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- PDB-3tyt: Crystal structure of a Heterogeneous nuclear ribonucleoprotein L ... -

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Basic information

Entry
Database: PDB / ID: 3tyt
TitleCrystal structure of a Heterogeneous nuclear ribonucleoprotein L (Hnrpl) from Mus musculus at 1.60 A resolution
ComponentsHeterogeneous nuclear ribonucleoprotein L
KeywordsRNA BINDING PROTEIN / Ferredoxin-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for Stem Cell Biology / Partnership for T-Cell Biology / STEMCELL / TCELL
Function / homology
Function and homology information


Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / ribonucleoprotein granule / pronucleus / regulation of alternative mRNA splicing, via spliceosome / pre-mRNA intronic binding / mRNA processing / transcription cis-regulatory region binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription ...Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / ribonucleoprotein granule / pronucleus / regulation of alternative mRNA splicing, via spliceosome / pre-mRNA intronic binding / mRNA processing / transcription cis-regulatory region binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / synapse / chromatin / RNA binding / nucleoplasm / 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 / : / RRM domain / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) ...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 / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a Heterogeneous nuclear ribonucleoprotein L (Hnrpl) from Mus musculus at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL) / Partnership for T-Cell Biology (TCELL)
History
DepositionSep 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Structure summary
Revision 1.2Oct 21, 2015Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,88416
Polymers23,0591
Non-polymers82515
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heterogeneous nuclear ribonucleoprotein L
hetero molecules

A: Heterogeneous nuclear ribonucleoprotein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,76732
Polymers46,1182
Non-polymers1,64930
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+2/31
Buried area6220 Å2
ΔGint-56 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.424, 127.424, 80.652
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-737-

HOH

DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. HOWEVER, THE PROTEIN APPEARS TO HAVE FORMED STABLE DIMERS IN THE CRYSTAL LATTICE.

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein L


Mass: 23059.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: BC027206, Hnrnpl, Hnrpl / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8R081
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 376-579 OF THE TARGET SEQUENCE. NUMBERING IS BASED ON THE UNIPROTKB Q8R081 VERSION 2 SEQUENCE.

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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: 4.1 Å3/Da / Density % sol: 69.99 % / Mosaicity: 0.16 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.6
Details: 2.0M NaCl, 10.0% PEG-6000, No Buffer pH 3.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 3, 2011
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→41.709 Å / Num. all: 51213 / Num. obs: 51213 / % possible obs: 100 % / Redundancy: 10.9 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.084 / Rsym value: 0.077 / Net I/av σ(I): 6.044 / Net I/σ(I): 15.4 / Num. measured all: 558136
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.6-1.6910.91.2811.170.67974173420.3861.2811.172.1100
1.69-1.79110.7650.717651769850.2290.7650.73.5100
1.79-1.91110.4620.4231.87204265680.1380.4620.4235.3100
1.91-2.07110.240.223.46755161450.0720.240.229.5100
2.07-2.26110.1480.1365.36213756410.0440.1480.13614.8100
2.26-2.53110.1010.0937.65673051620.030.1010.09319.1100
2.53-2.92110.0820.0768.45017245700.0240.0820.07624.4100
2.92-3.5810.90.0590.05510.44261639080.0180.0590.05534.6100
3.58-5.0610.70.0470.04313.23308030980.0140.0470.04347.6100
5.06-41.7099.80.0430.03915.11755017940.0130.0430.03945.398.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
MOLREPphasing
SCALA3.3.15data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→41.709 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.453 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. CHLORIDE (CL) IONS AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 2597 5.1 %RANDOM
Rwork0.1762 48577 --
obs0.1777 51174 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 78.52 Å2 / Biso mean: 35.6183 Å2 / Biso min: 17.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1588 0 48 216 1852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221768
X-RAY DIFFRACTIONr_bond_other_d0.0010.021264
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9682384
X-RAY DIFFRACTIONr_angle_other_deg0.96133096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02624.87882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68115313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.522158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211989
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02354
X-RAY DIFFRACTIONr_mcbond_it0.9171.51075
X-RAY DIFFRACTIONr_mcbond_other0.4391.5429
X-RAY DIFFRACTIONr_mcangle_it1.6421748
X-RAY DIFFRACTIONr_scbond_it2.6813692
X-RAY DIFFRACTIONr_scangle_it4.2664.5621
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 184 -
Rwork0.265 3531 -
all-3715 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: 43.21 Å / Origin y: -43.055 Å / Origin z: 9.359 Å
111213212223313233
T0.1071 Å2-0.0999 Å2-0.0283 Å2-0.1121 Å20.0114 Å2--0.0544 Å2
L1.9503 °20.8208 °20.131 °2-1.1535 °2-0.3278 °2--1.6458 °2
S-0.1445 Å °0.1994 Å °0.0898 Å °-0.2223 Å °0.1794 Å °0.1931 Å °0.2325 Å °-0.2669 Å °-0.0349 Å °

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