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- PDB-6d12: Crystal structure of C-terminal xRRM domain of human Larp7 bound ... -

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Basic information

Entry
Database: PDB / ID: 6d12
TitleCrystal structure of C-terminal xRRM domain of human Larp7 bound to 7SK stem-loop 4 RNA
Components
  • La-related protein 7
  • human 7SK RNA stem-loop 4
KeywordsRNA BINDING PROTEIN/RNA / RNA RECOGNITION MOTIF / RRM / RNA APICAL LOOP / RNA BINDING PROTEIN-RNA complex
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
RNA / RNA (> 10) / La-related protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.205 Å
Model details7SK protein in complex with RNA
AuthorsEichhorn, C.D. / Cascio, D. / Sawaya, M.R. / Feigon, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM107567 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis for recognition of human 7SK long noncoding RNA by the La-related protein Larp7.
Authors: Eichhorn, C.D. / Yang, Y. / Repeta, L. / Feigon, J.
History
DepositionApr 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: La-related protein 7
B: La-related protein 7
C: human 7SK RNA stem-loop 4


Theoretical massNumber of molelcules
Total (without water)38,3103
Polymers38,3103
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, native gel electrophoresis showed a reduced mobility that saturated at a ratio of 2:1 showing that 2 proteins bind 1 RNA molecule, light scattering, Dynamic ...Evidence: native gel electrophoresis, native gel electrophoresis showed a reduced mobility that saturated at a ratio of 2:1 showing that 2 proteins bind 1 RNA molecule, light scattering, Dynamic light scattering experiments indicated that the RNA-protein complex was the correct molecular weight, indicating that the complex formed a homogeneous sample and did not aggregate.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-17 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.910, 34.030, 95.010
Angle α, β, γ (deg.)90.000, 95.180, 90.000
Int Tables number4
Space group name H-MP1211

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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: 13006.630 Da / Num. of mol.: 2 / Fragment: RNA binding domain / Mutation: L475M, E501L, Q504L, L521M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LARP7, HDCMA18P / Plasmid: pETXa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4G0J3
#2: RNA chain human 7SK RNA stem-loop 4


Mass: 12296.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.16 % / Description: rods approx 20x20x50 um
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: 0.05M Na Cacodylate,0.08M Mg acetate, 24% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→94.622 Å / Num. obs: 15929 / % possible obs: 99.9 % / Redundancy: 7.547 % / Biso Wilson estimate: 35.16 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.169 / Rrim(I) all: 0.181 / Χ2: 0.82 / Net I/σ(I): 6.54 / Num. measured all: 120222 / Scaling rejects: 65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.267.481.1911.438879118811870.721.27999.9
2.26-2.327.3141.0781.598038110310990.7621.15999.6
2.32-2.397.910.8362.048804111211130.8970.895100
2.39-2.467.9120.7262.368585108610850.8870.77799.9
2.46-2.547.760.6522.637985102910290.9150.698100
2.54-2.637.6380.4893.317806102210220.9410.525100
2.63-2.737.4470.4413.5869939399390.9450.474100
2.73-2.847.2990.3064.7571249789760.9720.32999.8
2.84-2.977.8990.2635.7269358778780.9850.281100
2.97-3.117.8220.2047.0167588658640.9870.21899.9
3.11-3.287.6680.1828.3163268258250.9910.195100
3.28-3.487.2650.1529.7156817847820.9910.16499.7
3.48-3.727.1190.14710.9952187337330.9890.159100
3.72-4.017.8450.14612.753666866840.9930.15699.7
4.01-4.47.6890.13413.9648676346330.990.14599.8
4.4-4.927.360.1214.342915845830.9930.12999.8
4.92-5.686.8350.10913.5834865105100.9940.118100
5.68-6.957.5180.12314.5733084414400.9950.13299.8
6.95-9.837.0740.10216.0924053453400.990.11198.6
9.83-94.6226.6040.09117.2713672082070.9980.09899.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALE20170615data scaling
PDB_EXTRACT3.24data extraction
XDS20170615data reduction
HKL2Map2016/1phasing
RefinementMethod to determine structure: MAD / Resolution: 2.205→94.622 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.23
RfactorNum. reflection% reflection
Rfree0.2673 719 5.03 %
Rwork0.2279 --
obs0.2299 14297 90.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.02 Å2 / Biso mean: 61.2933 Å2 / Biso min: 15.67 Å2
Refinement stepCycle: final / Resolution: 2.205→94.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 816 0 46 2421
Biso mean---36.21 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082501
X-RAY DIFFRACTIONf_angle_d0.9993580
X-RAY DIFFRACTIONf_chiral_restr0.056440
X-RAY DIFFRACTIONf_plane_restr0.007313
X-RAY DIFFRACTIONf_dihedral_angle_d19.5521030
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.205-2.37520.3614790.27191559163853
2.3752-2.61430.3541590.292929573116100
2.6143-2.99260.33281580.275929813139100
2.9926-3.77040.26671530.216630063159100
3.7704-94.70890.21741700.196230753245100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8531-0.484-0.34832.96360.21944.2613-0.08-0.29960.40370.4486-0.0502-0.2972-0.55-0.02180.12570.3943-0.0096-0.07290.1926-0.02830.24112.7692.624819.2354
23.08390.2421-1.16554.39210.82712.55870.02370.14-0.0894-0.2574-0.0771-0.09830.1437-0.12740.05450.2018-0.0038-0.09420.1944-0.01730.20753.5366-2.221589.0625
3-1.5386-0.188-1.9751-0.46841.65733.45610.06940.14740.4445-1.04960.2099-1.1162-0.3938-1.3369-0.14711.65830.21370.24811.3327-0.24670.41014.95840.168554.1811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 446 through 545)A446 - 545
2X-RAY DIFFRACTION2(chain 'B' and resid 446 through 548)B446 - 548
3X-RAY DIFFRACTION3(chain 'C' and resid 303 through 340)C303 - 340

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