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- PDB-2lhn: RNA-binding zinc finger protein -

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Basic information

Entry
Database: PDB / ID: 2lhn
TitleRNA-binding zinc finger protein
ComponentsNuclear polyadenylated RNA-binding protein NAB2
KeywordsNUCLEAR PROTEIN / RNA-BINDING PROTEIN
Function / homology
Function and homology information


: / ribonuclease P RNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 7S RNA binding / poly(A) binding / positive regulation of transcription by RNA polymerase III / poly(A)+ mRNA export from nucleus / regulation of mRNA stability / 5S rRNA binding / tRNA binding ...: / ribonuclease P RNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 7S RNA binding / poly(A) binding / positive regulation of transcription by RNA polymerase III / poly(A)+ mRNA export from nucleus / regulation of mRNA stability / 5S rRNA binding / tRNA binding / mRNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
CCCH zinc finger - #40 / CCCH zinc finger / Nuclear abundant poly(A) RNA-binding protein Nab2, N-terminal / Nuclear polyadenylated RNA-binding 2 protein, CCCH zinc finger 1 / Nab2/ZC3H14, N-terminal domain superfamily / : / : / Nuclear abundant poly(A) RNA-bind protein 2 (Nab2) / Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1 / RNA-binding, Nab2-type zinc finger ...CCCH zinc finger - #40 / CCCH zinc finger / Nuclear abundant poly(A) RNA-binding protein Nab2, N-terminal / Nuclear polyadenylated RNA-binding 2 protein, CCCH zinc finger 1 / Nab2/ZC3H14, N-terminal domain superfamily / : / : / Nuclear abundant poly(A) RNA-bind protein 2 (Nab2) / Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1 / RNA-binding, Nab2-type zinc finger / Nab2-type CCCH zinc finger 4 / Nuclear polyadenylated RNA-binding protein Nab2/ZC3H14 / RNA-binding, Nab2-type zinc finger / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Nuclear polyadenylated RNA-binding protein NAB2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsBrockmann, C. / Neuhaus, D. / Stewart, M.
CitationJournal: Structure / Year: 2012
Title: Structural Basis for Polyadenosine-RNA Binding by Nab2 Zn Fingers and Its Function in mRNA Nuclear Export.
Authors: Brockmann, C. / Soucek, S. / Kuhlmann, S.I. / Mills-Lujan, K. / Kelly, S.M. / Yang, J.C. / Iglesias, N. / Stutz, F. / Corbett, A.H. / Neuhaus, D. / Stewart, M.
History
DepositionAug 12, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Nuclear polyadenylated RNA-binding protein NAB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4244
Polymers9,2281
Non-polymers1963
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nuclear polyadenylated RNA-binding protein NAB2


Mass: 9227.789 Da / Num. of mol.: 1 / Fragment: Zinc finger domain residues 409-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: NAB2, YGL122C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P32505
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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
1112D 1H-15N HSQC
1212D 1H-15N HSQC lomg-range optimised
1312D 1H-13C HSQC
1412D 1H-13C HSQC aliphatic
1512D 1H-13C HSQC aromatic
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY (50ms mixing)
11213D 1H-15N NOESY (120 ms mixing)
11313D 1H-13C NOESY aliphatic (150 ms mixing)
11413D 1H-13C NOESY aromatic (150 ms mixing)
11522D 1H-15N HSQC IPAP
11623D HNCO IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM [U-2H] TRIS, 50 mM arginine, 50 mM glutamic acid, 10 uM zinc chloride, 5 mM [U-2H] mercaptoethanol, 50 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
250 mM [U-2H] TRIS, 50 mM arginine, 50 mM glutamic acid, 10 uM zinc chloride, 5 mM [U-2H] mercaptoethanol, 50 mM sodium chloride, 25 mg/ml tobacco mosaic virus, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMTRIS-1[U-2H]1
50 mMarginine-21
50 mMglutamic acid-31
10 uMzinc chloride-41
5 mMmercaptoethanol-5[U-2H]1
50 mMsodium chloride-61
50 mMTRIS-7[U-2H]2
50 mMarginine-82
50 mMglutamic acid-92
10 uMzinc chloride-102
5 mMmercaptoethanol-11[U-2H]2
50 mMsodium chloride-122
25 mg/mLtobacco mosaic virus-132
Sample conditionsIonic strength: 0.125 / pH: 6.75 / Pressure: ambient / Temperature: 290 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
AnalysisCCPNchemical shift assignment
AnalysisCCPNdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 858 / NOE intraresidue total count: 2 / NOE long range total count: 277 / NOE medium range total count: 132 / NOE sequential total count: 371
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.43 Å

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