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- PDB-3s01: Crystal structure of a Heterogeneous nuclear ribonucleoprotein L ... -

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Basic information

Entry
Database: PDB / ID: 3s01
TitleCrystal structure of a Heterogeneous nuclear ribonucleoprotein L (Hnrpl) from Mus musculus at 2.15 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 / STEMCELL / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


Processing of Capped Intron-Containing Pre-mRNA / mRNA CDS binding / ribonucleoprotein granule / mRNA Splicing - Major Pathway / pronucleus / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / pre-mRNA intronic binding / mRNA 3'-UTR binding / mRNA processing ...Processing of Capped Intron-Containing Pre-mRNA / mRNA CDS binding / ribonucleoprotein granule / mRNA Splicing - Major Pathway / pronucleus / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / pre-mRNA intronic binding / mRNA 3'-UTR binding / mRNA processing / transcription cis-regulatory region binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / mRNA binding / synapse / chromatin / perinuclear region of cytoplasm / 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 / 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
ISOPROPYL ALCOHOL / Heterogeneous nuclear ribonucleoprotein L
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 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 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL) / Partnership for T-Cell Biology (TCELL)
History
DepositionMay 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Oct 21, 2015Group: Database references / Structure summary
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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)24,3774
Polymers24,1651
Non-polymers2123
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.672, 37.964, 57.953
Angle α, β, γ (deg.)90.00, 105.44, 90.00
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein L / hnRNP L


Mass: 24164.891 Da / Num. of mol.: 1 / Fragment: RRM 3 domain containg residues 376-586
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
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 376-586 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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10.00% 2-propanol, 20.00% polyethylene glycol 4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97938
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 10, 2011 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979381
ReflectionResolution: 2.15→29.512 Å / Num. obs: 11314 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.714 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.15-2.230.4521.942322242196.5
2.23-2.320.3512.441082144199
2.32-2.420.2972.9393520481100
2.42-2.550.2493.242062195198.9
2.55-2.710.2043.842312196199
2.71-2.920.1485.341622156199.2
2.92-3.210.107740832115198.2
3.21-3.670.06211.141072126197.5
3.67-4.610.04614.640652108197.5
4.61-29.5120.0416.141412137195.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.8.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.15→29.512 Å / Cor.coef. Fo:Fc: 0.9523 / Cor.coef. Fo:Fc free: 0.9262 / Occupancy max: 1 / Occupancy min: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. 2-PROPANOL (IPA) AND GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTIONS ARE MODELED. 5. THE MAD PHASES (HL COEFFICIENTS) WERE USED AS RESTRAINTS DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 534 4.73 %RANDOM
Rwork0.1586 ---
obs0.1607 11283 --
Displacement parametersBiso max: 105.56 Å2 / Biso mean: 29.8723 Å2 / Biso min: 12.16 Å2
Baniso -1Baniso -2Baniso -3
1--5.3714 Å20 Å2-0.5945 Å2
2--3.2102 Å20 Å2
3---2.1612 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 14 126 1756
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d776SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes248HARMONIC5
X-RAY DIFFRACTIONt_it1684HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion209SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2000SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1684HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2274HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.53
X-RAY DIFFRACTIONt_other_torsion2.65
LS refinement shellResolution: 2.15→2.35 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2478 142 5.32 %
Rwork0.1771 2526 -
all0.181 2668 -
Refinement TLS params.Method: refined / Origin x: -7.8905 Å / Origin y: 12.0963 Å / Origin z: 13.1495 Å
111213212223313233
T-0.0453 Å2-0.0086 Å20.0133 Å2--0.0579 Å20.0045 Å2---0.0703 Å2
L1.2298 °2-0.2601 °2-0.1619 °2-1.1848 °20.2012 °2--1.1019 °2
S-0.0338 Å °0.0594 Å °0.0116 Å °-0.0632 Å °-0.0019 Å °-0.0371 Å °-0.0606 Å °-0.074 Å °0.0358 Å °
Refinement TLS groupSelection details: { A|0 - A|586 }

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