[English] 日本語
Yorodumi
- PDB-4qmf: Structure of the Krr1 and Faf1 complex from Saccharomyces cerevisiae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qmf
TitleStructure of the Krr1 and Faf1 complex from Saccharomyces cerevisiae
Components
  • KRR1 small subunit processome component
  • Protein FAF1
KeywordsRNA BINDING PROTEIN / protein-protein complex / K-homology domain / ribosome biogenesis
Function / homology
Function and homology information


preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / nucleolus ...preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / nucleolus / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / : / : / KRR1 small subunit processome component, second KH domain / Ribosomal RNA assembly KRR1 / K Homology domain, type 1 / Krr1, KH1 domain / Krr1 KH1 domain / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily ...: / : / : / KRR1 small subunit processome component, second KH domain / Ribosomal RNA assembly KRR1 / K Homology domain, type 1 / Krr1, KH1 domain / Krr1 KH1 domain / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
KRR1 small subunit processome component / Protein FAF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.804 Å
AuthorsZheng, S. / Ye, K.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Interaction between ribosome assembly factors Krr1 and Faf1 is essential for formation of small ribosomal subunit in yeast
Authors: Zheng, S. / Lan, P. / Liu, X. / Ye, K.
History
DepositionJun 16, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
D: KRR1 small subunit processome component
B: KRR1 small subunit processome component
A: Protein FAF1
C: Protein FAF1


Theoretical massNumber of molelcules
Total (without water)55,3224
Polymers55,3224
Non-polymers00
Water25214
1
D: KRR1 small subunit processome component
C: Protein FAF1


Theoretical massNumber of molelcules
Total (without water)27,6612
Polymers27,6612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-7 kcal/mol
Surface area11410 Å2
MethodPISA
2
B: KRR1 small subunit processome component
A: Protein FAF1


Theoretical massNumber of molelcules
Total (without water)27,6612
Polymers27,6612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-6 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.097, 67.923, 81.414
Angle α, β, γ (deg.)90.00, 95.53, 90.00
Int Tables number4
Space group name H-MP1211
Detailsheterodimer of Krr1 and Faf1

-
Components

#1: Protein KRR1 small subunit processome component / KRR-R motif-containing protein 1 / Ribosomal RNA assembly protein KRR1


Mass: 21999.906 Da / Num. of mol.: 2 / Fragment: UNP residues 32-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: KRR1, YCL059C, YCL59C / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P25586
#2: Protein/peptide Protein FAF1 / Forty S assembly factor


Mass: 5661.330 Da / Num. of mol.: 2 / Fragment: UNP residues 145-169, 199-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: FAF1, YIL019W / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P40546
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M tri-ammonium citrate, 20% (w/v) PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 13065 / Num. obs: 13000 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 34.16 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 17.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.8-2.853.90.6324.341100
2.85-2.93.90.475.411100
2.9-2.963.90.4365.78199.8
2.96-3.023.90.347.031100
3.02-3.083.90.2987.961100
3.08-3.153.90.2619.071100
3.15-3.233.80.26410.1199.1
3.23-3.323.80.20511.91100
3.32-3.423.80.20412.91100
3.42-3.533.80.16814.9199.7
3.53-3.653.70.1517.5199.1
3.65-3.83.80.12719.5199.2
3.8-3.973.60.1221.3199.4
3.97-4.183.70.08523.4199.4
4.18-4.443.60.0726.3198
4.44-4.793.50.06227.7199.5
4.79-5.273.90.05828.51100
5.27-6.033.90.05928199.7
6.03-7.593.80.04929.21100
7.59-503.50.03830.1196.6

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.804→40.172 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 29.1 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2779 640 4.93 %
Rwork0.2324 --
obs0.2346 12974 98.06 %
all-13237 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.804→40.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 0 14 3161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033195
X-RAY DIFFRACTIONf_angle_d0.6444296
X-RAY DIFFRACTIONf_dihedral_angle_d16.3381252
X-RAY DIFFRACTIONf_chiral_restr0.025499
X-RAY DIFFRACTIONf_plane_restr0.003540
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8044-3.02090.35041320.2765232393
3.0209-3.32480.30371260.25672495100
3.3248-3.80550.3191400.2417248399
3.8055-4.79330.23541200.2113248699
4.7933-40.17580.24811220.214254799

+
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://pdbjlvh1.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