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- PDB-2lxu: Solution NMR Structure of the eukaryotic RNA recognition motif, R... -

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Basic information

Entry
Database: PDB / ID: 2lxu
TitleSolution NMR Structure of the eukaryotic RNA recognition motif, RRM1, from the heterogeneous nuclear ribonucleoprotein H from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8614A
ComponentsHeterogeneous nuclear ribonucleoprotein H
KeywordsRNA BINDING PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


poly(U) RNA binding / FGFR2 alternative splicing / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding ...poly(U) RNA binding / FGFR2 alternative splicing / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol
Similarity search - Function
Zinc finger, CHHC-type / RNPHF zinc finger / 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 ...Zinc finger, CHHC-type / RNPHF zinc finger / 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
Heterogeneous nuclear ribonucleoprotein H
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsRamelot, T.A. / Yang, Y. / Pederson, K. / Shastry, R. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Prestegard, J.H. ...Ramelot, T.A. / Yang, Y. / Pederson, K. / Shastry, R. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of the eukaryotic RNA recognition motif, RRM1, from the heterogeneous nuclear ribonucleoprotein H from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8614A
Authors: Ramelot, T.A. / Yang, Y. / Pederson, K. / Shastry, R. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Kennedy, M.A.
History
DepositionAug 31, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein H


Theoretical massNumber of molelcules
Total (without water)12,1691
Polymers12,1691
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein H / hnRNP H / Heterogeneous nuclear ribonucleoprotein H / N-terminally processed


Mass: 12168.548 Da / Num. of mol.: 1 / Fragment: UNP residues 7-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPH1, HNRPH, HNRPH1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: P31943

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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-13C HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-15N NOESY
1913D C(CO)NH
11013D HBHA(CO)NH
11113D (H)CCH-TOCSY
11233D (H)CCH-TOCSY
11333D NUS 1H-13C NOESY aliphatic
11412D 1H-15N HSQC NH2 only
11534D 13C-13C-HMQC-NOESY-HMQC
11611D T1 Nhsqc array
11711D T2 Nhsqc array
11822D 1H-15N HSQC
11922D 1H-13C HSQC aliphatic
12012D 1H-13C HSQC arom CT
12112D 1H-13C HSQC arom noCT
12222D 1H-15N HSQC His
12322D 1H-15N heteronuclear NOE interleaved

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] HR8614A.007, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [biosynthetically directed-5% 13C; U-100% 15N] HR8614A.008, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] HR8614A.007, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMHR8614A.007-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
50 uMDSS-61
0.8 mMHR8614A.008-7[biosynthetically directed-5% 13C; U-100% 15N]2
20 mMMES-82
100 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
50 uMDSS-122
1.0 mMHR8614A.007-13[U-100% 13C; U-100% 15N]3
20 mMMES-143
100 mMsodium chloride-153
5 mMcalcium chloride-163
10 mMDTT-173
50 uMDSS-183
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNScns_solve_1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNScns_solve_1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNScns_solve_1.3Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructureASDP-1.0Huang, Tejero, Powers and Montelionedata analysis
AutoStructureASDP-1.0Huang, Tejero, Powers and Montelionerefinement
NMRPipeNMRPipe-201109Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin2.1.4 and 3.1Bruker Biospincollection
VnmrJ1.1 DVariancollection
PINEPINE Server v.2.0Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
Sparky3.113Goddarddata analysis
TALOS+1.2009.0721.18Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESpales_linux 2000PALES (Zweckstetter, Bax)geometry optimization
PSVS1.4Bhattacharya, Montelionestructure validation
FMCGUIfmcgui_2.5_linuxLemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagan, and Arrowsmithstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: REFINEMENT IN EXPLICIT WATER
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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