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- PDB-5knw: Solution NMR structure of human LARP7 xRRM2 -

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Basic information

Entry
Database: PDB / ID: 5knw
TitleSolution NMR structure of human LARP7 xRRM2
ComponentsLa-related protein 7
KeywordsRNA BINDING PROTEIN / xRRM / RRM / 7SK
Function / homology
Function and homology information


U6 2'-O-snRNA methylation / 7SK snRNP / positive regulation of snRNA transcription by RNA polymerase II / 7SK snRNA binding / box C/D sno(s)RNA 3'-end processing / positive regulation of protein localization to Cajal body / negative regulation of viral transcription / regulation of mRNA splicing, via spliceosome / negative regulation of transcription elongation by RNA polymerase II / U6 snRNA binding ...U6 2'-O-snRNA methylation / 7SK snRNP / positive regulation of snRNA transcription by RNA polymerase II / 7SK snRNA binding / box C/D sno(s)RNA 3'-end processing / positive regulation of protein localization to Cajal body / negative regulation of viral transcription / regulation of mRNA splicing, via spliceosome / negative regulation of transcription elongation by RNA polymerase II / U6 snRNA binding / RNA splicing / mRNA processing / spermatogenesis / cell differentiation / ribonucleoprotein complex / mRNA binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
LARP7, RNA recognition motif 1 / LARP7, RNA recognition motif 2 / La-related protein 7, La domain / RNA binding motif / Lupus La protein / xRRM domain profile. / La protein, xRRM domain / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function ...LARP7, RNA recognition motif 1 / LARP7, RNA recognition motif 2 / La-related protein 7, La domain / RNA binding motif / Lupus La protein / xRRM domain profile. / La protein, xRRM domain / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
La-related protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsEichhorn, C.D. / Feigon, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107567 United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: hLARP7 C-terminal domain contains an xRRM that binds the 3' hairpin of 7SK RNA.
Authors: Eichhorn, C.D. / Chug, R. / Feigon, J.
History
DepositionJun 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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 1.5May 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: La-related protein 7


Theoretical massNumber of molelcules
Total (without water)14,3951
Polymers14,3951
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10330 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein La-related protein 7 / La ribonucleoprotein domain family member 7 / P-TEFb-interaction protein for 7SK stability / PIP7S


Mass: 14395.445 Da / Num. of mol.: 1 / Fragment: residues 445-561
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LARP7, HDCMA18P
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q4G0J3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
1121isotropic12D 1H-15N HSQC
1111isotropic13D HNCA
121isotropic13D CBCA(CO)NH
1101isotropic13D CC(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D HBHA(CO)NH
151isotropic13d HN(CA)CO
161isotropic13D 1H-15N NOESY
1161isotropic12D 1H-13C HSQC
171isotropic13D 1H-13C NOESY aliphatic
1151isotropic13D 1H-13C NOESY aromatic
191isotropic13D (H)CCH-TOCSY
181isotropic13D (H)CCH-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-99% 13C; U-99% 15N] hLARP7 xRRM2, 0.8 mM [U-99% 15N] hLARP7 xRRM2, 90% H2O/10% D2O13C,15N_label_H2O90% H2O/10% D2O
solution20.8 mM [U-99% 13C; U-99% 15N] hLARP7 xRRM2, 100% D2O13C,15N_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMhLARP7 xRRM2-1[U-99% 13C; U-99% 15N]1
0.8 mMhLARP7 xRRM2-2[U-99% 15N]1
0.8 mMhLARP7 xRRM2[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 100 mM / Label: condition1 / pH: 6.1 / Pressure: 760 mmHg / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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