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- PDB-7evr: Crystal structure of hnRNP L RRM2 in complex with SETD2 -

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Basic information

Entry
Database: PDB / ID: 7evr
TitleCrystal structure of hnRNP L RRM2 in complex with SETD2
Components
  • Heterogeneous nuclear ribonucleoprotein L
  • SHI domain from Histone-lysine N-methyltransferase SETD2
KeywordsRNA BINDING PROTEIN / complex
Function / homology
Function and homology information


mesoderm morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / coronary vasculature morphogenesis / cell migration involved in vasculogenesis / ribonucleoprotein granule / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / embryonic placenta morphogenesis / histone H3K36 trimethyltransferase activity ...mesoderm morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / coronary vasculature morphogenesis / cell migration involved in vasculogenesis / ribonucleoprotein granule / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / embryonic placenta morphogenesis / histone H3K36 trimethyltransferase activity / pericardium development / regulation of mRNA export from nucleus / stem cell development / histone H3K36 methyltransferase activity / nucleosome organization / response to type I interferon / protein-lysine N-methyltransferase activity / embryonic cranial skeleton morphogenesis / positive regulation of ossification / response to alkaloid / regulation of protein localization to chromatin / response to metal ion / histone H3 methyltransferase activity / regulation of alternative mRNA splicing, via spliceosome / regulation of double-strand break repair via homologous recombination / endodermal cell differentiation / regulation of RNA splicing / positive regulation of interferon-alpha production / Processing of Capped Intron-Containing Pre-mRNA / alpha-tubulin binding / pre-mRNA intronic binding / mismatch repair / RNA processing / forebrain development / positive regulation of autophagy / mRNA Splicing - Major Pathway / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of cytokinesis / stem cell differentiation / neural tube closure / transcription elongation by RNA polymerase II / : / PKMTs methylate histone lysines / mRNA processing / chromosome / regulation of gene expression / angiogenesis / defense response to virus / transcription cis-regulatory region binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / mRNA binding / regulation of DNA-templated transcription / chromatin / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / cytoplasm
Similarity search - Function
hnRNP-L, RNA recognition motif 3 / hnRNP-L, RNA recognition motif 4 / hnRNP-L, RNA recognition motif 1 / hnRNP-L, RNA recognition motif 2 / : / RRM domain / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / Histone-lysine N-methyltransferase SETD2, animal ...hnRNP-L, RNA recognition motif 3 / hnRNP-L, RNA recognition motif 4 / hnRNP-L, RNA recognition motif 1 / hnRNP-L, RNA recognition motif 2 / : / RRM domain / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / TFIIS/LEDGF domain superfamily / Post-SET domain / Post-SET domain profile. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW domain / SET domain / SET domain superfamily / SET domain profile. / SET 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
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoprotein L / Histone-lysine N-methyltransferase SETD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, F.D. / Wang, S.M.
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of the interaction between SETD2 methyltransferase and hnRNP L paralogs for governing co-transcriptional splicing.
Authors: Bhattacharya, S. / Wang, S. / Reddy, D. / Shen, S. / Zhang, Y. / Zhang, N. / Li, H. / Washburn, M.P. / Florens, L. / Shi, Y. / Workman, J.L. / Li, F.
History
DepositionMay 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein L
B: SHI domain from Histone-lysine N-methyltransferase SETD2
C: Heterogeneous nuclear ribonucleoprotein L
D: SHI domain from Histone-lysine N-methyltransferase SETD2


Theoretical massNumber of molelcules
Total (without water)30,8294
Polymers30,8294
Non-polymers00
Water5,981332
1
A: Heterogeneous nuclear ribonucleoprotein L
B: SHI domain from Histone-lysine N-methyltransferase SETD2


Theoretical massNumber of molelcules
Total (without water)15,4142
Polymers15,4142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-8 kcal/mol
Surface area6820 Å2
MethodPISA
2
C: Heterogeneous nuclear ribonucleoprotein L
D: SHI domain from Histone-lysine N-methyltransferase SETD2


Theoretical massNumber of molelcules
Total (without water)15,4142
Polymers15,4142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-8 kcal/mol
Surface area6720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.776, 38.789, 68.982
Angle α, β, γ (deg.)90.000, 100.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein L / hnRNP L


Mass: 12626.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPL, HNRPL, P/OKcl.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P14866
#2: Protein/peptide SHI domain from Histone-lysine N-methyltransferase SETD2 / HIF-1 / Huntingtin yeast partner B / Huntingtin-interacting protein 1 / HIP-1 / Huntingtin- ...HIF-1 / Huntingtin yeast partner B / Huntingtin-interacting protein 1 / HIP-1 / Huntingtin-interacting protein B / Lysine N-methyltransferase 3A / Protein-lysine N-methyltransferase SETD2 / SET domain-containing protein 2 / hSET2 / p231HBP


Mass: 2788.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9BYW2, [histone H3]-lysine36 N-trimethyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.8M Potassium/Sodium phosphate, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 27697 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 15.64 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.06 / Rrim(I) all: 0.141 / Χ2: 1.024 / Net I/σ(I): 4.6 / Num. measured all: 142925
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.834.90.46613540.9150.2180.5160.55998.1
1.83-1.865.10.45513530.90.2110.5030.54599.6
1.86-1.95.20.43113710.9110.20.4760.59399.9
1.9-1.945.20.37413940.9010.1750.4140.70999.7
1.94-1.985.20.31813350.9320.150.3530.678100
1.98-2.034.90.29714280.940.1450.3320.72999.9
2.03-2.084.90.26613470.9530.1280.2960.86699.9
2.08-2.135.40.22213810.9710.1020.2450.896100
2.13-2.25.40.20113750.9730.0920.2220.856100
2.2-2.275.30.21613780.9710.0990.2381.02599.9
2.27-2.355.20.17613660.9810.0820.1950.96100
2.35-2.4450.16413880.9740.080.1830.992100
2.44-2.5550.15114000.980.0720.1681.084100
2.55-2.695.40.14613560.9810.0660.161.09899.9
2.69-2.865.40.1314010.9830.060.1441.15100
2.86-3.085.30.11213850.9890.0520.1241.259100
3.08-3.3950.09613900.9890.0460.1071.54599.9
3.39-3.885.40.08314290.9940.0380.0921.67199.9
3.88-4.8850.07214010.9920.0350.0811.662100
4.88-405.10.07314650.9930.0350.0811.47199.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZZY

3zzy


Resolution: 1.8→39.78 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 1373 4.96 %
Rwork0.1582 26308 -
obs0.1602 27681 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.19 Å2 / Biso mean: 19.619 Å2 / Biso min: 7.65 Å2
Refinement stepCycle: final / Resolution: 1.8→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 0 332 2276
Biso mean---30.49 -
Num. residues----251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.860.25541320.22272534266697
1.86-1.940.24521510.190126162767100
1.94-2.030.25491230.168726392762100
2.03-2.130.18831300.160126032733100
2.13-2.270.23371470.151526162763100
2.27-2.440.18021410.154526112752100
2.44-2.690.2141320.165426272759100
2.69-3.080.19781490.161626422791100
3.08-3.880.16671300.141926942824100
3.88-39.780.17651380.148427262864100

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