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- PDB-7evs: Crystal structure of hnRNP LL RRM2 in complex with SETD2 -

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Basic information

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


mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis / regulation of mRNA export from nucleus ...mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis / regulation of mRNA export from nucleus / pericardium development / stem cell development / nucleosome organization / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / response to type I interferon / positive regulation of ossification / embryonic cranial skeleton morphogenesis / response to alkaloid / regulation of protein localization to chromatin / response to metal ion / histone H3 methyltransferase activity / regulation of double-strand break repair via homologous recombination / endodermal cell differentiation / regulation of RNA splicing / alpha-tubulin binding / positive regulation of interferon-alpha production / mismatch repair / positive regulation of autophagy / forebrain development / Transferases; Transferring one-carbon groups; Methyltransferases / positive regulation of RNA splicing / regulation of cytokinesis / neural tube closure / transcription elongation by RNA polymerase II / stem cell differentiation / response to organic cyclic compound / mRNA processing / PKMTs methylate histone lysines / chromosome / regulation of gene expression / angiogenesis / defense response to virus / mRNA binding / regulation of DNA-templated transcription / RNA binding / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm
Similarity search - Function
hnRPLL, RNA recognition motif 3 / hnRPLL, RNA recognition motif 1 / hnRPLL, RNA recognition motif 2 / hnRPLL, RNA recognition motif 4 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / Histone-lysine N-methyltransferase SETD2, animal / RRM-like domain / Set2 Rpb1 interacting domain / Set2 Rpb1 interacting domain superfamily ...hnRPLL, RNA recognition motif 3 / hnRPLL, RNA recognition motif 1 / hnRPLL, RNA recognition motif 2 / hnRPLL, RNA recognition motif 4 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / Histone-lysine N-methyltransferase SETD2, animal / RRM-like domain / Set2 Rpb1 interacting domain / Set2 Rpb1 interacting domain superfamily / SRI (Set2 Rpb1 interacting) domain / SETD2/Set2, SET domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / TFIIS/LEDGF domain superfamily / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / SET domain superfamily / WW domain / SET domain / 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-like / Histone-lysine N-methyltransferase SETD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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-like
B: Heterogeneous nuclear ribonucleoprotein L-like
C: SHI domain from Histone-lysine N-methyltransferase SETD2
D: SHI domain from Histone-lysine N-methyltransferase SETD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0566
Polymers27,8644
Non-polymers1922
Water6,341352
1
A: Heterogeneous nuclear ribonucleoprotein L-like
C: SHI domain from Histone-lysine N-methyltransferase SETD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0283
Polymers13,9322
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-6 kcal/mol
Surface area6140 Å2
MethodPISA
2
B: Heterogeneous nuclear ribonucleoprotein L-like
D: SHI domain from Histone-lysine N-methyltransferase SETD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0283
Polymers13,9322
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-18 kcal/mol
Surface area6270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.676, 41.685, 42.636
Angle α, β, γ (deg.)85.020, 89.570, 71.120
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein L-like / hnRNPLL / Stromal RNA-regulating factor


Mass: 12623.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPLL, HNRPLL, SRRF, BLOCK24 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WVV9
#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: 1308.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BYW2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.3M Ammonium Sulfate, 20% PEG 4000

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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: Jan 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 34584 / % possible obs: 96.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.62 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.04 / Rrim(I) all: 0.075 / Χ2: 0.964 / Net I/σ(I): 7.9 / Num. measured all: 118064
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.633.30.31416640.9080.1990.3730.83194.3
1.63-1.663.40.30917100.9120.1930.3660.83294.1
1.66-1.693.40.27416930.9150.1710.3240.86395.5
1.69-1.723.40.23717300.9350.1490.280.88995.5
1.72-1.763.40.20316780.9580.1290.2420.88395.8
1.76-1.83.40.1817510.9710.1140.2140.92395.8
1.8-1.853.20.17216880.9680.1140.2071.03295.6
1.85-1.93.30.14417490.9780.0910.1711.06696.1
1.9-1.953.40.1417160.9740.0880.1661.13596.5
1.95-2.023.60.11517080.9820.0720.1361.08995.7
2.02-2.093.50.10617400.9820.0670.1261.17996.5
2.09-2.173.50.117050.980.0620.1181.22796.9
2.17-2.273.40.08617380.9870.0550.1031.20197.3
2.27-2.393.30.08317610.9860.0520.0991.17897.5
2.39-2.543.40.07417430.990.0460.0881.13997.6
2.54-2.743.60.06917620.9910.0420.0810.99197.9
2.74-3.013.50.0617740.9920.0370.070.92598.3
3.01-3.453.30.05217530.9940.0330.0610.77398.4
3.45-4.343.50.04417580.9950.0270.0520.61198.4
4.34-403.50.04317630.9950.0270.0510.5398.1

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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: 7EVR

7evr


Resolution: 1.6→30.21 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2036 1732 5.06 %
Rwork0.1776 32498 -
obs0.1789 34230 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.86 Å2 / Biso mean: 18.2087 Å2 / Biso min: 5.97 Å2
Refinement stepCycle: final / Resolution: 1.6→30.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 10 352 2083
Biso mean--37.01 28.1 -
Num. residues----227
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.650.26121630.23252483264690
1.65-1.70.22911690.20792612278194
1.7-1.760.21521440.18962675281995
1.76-1.830.21521320.192724285695
1.83-1.910.24611240.18652719284396
1.91-2.020.23461390.18732707284696
2.02-2.140.17671750.17732706288197
2.14-2.310.21521190.17782787290697
2.31-2.540.19081400.18042736287698
2.54-2.910.21821570.17642749290698
2.91-3.660.16161430.16542801294499
3.66-30.210.2081270.16462799292698

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