[English] 日本語
Yorodumi
- PDB-1zh5: Structural basis for recognition of UUUOH 3'-terminii of nascent ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zh5
TitleStructural basis for recognition of UUUOH 3'-terminii of nascent RNA pol III transcripts by La autoantigen
Components
  • 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'
  • Lupus La protein
KeywordsTRANSCRIPTION/RNA / TRANSCRIPTION-RNA complex
Function / homology
Function and homology information


nuclear histone mRNA catabolic process / histone mRNA metabolic process / tRNA 3'-end processing / protein localization to cytoplasmic stress granule / RNA Polymerase III Transcription Termination / IRES-dependent viral translational initiation / tRNA export from nucleus / RNA Polymerase III Abortive And Retractive Initiation / tRNA 5'-leader removal / tRNA modification ...nuclear histone mRNA catabolic process / histone mRNA metabolic process / tRNA 3'-end processing / protein localization to cytoplasmic stress granule / RNA Polymerase III Transcription Termination / IRES-dependent viral translational initiation / tRNA export from nucleus / RNA Polymerase III Abortive And Retractive Initiation / tRNA 5'-leader removal / tRNA modification / sequence-specific mRNA binding / poly(U) RNA binding / tRNA processing / positive regulation of translation / cytoplasmic stress granule / tRNA binding / chromosome, telomeric region / ribonucleoprotein complex / mRNA binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA binding motif / Lupus La protein / La protein, xRRM domain / xRRM domain profile. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RRM (RNA recognition motif) domain ...RNA binding motif / Lupus La protein / La protein, xRRM domain / xRRM domain profile. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RRM (RNA recognition motif) domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / Lupus La protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsTeplova, M. / Yuan, Y.R. / Ilin, S. / Malinina, L. / Phan, A.T. / Teplov, A. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2006
Title: Structural Basis for Recognition and Sequestration of UUU(OH) 3' Temini of Nascent RNA Polymerase III Transcripts by La, a Rheumatic Disease Autoantigen.
Authors: Teplova, M. / Yuan, Y.R. / Phan, A.T. / Malinina, L. / Ilin, S. / Teplov, A. / Patel, D.J.
History
DepositionApr 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'
D: 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'
A: Lupus La protein
B: Lupus La protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9417
Polymers51,6534
Non-polymers2883
Water8,197455
1
D: 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'
A: Lupus La protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0184
Polymers25,8262
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'
B: Lupus La protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9223
Polymers25,8262
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.209, 55.030, 57.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: RNA chain 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'


Mass: 2787.631 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Lupus La protein / Sjogren syndrome type B antigen / SS-B / La ribonucleoprotein / La autoantigen


Mass: 23038.621 Da / Num. of mol.: 2 / Fragment: N-terminal domain (residues 1-194)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SSB / Production host: Escherichia coli (E. coli) / References: UniProt: P05455
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 8000, lithium sulfate, potassium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2lithium sulfate11
3potassium chloride11
4sodium acetate11
5H2011
6PEG 800012
7lithium sulfate12
8potassium chloride12
9sodium acetate12
10H2012

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONNSLS X2520.9798, 0.9795, 0.9611
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDFeb 16, 2005mirrors
ADSC QUANTUM 3152CCDJan 26, 2005mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97981
30.97951
40.96111
ReflectionResolution: 1.85→20 Å / Num. obs: 42919 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rsym value: 0.103 / Net I/σ(I): 14.9
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4221 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CBASSdata collection
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→19.92 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.914 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.148 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24528 2192 5.1 %RANDOM
Rwork0.20022 ---
obs0.20252 40918 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 366 15 455 3886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223530
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6812.1124826
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83125.033153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40415620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7541516
X-RAY DIFFRACTIONr_chiral_restr0.1130.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022478
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21228
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22329
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.911.51942
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37723001
X-RAY DIFFRACTIONr_scbond_it2.16731916
X-RAY DIFFRACTIONr_scangle_it3.2664.51825
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 166 -
Rwork0.224 2943 -
obs--99.36 %
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)
11.4356-0.3842-0.64452.077-0.25592.4255-0.0733-0.0099-0.11970.08960.0165-0.00370.08010.01140.0568-0.0652-0.0028-0.0047-0.0551-0.0014-0.037958.6822-21.9858-41.7795
22.2560.2054-0.94111.5820.12682.04630.1042-0.07050.1462-0.04380.0541-0.182-0.26960.1427-0.1583-0.0487-0.00990.002-0.07-0.0116-0.027260.68243.0083-39.5119
30.6115-0.08060.44611.83110.17462.6953-0.0872-0.04650.05850.06170.02460.0416-0.1607-0.04380.0626-0.045-0.00220.0052-0.0478-0.0035-0.046922.58217.4302-45.1746
42.38540.05021.65881.3763-0.59583.63580.150.0008-0.2106-0.10710.09610.16190.3847-0.1393-0.2461-0.0434-0.0053-0.0125-0.08180.0047-0.007120.188-7.4518-44.0297
51.4286-0.2563-0.01480.23190.00740.0003-0.00990.29750.0272-0.0375-0.0310.0169-0.02920.02060.0409-0.00490.0182-0.00920.0824-0.0071-0.022640.9898-2.1759-48.1384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC6 - 997 - 100
2X-RAY DIFFRACTION2AC100 - 189101 - 190
3X-RAY DIFFRACTION3BD7 - 998 - 100
4X-RAY DIFFRACTION4BD100 - 189101 - 190
5X-RAY DIFFRACTION5CA1 - 91 - 9
6X-RAY DIFFRACTION5DB1 - 91 - 9

+
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