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- PDB-2jrs: Solution NMR Structure of CAPER RRM2 Domain. Northeast Structural... -

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Basic information

Entry
Database: PDB / ID: 2jrs
TitleSolution NMR Structure of CAPER RRM2 Domain. Northeast Structural Genomics Target HR4730A
ComponentsRNA-binding protein 39
KeywordsRNA BINDING PROTEIN / RNA Binding Motif of RBM39_HUMAN (CAPER) / RRM2 Domain / Solution NMR Structure / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


RS domain binding / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / centriolar satellite / RNA processing / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / microtubule cytoskeleton / nuclear speck ...RS domain binding / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / centriolar satellite / RNA processing / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / microtubule cytoskeleton / nuclear speck / protein-containing complex / RNA binding / nucleoplasm
Similarity search - Function
Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-binding protein 39
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsRossi, P. / Zhao, L. / Nwosu, C. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. ...Rossi, P. / Zhao, L. / Nwosu, C. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of CAPER RRM2 Domain.
Authors: Rossi, P. / Xiao, R. / Acton, T.B. / Montelione, G.T.
History
DepositionJun 28, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein 39


Theoretical massNumber of molelcules
Total (without water)12,0621
Polymers12,0621
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA-binding protein 39 / RNA-binding motif protein 39 / RNA-binding region-containing protein 2 / Hepatocellular carcinoma ...RNA-binding motif protein 39 / RNA-binding region-containing protein 2 / Hepatocellular carcinoma protein 1 / Splicing factor HCC1


Mass: 12061.732 Da / Num. of mol.: 1 / Fragment: RRM2 Domain: Residues 235-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM39, HCC1, RNPC2 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q14498

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: RBM39_HUMAN (CAPER), RRM2 residue 235-331. Solution NMR Structure
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1312D 1H-13C HSQC
1412D 1H-15N HSQC
1522D 1H-13C HSQC stereospecific methyl
162HETnoe
1713D HN(CA)CB
1813D HN(COCA)CB
1913D HNCO
11013D HBHA(CO)NH
11113D (H)CCH-TOCSY
11213D (H)CCH-COSY
11313D CCH-TOCSY
NMR detailsText: STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS MADE WITH ITERATIVE METHOD USING CHEMICAL SHIFTS (TALOS) FOR DIHEDRAL ANGLE INFERENCE, AND DYANA FOR SIMULATED ...Text: STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS MADE WITH ITERATIVE METHOD USING CHEMICAL SHIFTS (TALOS) FOR DIHEDRAL ANGLE INFERENCE, AND DYANA FOR SIMULATED ANNEALING MD LOWEST TARGET FUNCTION SELECTED. CONVERGED STRUCTURES ARE FURTHER REFINED USING NIH-XPLOR FOLLOWED BY CNS IN EXPLICIT WATER SHELL (NIELGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (EXCLUDING N-TERM TAG): BACKBONE 99.19%, SIDECHAIN 94.31%, AROMATIC (SC) 100%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1252 NOE, 44 H-BOND, 84 DIHEDRAL. 100 STRUCTURES CALCULATED 20 LOWEST ENERGY SUBMITTED. MAX NOE VIOLATION 0.30 A (1 MODEL), MAX DIHEDRAL VIOLATION 4.0 DEG. 5 CLOSE CONTACTS TOTAL PER 20 MODELS. STRUCTURE QUALITY FACTOR PSVS 1.3: ORDERED RESIDUES RANGES - ALPHA HELIX (40-47, 78-88), B-STRAND (53-61, 66-75, 27-32, 99-101) [S(PHI)+S(PSI)] > 1.8. RMSD 0.4 BB, 1.0 ALL HEAVY ATOMS. RAMACHANDRAN: 85.4% MOST FAV, 12.4% ADDTL ALLOW, 2.3 GENEROUSLY ALLOW, 0.0% DISALLOW. PROCHECK (PSI-PHI): -0.46/-1.49 (RAW/Z), PROCHECK (ALL): -0.24/-1.42 (RAW/Z), MOLPROBITY CLASH: 15.06/-1.06 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.959, PRECISION: 0.935, F-MEASURE: 0.947, DP-SCORE: 0.775.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3 mM [U-100% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
21.1 mM [U-5% 13C; U-100% 15N] protein, 0.02 % sodium azide, 20 mM MES, 100 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMHR4730A[U-100% 13C; U-100% 15N]1
0.02 %sodium azide1
20 mMMES1
100 mMsodium chloride1
5 mMCalcium Chloride1
10 mMDTT1
1.1 mMHR4730A[U-5% 13C; U-100% 15N]2
0.02 %sodium azide2
20 mMMES2
100 mMsodium chloride2
5 mMCalcium Chloride2
10 mMDTT2
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructure2.1.1Huang, Tejero, Powers and Montelionestructure solution
NMRPipe2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky2.112Goddarddata analysis
TopSpin1.3Bruker Biospincollection
CNSSOLVE1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorerefinement
DYANAGuntert, Mumenthaler and Wuthrichstructure solution
PSVS1.3Bhattacharya and Montelionevalidation
PdbStat5(PDBStat) Tejerodata analysis
MOLMOL2K.2Koradi, Billeter and Wuthrichvisualization
MolProbityRichardsonvalidation
ProcheckNMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thvalidation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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