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- PDB-9ngx: Structure of the 5'SL-bound La Domain of the Human La-related Pro... -

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Basic information

Entry
Database: PDB / ID: 9ngx
TitleStructure of the 5'SL-bound La Domain of the Human La-related Protein 6
ComponentsLa-related protein 6
KeywordsRNA BINDING PROTEIN / La / La-related protein / LARP / LARP6 / Collagen synthesis / Fibrosis
Function / homology
Function and homology information


sequence-specific mRNA binding / myosin binding / positive regulation of collagen biosynthetic process / RNA processing / mRNA 5'-UTR binding / RNA stem-loop binding / regulation of translation / ribonucleoprotein complex / mRNA binding / nucleus / cytoplasm
Similarity search - Function
La-related protein 6, RNA recognition motif / SUZ-C motif / SUZ-C domain / SUZ-C domain profile. / Lupus La protein / 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. ...La-related protein 6, RNA recognition motif / SUZ-C motif / SUZ-C domain / SUZ-C domain profile. / Lupus La protein / 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-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 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics / molecular dynamics
AuthorsGordon, B.H. / Silvers, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142912 United States
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Noncanonical RNA binding of human La-related protein 6.
Authors: Gordon, B.H. / Ogunkunle, V.S. / Silvers, R.
History
DepositionFeb 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: La-related protein 6


Theoretical massNumber of molelcules
Total (without water)12,6391
Polymers12,6391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400target function
RepresentativeModel #1target function

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Components

#1: Protein La-related protein 6 / Acheron / Achn / La ribonucleoprotein domain family member 6


Mass: 12639.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LARP6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BRS8
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCA
131isotropic13D HN(CA)CB
141isotropic13D HNCO
151isotropic13D HN(CA)CO
181isotropic13D H(CC)(CO)NH
171isotropic13D (H)CC(CO)NH
161isotropic13D (H)CCH-COSY
192isotropic12D 1H-13C HSQC
1112isotropic13D (H)CCH-TOCSY
1102isotropic13D (H)CCH-TOCSY
1123isotropic12D 1H-15N HSQC
1134isotropic13D 1H-15N NOESY
1144isotropic13D 1H-13C NOESY
1155isotropic12D 1H-13C HSQC aliphatic
1185isotropic12D 1H-13C HSQC aromatic
1175isotropic13D 1H-13C NOESY aliphatic
1165isotropic13D 1H-13C NOESY aromatic
1196isotropic12D 1H-13C HSQC aliphatic
1206isotropic12D 1H-13C HSQC aromatic
1216isotropic13D 1H-13C NOESY aliphatic
1226isotropic13D 1H-13C NOESY aromatic
1237isotropic12D 1H-15N HSQC
1247isotropic12D 1H-13C HSQC
1268isotropic12D 1H-13C CTHSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.7 mM [U-98% 13C; U-98% 15N] LARP6(79-183), 1.7 mM A2M5, 10 mM MES, 50 mM potassium chloride, 0.01 mg/mL DSS, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution2370 uM [U-98% 13C; U-98% 15N] LARP6(79-183), 370 uM A2M5, 10 mM MES, 50 mM potassium chloride, 0.01 mg/mL DSS, 100% D2Osample_2100% D2O
solution3300 uM [U-98% 15N] LARP6(79-183), 300 uM A2M5, 10 mM MES, 50 mM potassium chloride, 0.01 mg/mL DSS, 90% H2O/10% D2Osample_390% H2O/10% D2O
solution41.1 mM [U-98% 13C; U-98% 15N] LARP6(79-183), 1.1 mM A2M5, 10 mM MES, 50 mM potassium chloride, 0.01 mg/mL DSS, 90% H2O/10% D2Osample_490% H2O/10% D2O
solution51.6 mM [U-98% 15N; 1,3-13C-glycerol] LARP6(79-183), 1.6 mM A2M5, 10 mM MES, 50 mM potassium chloride, 0.01 mg/mL DSS, 100% D2Osample_5100% D2O
solution61.3 mM [U-98% 15N; 2-13C-glycerol] LARP6(79-183), 1.3 mM A2M5, 10 mM MES, 50 mM potassium chloride, 0.01 mg/mL DSS, 100% D2Osample_6100% D2O
solution71.9 mM [13C, 15N]-Arg LARP6(79-183), 1.9 mM A2M5, 10 mM MES, 50 mM potassium chloride, 0.01 mg/mL DSS, 90% H2O/10% D2Osample_790% H2O/10% D2O
solution81 mM [13C]-Pro LARP6(79-183), 1 mM A2M5, 10 mM MES, 50 mM potassium chloride, 0.01 mg/mL DSS, 90% H2O/10% D2Osample_890% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.7 mMLARP6(79-183)[U-98% 13C; U-98% 15N]1
1.7 mMA2M5natural abundance1
10 mMMESnatural abundance1
50 mMpotassium chloridenatural abundance1
0.01 mg/mLDSSnatural abundance1
370 uMLARP6(79-183)[U-98% 13C; U-98% 15N]2
370 uMA2M5natural abundance2
10 mMMESnatural abundance2
50 mMpotassium chloridenatural abundance2
0.01 mg/mLDSSnatural abundance2
300 uMLARP6(79-183)[U-98% 15N]3
300 uMA2M5natural abundance3
10 mMMESnatural abundance3
50 mMpotassium chloridenatural abundance3
0.01 mg/mLDSSnatural abundance3
1.1 mMLARP6(79-183)[U-98% 13C; U-98% 15N]4
1.1 mMA2M5natural abundance4
10 mMMESnatural abundance4
50 mMpotassium chloridenatural abundance4
0.01 mg/mLDSSnatural abundance4
1.6 mMLARP6(79-183)[U-98% 15N; 1,3-13C-glycerol]5
1.6 mMA2M5natural abundance5
10 mMMESnatural abundance5
50 mMpotassium chloridenatural abundance5
0.01 mg/mLDSSnatural abundance5
1.3 mMLARP6(79-183)[U-98% 15N; 2-13C-glycerol]6
1.3 mMA2M5natural abundance6
10 mMMESnatural abundance6
50 mMpotassium chloridenatural abundance6
0.01 mg/mLDSSnatural abundance6
1.9 mMLARP6(79-183)[13C, 15N]-Arg7
1.9 mMA2M5natural abundance7
10 mMMESnatural abundance7
50 mMpotassium chloridenatural abundance7
0.01 mg/mLDSSnatural abundance7
1 mMLARP6(79-183)[13C]-Pro8
1 mMA2M5natural abundance8
10 mMMESnatural abundance8
50 mMpotassium chloridenatural abundance8
0.01 mg/mLDSSnatural abundance8
Sample conditionsIonic strength: 50 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.6.5Bruker Biospincollection
TopSpin4.3.0Bruker Biospinprocessing
NMRFAM-SPARKYNational Magnetic Resonance Facility at Madisonchemical shift assignment
NMRFAM-SPARKYNational Magnetic Resonance Facility at Madisonpeak picking
ARTINAKlukowski, P., Riek, R. and Guntert, P.peak picking
TALOS-N4.12Y. Shen and A. Baxgeometry optimization
CYANA3.98.15Guntert, Mumenthaler and Wuthrichstructure calculation
Amber22Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
Refinement
MethodSoftware ordinalDetails
torsion angle dynamics6simulated annealing
molecular dynamics7
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

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