[English] 日本語
Yorodumi
- PDB-6eld: Crystal structure of TIA-1 RRM1 in complex with U1C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6eld
TitleCrystal structure of TIA-1 RRM1 in complex with U1C
ComponentsNucleolysin TIA-1 isoform p40,U1 small nuclear ribonucleoprotein C
KeywordsRNA BINDING PROTEIN / RRM domain / Protein-RNA interaction
Function / homology
Function and homology information


protein localization to cytoplasmic stress granule / nuclear stress granule / mRNA 3'-UTR AU-rich region binding / poly(A) binding / regulation of mRNA splicing, via spliceosome / commitment complex / positive regulation of epithelial cell apoptotic process / U1 snRNP / FGFR2 alternative splicing / negative regulation of cytokine production ...protein localization to cytoplasmic stress granule / nuclear stress granule / mRNA 3'-UTR AU-rich region binding / poly(A) binding / regulation of mRNA splicing, via spliceosome / commitment complex / positive regulation of epithelial cell apoptotic process / U1 snRNP / FGFR2 alternative splicing / negative regulation of cytokine production / pre-mRNA 5'-splice site binding / U2-type prespliceosome / regulation of alternative mRNA splicing, via spliceosome / mRNA 5'-splice site recognition / Cajal body / spliceosomal snRNP assembly / stress granule assembly / mRNA Splicing - Major Pathway / RNA splicing / mRNA 3'-UTR binding / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / cytoplasmic stress granule / single-stranded RNA binding / negative regulation of translation / ribonucleoprotein complex / mRNA binding / apoptotic process / protein homodimerization activity / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
TIA-1, RNA recognition motif 1 / TIA-1, RNA recognition motif 2 / TIAR, RNA recognition motif 3 / U1 small nuclear ribonucleoprotein C / U1-C, C2H2-type zinc finger / U1 zinc finger / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / RNA recognition motif domain, eukaryote / RNA recognition motif ...TIA-1, RNA recognition motif 1 / TIA-1, RNA recognition motif 2 / TIAR, RNA recognition motif 3 / U1 small nuclear ribonucleoprotein C / U1-C, C2H2-type zinc finger / U1 zinc finger / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / RNA recognition motif domain, eukaryote / RNA recognition motif / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger C2H2 superfamily / 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
Similarity search - Domain/homology
U1 small nuclear ribonucleoprotein C / Cytotoxic granule associated RNA binding protein TIA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.485 Å
AuthorsJagtap, P.K.A. / Sattler, M.
CitationJournal: To Be Published
Title: Crystal structure of TIA-1 RRM1 in complex with U1C
Authors: Jagtap, P.K.A. / Sattler, M.
History
DepositionSep 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleolysin TIA-1 isoform p40,U1 small nuclear ribonucleoprotein C


Theoretical massNumber of molelcules
Total (without water)15,2421
Polymers15,2421
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.110, 71.110, 60.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

-
Components

#1: Protein Nucleolysin TIA-1 isoform p40,U1 small nuclear ribonucleoprotein C / RNA-binding protein TIA-1 / T-cell-restricted intracellular antigen-1 / TIA-1 / p40-TIA-1 / U1C


Mass: 15242.138 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein is a chimeric protein made from TIA-1 RRM1 and U1C protein from human fused together with GS linker
Source: (gene. exp.) Homo sapiens (human) / Gene: TIA1, SNRPC / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P31483, UniProt: P09234
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.67 % / Description: Rod shaped crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 10% PEG6000 and 10% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.485→43.223 Å / Num. obs: 6053 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 6.16 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.066 / Χ2: 1.095 / Net I/σ(I): 16.85
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.49-2.555.5140.7631.814010.8160.83686.6
2.55-2.626.3220.712.314500.7440.77199.1
2.62-2.76.1710.5243.134270.8630.57199.1
2.7-2.785.7520.4183.674040.9190.45898.3
2.78-2.876.3660.344.84210.9350.36998.1
2.87-2.976.4020.2356.763830.9870.25498.5
2.97-3.086.3940.1868.733730.9820.20198.9
3.08-3.216.4630.14211.293650.9890.15398.9
3.21-3.356.0430.10914.233480.9940.11898
3.35-3.515.830.08619.033300.9950.09397.6
3.51-3.76.4830.07122.893170.9970.07698.8
3.7-3.936.3660.05628.672950.9980.0697.4
3.93-4.26.0790.05232.872800.9990.05696.6
4.2-4.545.7370.04434.962550.9970.04897.7
4.54-4.976.2890.04238.62390.9980.04596.4
4.97-5.566.3730.03837.652200.9990.04196.5
5.56-6.426.2190.03737.971920.9990.0497
6.42-7.866.1730.03241.251620.9990.03494.7
7.86-11.116.1150.02845.071220.9990.0393.1
11.11-43.2236.2030.02449.066910.02688.5

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O2V

5o2v


Resolution: 2.485→43.223 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.8
RfactorNum. reflection% reflection
Rfree0.2422 303 5.01 %
Rwork0.1969 --
obs0.1992 6052 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.93 Å2 / Biso mean: 77.367 Å2 / Biso min: 40.93 Å2
Refinement stepCycle: final / Resolution: 2.485→43.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 0 3 824
Biso mean---60.19 -
Num. residues----107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001837
X-RAY DIFFRACTIONf_angle_d0.3391133
X-RAY DIFFRACTIONf_chiral_restr0.035126
X-RAY DIFFRACTIONf_plane_restr0.002146
X-RAY DIFFRACTIONf_dihedral_angle_d18.277499
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 97 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4853-3.13110.28261500.256528583008
3.1311-43.22950.23271530.182528913044
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)
16.41580.37470.48916.94232.6153.5613-0.31150.3164-0.5274-1.3736-0.02820.66920.1625-0.16850.2990.5992-0.0409-0.04450.6069-0.05060.43122.543330.4607-6.7257
22.6394-3.08342.23866.41470.47469.3593-0.24940.3999-0.39140.48710.29680.54890.2881-0.2412-0.03010.5716-0.1253-0.03190.43290.0540.61899.994721.58440.5812
36.9815-4.3343-2.61423.951-1.24029.621-0.43780.25010.2420.01030.58230.4530.1853-0.5378-0.11880.4757-0.01480.00810.65790.03140.4640.185535.3756-1.9053
43.02662.676-0.75884.79121.7022.7723-0.2869-1.4553-0.49520.48190.39440.28750.4012-0.975-0.13010.51820.04520.09240.68880.16470.4197-0.469228.85296.318
58.8046-3.3952-1.14794.058-1.27058.1449-0.1193-0.5038-0.3021-0.16450.2127-0.0585-0.0817-0.5715-0.05270.5512-0.07140.010.69830.00140.43161.390335.16060.9841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 67 through 85 )A67 - 85
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 137 )A111 - 137
3X-RAY DIFFRACTION3chain 'A' and (resid 2 through 19 )A2 - 19
4X-RAY DIFFRACTION4chain 'A' and (resid 20 through 29 )A20 - 29
5X-RAY DIFFRACTION5chain 'A' and (resid 30 through 66 )A30 - 66

+
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