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- PDB-3to8: Crystal structure of the two C-terminal RRM domains of heterogene... -

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Basic information

Entry
Database: PDB / ID: 3to8
TitleCrystal structure of the two C-terminal RRM domains of heterogeneous nuclear ribonucleoprotein L (hnRNP L)
ComponentsHeterogeneous nuclear ribonucleoprotein L
KeywordsRNA BINDING PROTEIN / RNA recognition motifs / Splicing
Function / homology
Function and homology information


ribonucleoprotein granule / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / pre-mRNA intronic binding / mRNA Splicing - Major Pathway / mRNA processing / transcription cis-regulatory region binding / ribonucleoprotein complex ...ribonucleoprotein granule / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / pre-mRNA intronic binding / mRNA Splicing - Major Pathway / mRNA processing / transcription cis-regulatory region binding / ribonucleoprotein complex / mRNA binding / negative regulation of DNA-templated transcription / chromatin / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / 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 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RRM (RNA recognition motif) domain / RNA recognition motif ...hnRNP-L, RNA recognition motif 3 / hnRNP-L, RNA recognition motif 4 / hnRNP-L, RNA recognition motif 1 / hnRNP-L, RNA recognition motif 2 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RRM (RNA recognition motif) 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Heterogeneous nuclear ribonucleoprotein L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsZhang, W.J. / Zeng, F.X. / Liu, Y.W. / Zhao, Y. / Niu, L.W. / Teng, M.K. / Li, X.
CitationJournal: To be Published
Title: Crystal structure of the two C-terminal RRM domains of heterogeneous nuclear ribonucleoprotein L (hnRNP L)
Authors: Zhang, W.J. / Zeng, F.X. / Liu, Y.W. / Zhao, Y. / Niu, L.W. / Teng, M.K. / Li, X.
History
DepositionSep 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0005
Polymers24,6141
Non-polymers3864
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.569, 56.545, 88.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein L / hnRNP L


Mass: 24613.797 Da / Num. of mol.: 1 / Fragment: C-TERMINAL RRM DOMAIN, UNP residues 380-589
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPL, HNRPL, P/OKcl.14 / Plasmid: Modified PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P14866
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsLIGAND PEG IN THIS ENTRY IS A PART OF PENTAERYTHRITOL ETHOXYLATE WHICH WAS USED IN CRYSTALLIZATION.

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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: 1.86 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% v/v Pentaerythritol ethoxylate (15/4 EO/OH), 0.05M Ammonium sulfate, 0.05M BIS-TRIS pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 17155 / Num. obs: 17147 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 23.816
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 4.75 / Num. unique all: 830 / Rsym value: 0.438 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ADC

2adc


Resolution: 1.82→47.69 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.623 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24274 865 5.1 %RANDOM
Rwork0.18963 ---
all0.19262 16253 --
obs0.19239 16234 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.016 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---1.15 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.82→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 24 71 1659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211669
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9482268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5485221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13124.44472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38215246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.411155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211301
X-RAY DIFFRACTIONr_mcbond_it0.5691.51068
X-RAY DIFFRACTIONr_mcangle_it1.00721711
X-RAY DIFFRACTIONr_scbond_it1.5653601
X-RAY DIFFRACTIONr_scangle_it2.4894.5553
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 62 -
Rwork0.199 1137 -
obs--98.68 %
Refinement TLS params.Method: refined / Origin x: -2.1439 Å / Origin y: 10.7082 Å / Origin z: -18.9336 Å
111213212223313233
T0.0039 Å2-0.0035 Å20.0054 Å2-0.0079 Å2-0.0024 Å2--0.0616 Å2
L1.3824 °2-0.2209 °2-0.113 °2-1.865 °2-0.1913 °2--2.1863 °2
S0.0252 Å °0.0361 Å °-0.0024 Å °-0.0331 Å °-0.0148 Å °-0.0087 Å °0.0131 Å °-0.0476 Å °-0.0104 Å °

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