[English] 日本語
Yorodumi
- PDB-3tyt: Crystal structure of a Heterogeneous nuclear ribonucleoprotein L ... -

+
Open data


ID or keywords:

Loading...

-
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 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 / mRNA binding / negative regulation of DNA-templated transcription / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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 / Chloride


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


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


Mass: 18.015 Da / Num. of mol.: 216 / 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 376-579 OF THE TARGET SEQUENCE. NUMBERING IS BASED ON THE UNIPROTKB Q8R081 VERSION 2 SEQUENCE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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 °

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more