[English] 日本語
Yorodumi
- PDB-3u28: Crystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u28
TitleCrystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae
Components
  • H/ACA ribonucleoprotein complex subunit 1
  • H/ACA ribonucleoprotein complex subunit 3
  • H/ACA ribonucleoprotein complex subunit 4
KeywordsISOMERASE/PROTEIN BINDING / pseudouridine synthase / pseudouridylation / H/ACA RNA / Nucleolus / ISOMERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


Telomere Extension By Telomerase / snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / snRNA pseudouridine synthesis / Isomerases; Intramolecular transferases; Transferring other groups / mRNA pseudouridine synthesis / box H/ACA snoRNA binding / pseudouridine synthase activity ...Telomere Extension By Telomerase / snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / snRNA pseudouridine synthesis / Isomerases; Intramolecular transferases; Transferring other groups / mRNA pseudouridine synthesis / box H/ACA snoRNA binding / pseudouridine synthase activity / rRNA modification / sno(s)RNA-containing ribonucleoprotein complex / telomerase RNA binding / snoRNA binding / 90S preribosome / chromosome, centromeric region / rRNA processing / microtubule / cell cycle / cell division / mRNA binding / nucleolus / DNA binding / RNA binding / cytoplasm
Similarity search - Function
Rhinovirus 14, subunit 4 - #300 / Probable tRNA pseudouridine synthase domain / H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 / H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain / Gar1/Naf1 RNA binding region / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / H/ACA ribonucleoprotein complex, subunit Nop10 ...Rhinovirus 14, subunit 4 - #300 / Probable tRNA pseudouridine synthase domain / H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 / H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain / Gar1/Naf1 RNA binding region / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / H/ACA ribonucleoprotein complex, subunit Nop10 / H/ACA ribonucleoprotein complex, subunit Nop10 superfamily / Nucleolar RNA-binding protein, Nop10p family / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / Uncharacterised domain CHP00451 / PUA domain / PUA domain / Pseudouridine synthase, catalytic domain superfamily / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / Rhinovirus 14, subunit 4 / PUA-like superfamily / Few Secondary Structures / Irregular / Thrombin, subunit H / Translation protein, beta-barrel domain superfamily / Roll / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H/ACA ribonucleoprotein complex subunit GAR1 / H/ACA ribonucleoprotein complex subunit CBF5 / H/ACA ribonucleoprotein complex subunit NOP10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYe, K. / Li, S.
CitationJournal: Genes Dev. / Year: 2011
Title: Reconstitution and structural analysis of the yeast box H/ACA RNA-guided pseudouridine synthase
Authors: Li, S. / Duan, J. / Li, D. / Yang, B. / Dong, M. / Ye, K.
History
DepositionOct 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H/ACA ribonucleoprotein complex subunit 4
B: H/ACA ribonucleoprotein complex subunit 3
C: H/ACA ribonucleoprotein complex subunit 1


Theoretical massNumber of molelcules
Total (without water)64,2503
Polymers64,2503
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-30 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.413, 59.386, 169.212
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein H/ACA ribonucleoprotein complex subunit 4 / Centromere-binding factor 5 / Centromere/microtubule-binding protein CBF5 / H/ACA snoRNP protein ...Centromere-binding factor 5 / Centromere/microtubule-binding protein CBF5 / H/ACA snoRNP protein CBF5 / Small nucleolar RNP protein CBF5 / p64'


Mass: 44981.797 Da / Num. of mol.: 1 / Fragment: UNP residues 3-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CBF5 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: P33322, Isomerases; Intramolecular transferases; Transferring other groups
#2: Protein H/ACA ribonucleoprotein complex subunit 3 / Nucleolar protein 10 / Nucleolar protein family A member 3 / snoRNP protein NOP10


Mass: 6649.745 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NOP10 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q6Q547
#3: Protein H/ACA ribonucleoprotein complex subunit 1 / snoRNP protein GAR1


Mass: 12618.431 Da / Num. of mol.: 1 / Fragment: UNP residues 32-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GAR1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P28007
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.13 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.04
Details: 0.2M sodium malonate, 7%(w/v) polyethylene glycol 3350, pH 8.04, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9796 Å
DetectorDetector: CCD / Date: Sep 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 39859 / % possible obs: 89.5 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 26.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 4.2 / % possible all: 78.8

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HVY

2hvy


Resolution: 1.9→19.92 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.105 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23343 1971 5 %RANDOM
Rwork0.20355 ---
obs0.20509 37603 89.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.503 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 0 279 4028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223820
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9795162
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0385470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65723.313163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79715694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3011531
X-RAY DIFFRACTIONr_chiral_restr0.1030.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212818
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8651.52361
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.54823825
X-RAY DIFFRACTIONr_scbond_it1.97631459
X-RAY DIFFRACTIONr_scangle_it3.3524.51337
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 102 -
Rwork0.245 2467 -
obs--79.86 %
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)
10.2429-0.0546-0.46530.2320.01931.46520.0003-0.03490.01980.05210.0046-0.0323-0.04790.1006-0.00480.1362-0.0066-0.01070.0865-0.00310.08082.919-4.312-29.356
212.35010.7535-15.42470.049-0.943519.29381.5805-1.4240.45070.1101-0.48750.0756-2.45851.5842-1.0930.3494-0.1045-0.04731.78640.51821.1917-10.632-27.541-2.358
31.0359-0.70750.07781.92960.45751.27050.0456-0.0382-0.08330.09540.007-0.00080.06730.0304-0.05260.1413-0.0078-0.01710.10380.00350.04992.503-27.922-7.879
41.92170.1758-0.251.1525-0.35110.8287-0.02560.0639-0.0462-0.03340.0207-0.0883-0.01060.05130.00490.118-0.00990.00250.0864-0.00470.078625.302-9.766-54.862
52.8785-1.10961.56331.7641-0.33152.0071-0.0158-0.0938-0.07750.0544-0.04020.18220.0115-0.08930.0560.1250.00040.00710.078-0.01310.0836-12.161-0.949-37.146
67.2373-2.8219-0.78592.6213-1.46075.7279-0.4457-0.30350.56850.21860.15970.124-0.9486-0.16590.2860.39960.0311-0.15170.0274-0.0640.3196-8.39112.181-16.764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 258
2X-RAY DIFFRACTION2A5 - 11
3X-RAY DIFFRACTION3A18 - 51
4X-RAY DIFFRACTION3A259 - 350
5X-RAY DIFFRACTION4C33 - 124
6X-RAY DIFFRACTION5B1 - 32
7X-RAY DIFFRACTION6B33 - 48

+
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