAY DIFFRACTION100
2.0643-2.12010.21341370.1712646X-RAY DIFFRACTION100
2.1201-2.18250.1861360.16762651X-RAY DIFFRACTION100
2.1825-2.25290.2361530.16592614X-RAY DIFFRACTION100
2.2529-2.33340.19131430.1672626X-RAY DIFFRACTION100
2.3334-2.42680.22911360.17662648X-RAY DIFFRACTION100
2.4268-2.53720.19011490.16812670X-RAY DIFFRACTION100
2.5372-2.67090.21861680.17512605X-RAY DIFFRACTION100
2.6709-2.83820.23051210.17682688X-RAY DIFFRACTION100
2.8382-3.05720.21351560.17582607X-RAY DIFFRACTION99
3.0572-3.36460.23691410.16812673X-RAY DIFFRACTION99
3.3646-3.85090.15531290.15692665X-RAY DIFFRACTION99
3.8509-4.84940.15991430.13822620X-RAY DIFFRACTION98
4.8494-33.76010.17951380.16512657X-RAY DIFFRACTION96
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)
1refined1.1836-0.33510.27170.32880.18930.5969-0.1049-0.12730.0880.02680.0375-0.0363-0.0393-0.0350.05760.09340.0084-0.05530.0202-0.01010.037352.4465-4.3495-3.9274
21.66071.2321-1.05433.0234-0.34570.59550.04550.21460.036-0.51680.106-0.1423-0.26170.2987-0.13330.2697-0.04340.05050.28320.05080.2088
30.67110.23510.13570.3686-0.14321.03720.03460.0062-0.0016-0.06840.0055-0.00450.1201-0.0811-0.04930.0852-0.0131-0.06610.02480.00090.0569
4-2.25710.9761-0.51411.38211.31292.39710.19510.4221-0.2191-0.17090.0095-0.4819-0.05910.4058-0.19910.21930.08440.01580.421-0.0610.2972
Refinement TLS groupSelection details: Chain D

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