[English] 日本語
Yorodumi
- PDB-4nsx: Crystal Structure of the Utp21 tandem WD Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nsx
TitleCrystal Structure of the Utp21 tandem WD Domain
ComponentsU3 small nucleolar RNA-associated protein 21
KeywordsPROTEIN BINDING / ribosome biogenesis / UTPB complex / 90S preribosome / Small subunit processome
Function / homology
Function and homology information


Pwp2p-containing subcomplex of 90S preribosome / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / maturation of SSU-rRNA / small-subunit processome / rRNA processing / nucleolus / nucleoplasm / nucleus
Similarity search - Function
Small-subunit processome, Utp21 / Utp21 specific WD40 associated putative domain / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...Small-subunit processome, Utp21 / Utp21 specific WD40 associated putative domain / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / U3 small nucleolar RNA-associated protein 21
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å
AuthorsZhang, C. / Ye, K.
CitationJournal: Plos One / Year: 2014
Title: Structure of Utp21 Tandem WD Domain Provides Insight into the Organization of the UTPB Complex Involved in Ribosome Synthesis
Authors: Zhang, C. / Lin, J. / Liu, W. / Chen, X. / Chen, R. / Ye, K.
History
DepositionNov 29, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: U3 small nucleolar RNA-associated protein 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2842
Polymers76,0951
Non-polymers1891
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.493, 63.540, 82.549
Angle α, β, γ (deg.)110.95, 95.83, 97.93
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein U3 small nucleolar RNA-associated protein 21 / U3 snoRNA-associated protein 21 / U three protein 21


Mass: 76095.398 Da / Num. of mol.: 1 / Fragment: Tandem WD domain 1-684
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: L8084.22, UTP21, YLR409C / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06078
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 15% PEG3350, 0.15M sodium citrate, pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 37483 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.142 / Rsym value: 0.142 / Net I/σ(I): 13.723
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.826 / Num. unique all: 1852 / Rsym value: 0.478 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→20 Å / SU ML: 0.19 / σ(F): 0.05 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 1760 4.97 %RANDOM
Rwork0.1869 ---
obs0.1888 35416 92.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 13 394 5381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035089
X-RAY DIFFRACTIONf_angle_d0.8346889
X-RAY DIFFRACTIONf_dihedral_angle_d13.3521858
X-RAY DIFFRACTIONf_chiral_restr0.059780
X-RAY DIFFRACTIONf_plane_restr0.003879
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.15670.29351280.2232221680
2.1567-2.22010.24771440.2136246788
2.2201-2.29170.23811250.2131237086
2.2917-2.37340.2411240.1998255789
2.3734-2.46830.25561500.2005251891
2.4683-2.58040.21421080.2059259992
2.5804-2.71610.26761240.2049265793
2.7161-2.88580.25151440.211263595
2.8858-3.10790.26111490.2038270296
3.1079-3.41920.25431410.1857271197
3.4192-3.91060.19061410.1747277798
3.9106-4.91460.16961300.1565270897
4.9146-200.20131520.1696273998

+
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