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- PDB-2jnb: Solution Structure of RNA-binding protein 15.5K -

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Basic information

Entry
Database: PDB / ID: 2jnb
TitleSolution Structure of RNA-binding protein 15.5K
ComponentsNHP2-like protein 1
KeywordsRNA BINDING PROTEIN / splicing / kink-turn RNA-binding protein / nhpx
Function / homology
Function and homology information


U4atac snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component / box C/D methylation guide snoRNP complex / U4 snRNA binding / U2-type precatalytic spliceosome / U3 snoRNA binding / rRNA modification in the nucleus and cytosol / precatalytic spliceosome ...U4atac snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component / box C/D methylation guide snoRNP complex / U4 snRNA binding / U2-type precatalytic spliceosome / U3 snoRNA binding / rRNA modification in the nucleus and cytosol / precatalytic spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / ATPase binding / ribosomal small subunit biogenesis / nucleolus / protein-containing complex / RNA binding / nucleoplasm / nucleus
Similarity search - Function
H/ACA ribonucleoprotein complex, subunit Nhp2-like / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like ...H/ACA ribonucleoprotein complex, subunit Nhp2-like / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSoss, S.E. / Flynn, P.F.
CitationJournal: Biochemistry / Year: 2007
Title: Functional Implications for a Prototypical K-Turn Binding Protein from Structural and Dynamical Studies of 15.5K
Authors: Soss, S.E. / Flynn, P.F.
History
DepositionJan 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NHP2-like protein 1


Theoretical massNumber of molelcules
Total (without water)16,0261
Polymers16,0261
Non-polymers00
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein NHP2-like protein 1 / High mobility group-like nuclear protein 2 homolog 1 / U4/U6.U5 tri-snRNP 15.5 kDa protein / OTK27 / hSNU13


Mass: 16025.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHP2L1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P55769

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1223D CBCA(CO)NH
1323D HNCO
1423D HNCA
1523D HN(CA)CB
1623D HN(CO)CA
2712D 1H-13C HSQC
2813D C(CO)NH
2913D HBHA(CO)NH
21013D (H)CCH-TOCSY
21113D (H)CCH-COSY
21213D 1H-15N NOESY
21313D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.1 % sodium azide, 100 mM sodium chloride, 100 mM sodium phosphate, 1.6 mM protein, 90% H2O, 10% D2O90% H2O/10% D2O
20.1 % sodium azide, 200 mM sodium chloride, 50 mM sodium phosphate, 0.9 mM [U-98% 13C, U-98% 15N] protein, 90% H2O, 10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 %sodium azide1
100 mMsodium chloride1
100 mMsodium phosphate1
1.6 mMentity1
0.1 %sodium azide2
200 mMsodium chloride2
50 mMsodium phosphate2
.9 mMentity[U-98% 13C; U-98% 15N]2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
12506ambient 293 K
22006ambient 293 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 INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
Felix97Accelrys Software Inc.processing
Sparky3.111Goddardchemical shift assignment
Sparky3.111Goddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
ProcheckNMRLaskowski and MacArthurdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1090 / NOE long range total count: 229 / NOE medium range total count: 148 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 100 / Protein psi angle constraints total count: 100
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.35 Å / Maximum upper distance constraint violation: 0.25 Å

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