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- PDB-6dg1: NMR structure of the second qRRM2 domain of human hnRNP H -

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Basic information

Entry
Database: PDB / ID: 6dg1
TitleNMR structure of the second qRRM2 domain of human hnRNP H
ComponentsqRRM2 domain of Heterogeneous nuclear ribonucleoprotein H2
KeywordsRNA BINDING PROTEIN / hnRNP H / Heterogeneous nuclear ribonucleoprotein H / HqRRM2 / qRRM2
Function / homology
Function and homology information


regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / postsynaptic density / ribonucleoprotein complex / RNA binding / nucleoplasm / membrane / 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 ...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 H2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSrinivasa, R.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM101979 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103622 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Differential Conformational Dynamics Encoded by the Inter-qRRM linker of hnRNP H.
Authors: Penumutchu, S. / Chiu, L.Y. / Meagher, J.L. / Hansen, A.L. / Stuckey, J.A. / Tolbert, B.S.
History
DepositionMay 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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:
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Assembly

Deposited unit
A: qRRM2 domain of Heterogeneous nuclear ribonucleoprotein H2


Theoretical massNumber of molelcules
Total (without water)11,7911
Polymers11,7911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5780 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 800structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein qRRM2 domain of Heterogeneous nuclear ribonucleoprotein H2 / hnRNP H2 / FTP-3 / Heterogeneous nuclear ribonucleoprotein H' / hnRNP H'


Mass: 11791.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPH2, FTP3, HNRPH2 / Production host: Escherichia coli (E. coli) / References: UniProt: P55795

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11H-15N HSQC
121isotropic1HNCA
131isotropic1HN(CO)CA
141isotropic1HN(CA)CB
151isotropic1CBCA(CO)NH
161isotropic1HNCO
171isotropic1HN(CA)CO
181isotropic1HBHA(CO)NH
191isotropic1(H)CCCH-TOCSY
1101isotropic1H(C)CCH-TOCSY
1111isotropic23D NOESY-(13C-1H)-HSQC
1121isotropic23D NOESY-(15N-1H)-HSQC

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Sample preparation

DetailsType: solution
Contents: 1.5 mM C13_N15 qRRM2 domain of hnRNP H, 90% H2O/10% D2O
Details: 20mM sodium phosphate, 20 mM NaCl, 4mM TCEP and 10 % D2O at pH 6.2
Label: [U-100% 13C; U-100% 15N] / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 mM / Component: qRRM2 domain of hnRNP H / Isotopic labeling: C13_N15
Sample conditionsIonic strength: 40 mM / Label: conditions_1 / pH: 6.2 / Pressure: 760 mmHg / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 800 / Conformers submitted total number: 10

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