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- PDB-3r27: Crystal structure of the first RRM domain of heterogeneous nuclea... -

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Basic information

Entry
Database: PDB / ID: 3r27
TitleCrystal structure of the first RRM domain of heterogeneous nuclear ribonucleoprotein L (HnRNP L)
ComponentsHeterogeneous nuclear ribonucleoprotein L
KeywordsPROTEIN BINDING / RBD Fold / Nucleus
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
Heterogeneous nuclear ribonucleoprotein L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsZhang, W. / Liu, Y. / Zeng, F. / Niu, L. / Teng, M. / Li, X.
CitationJournal: To be Published
Title: Crystal structure of the first RRM domain of heterogeneous nuclear ribonucleoprotein L (HnRNP L)
Authors: Zhang, W. / Liu, Y. / Zeng, F. / Niu, L. / Teng, M. / Li, X.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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
B: Heterogeneous nuclear ribonucleoprotein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6657
Polymers22,2052
Non-polymers4605
Water1,47782
1
A: Heterogeneous nuclear ribonucleoprotein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2873
Polymers11,1021
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heterogeneous nuclear ribonucleoprotein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3794
Polymers11,1021
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.170, 43.170, 78.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein L / hnRNP L


Mass: 11102.481 Da / Num. of mol.: 2 / Fragment: THE FIRST RRM DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPL, HNRPL, P/OKcl.14 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P14866
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 1.9 Å3/Da / Density % sol: 35.35 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 25%w/v Polyethylene glycol 3,350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 6, 2009
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→78.57 Å / Num. all: 10581 / Num. obs: 10541 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 14
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1521 / Rsym value: 0.037 / % possible all: 97.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WEX

1wex


Resolution: 2.04→39.25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.894 / SU B: 11.931 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25473 502 4.8 %RANDOM
Rwork0.20437 ---
obs0.20682 9988 99.81 %-
all-10007 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.021 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.36 Å20 Å2
2--0.72 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.04→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 30 82 1390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221329
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.9721803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.7525.35756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92115204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.141154
X-RAY DIFFRACTIONr_chiral_restr0.080.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021990
X-RAY DIFFRACTIONr_mcbond_it0.4221.5838
X-RAY DIFFRACTIONr_mcangle_it0.8521358
X-RAY DIFFRACTIONr_scbond_it1.4683491
X-RAY DIFFRACTIONr_scangle_it2.4074.5445
LS refinement shellResolution: 2.04→2.089 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 42 -
Rwork0.321 719 -
obs--97.56 %
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)
11.0183-0.39720.20210.73330.16230.9733-0.04040.02280.0020.05120.04230.00970.03410.0193-0.00180.04310.00380.00230.02980.00360.00748.7077-7.3571-4.5541
20.2782-0.15510.166910.17680.87450.0201-0.01030.014-0.0111-0.0214-0.01110.05180.02510.00130.03790.0060.00660.045-0.00130.01172.102413.9127-14.5011
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A97 - 182
2X-RAY DIFFRACTION2B97 - 183

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