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- PDB-2gqe: Molecular characterization of the Ran binding zinc finger domain -

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Basic information

Entry
Database: PDB / ID: 2gqe
TitleMolecular characterization of the Ran binding zinc finger domain
ComponentsNuclear pore complex protein Nup153
KeywordsTRANSPORT PROTEIN / Zinc finger / Ran / Nuclear Pore / zinc knuckle / nucleoporin / pore / transport / NUP153 / NUP358 / RanBP2
Function / homology
Function and homology information


negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA ...negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / SUMOylation of DNA damage response and repair proteins / nuclear pore / protein-membrane adaptor activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / viral penetration into host nucleus / protein import into nucleus / host cell / nuclear envelope / snRNP Assembly / nuclear membrane / amyloid fibril formation / symbiont entry into host cell / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / DNA binding / nucleoplasm / identical protein binding / membrane / metal ion binding / cytosol
Similarity search - Function
Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type
Similarity search - Domain/homology
Nuclear pore complex protein Nup153
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHiga, M.M. / Alam, S.L. / Sundquist, W.I. / Ullman, K.S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Molecular Characterization of the Ran-binding Zinc Finger Domain of Nup153.
Authors: Higa, M.M. / Alam, S.L. / Sundquist, W.I. / Ullman, K.S.
History
DepositionApr 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear pore complex protein Nup153
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5582
Polymers3,4921
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100lowest target function, least violations, favorable non-bonded energies
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Nuclear pore complex protein Nup153 / Nucleoporin Nup153 / 153 kDa nucleoporin


Mass: 3492.093 Da / Num. of mol.: 1 / Fragment: second zinc finger, residues 722-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP153 / Plasmid: pGex2T variant with TEV cleavage site / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon plus / References: UniProt: P49790
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1213D 15N-separated NOESY
131HNHA
141HNCO
151HN(CO)CA
161HN(CA)CB
171CBCA(CO)NH
181HNHB
191HN(CO)HB
1101LRCC
1111HSQC
1121HSQC-TROSY
1131(H)CCH-TOCSY
1141(H)C(CO)NH-TOCSY
1151H(CCO)NH-TOCSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.3 mM hZnF2 U-15N, 13C, 20mM D-Tris, pH 7.0, 50mM NaCl, 1mM D-BME, 10 micromolr ZnCl2, 90%H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 70mM, 20mM Tris, 50mM NaCl / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1GUNTERT, P. ET AL.refinement
CYANA2.1GUNTERT, P. ET AL.structure solution
Felixprocessing
Sparky3.11.2Goddard, T.D. et al.data analysis
VNMR2.3Ccollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: Using CYANA automated NOESY assignments
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest target function, least violations, favorable non-bonded energies
Conformers calculated total number: 100 / Conformers submitted total number: 20

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