[English] 日本語
Yorodumi
- PDB-4v7f: Arx1 pre-60S particle. -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 4v7f
TitleArx1 pre-60S particle.
Components
  • (60S ribosomal protein ...) x 37
  • (Ribosome biogenesis protein ...) x 2
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Eukaryotic translation initiation factor 6
  • Nucleolar GTP-binding protein 1
  • Ribosome assembly protein 4
  • mRNA turnover protein 4
  • metalloprotease ARX1
KeywordsRIBOSOME / 60S biogenesis / 5S rRNA
Function / homologyRibosome assembly factor Mrt4 / Ribosomal protein L32e superfamily / Ribosomal protein L15 / OBG-type guanine nucleotide-binding (G) domain / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L30 signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily ...Ribosome assembly factor Mrt4 / Ribosomal protein L32e superfamily / Ribosomal protein L15 / OBG-type guanine nucleotide-binding (G) domain / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L30 signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / Creatinase/aminopeptidase-like / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein L22/L17 superfamily / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L24e/L24 superfamily / 50S ribosomal protein L30e-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L35A superfamily / Ribosomal protein L5 domain superfamily / Ribosomal protein L39e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L30e, conserved site / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L13, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L4 domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L1, conserved site / Ribosomal protein L1-like / Ribosomal protein L15e core domain superfamily / Nucleolar GTP-binding protein 1 / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L27e superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L6, alpha-beta domain / Ribosomal L18 C-terminal region / Ribosomal L27e protein family / Ribosomal L37ae protein family / Ribosomal L38e protein family / Ribosomal protein L37e / eIF-6 family / Ribosomal protein L14 / Ribosomal protein L23, N-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal Proteins L2, C-terminal domain / Nucleolar GTP-binding protein 1 (NOG1) / Ribosomal L30 N-terminal domain / NLE (NUC135) domain / NOGCT (NUC087) domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein 60S L18 and 50S L18e / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ribosomal protein L39e signature. / Ribosomal protein L5 signature. / Ribosomal protein L11 signature. / Ribosomal protein L22 signature. / Ribosomal protein L2 signature. / Ribosomal protein L3 signature. / Ribosomal protein L15 signature. / Ribosomal protein L19e signature. / Ribosomal L22e protein family / Ribosomal protein L32 / Ribosomal protein L22p/L17e / ribosomal L5P family C-terminus / Ribosomal protein L14p/L23e / Ribosomal protein L23 / Ribosomal protein L5
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8.7 Å resolution
AuthorsLeidig, C. / Thoms, M. / Holdermann, I. / Bradatsch, B. / Berninghausen, O. / Bange, G. / Sinning, I. / Hurt, E. / Beckmann, R.
CitationJournal: Nat Commun / Year: 2014
Title: 60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle.
Authors: Christoph Leidig / Matthias Thoms / Iris Holdermann / Bettina Bradatsch / Otto Berninghausen / Gert Bange / Irmgard Sinning / Ed Hurt / Roland Beckmann
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 10, 2013 / Release: Jul 9, 2014
RevisionDateData content typeGroupProviderType
1.0Jul 9, 2014Structure modelrepositoryInitial release
1.1Dec 10, 2014Structure modelOther
1.2Apr 15, 2015Structure modelOther

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2528
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: 25S ribosomal RNA
2: 5.8S ribosomal RNA
3: 5S ribosomal RNA
A: 60S ribosomal protein L1
B: 60S ribosomal protein L2
C: 60S ribosomal protein L3
D: 60S ribosomal protein L4
E: 60S ribosomal protein L11
F: 60S ribosomal protein L9
G: 60S ribosomal protein L6
H: 60S ribosomal protein L8
I: 60S ribosomal protein L12
J: 60S ribosomal protein L16
K: 60S ribosomal protein L13
L: 60S ribosomal protein L23
M: 60S ribosomal protein L14
N: 60S ribosomal protein L28
O: 60S ribosomal protein L15
P: 60S ribosomal protein L5
Q: 60S ribosomal protein L18
R: 60S ribosomal protein L19
S: 60S ribosomal protein L20
T: 60S ribosomal protein L21
U: 60S ribosomal protein L17
V: 60S ribosomal protein L22
W: 60S ribosomal protein L25
X: 60S ribosomal protein L26
Y: 60S ribosomal protein L27
Z: 60S ribosomal protein L35
a: 60S ribosomal protein L7
b: 60S ribosomal protein L30
c: 60S ribosomal protein L31
d: 60S ribosomal protein L32
e: 60S ribosomal protein L33
f: 60S ribosomal protein L34
g: 60S ribosomal protein L36
h: 60S ribosomal protein L37
i: 60S ribosomal protein L38
j: 60S ribosomal protein L39
k: 60S ribosomal protein L43
l: metalloprotease ARX1
m: Eukaryotic translation initiation factor 6
n: mRNA turnover protein 4
o: Nucleolar GTP-binding protein 1
p: Ribosome biogenesis protein RLP24
q: Ribosome assembly protein 4
r: Ribosome biogenesis protein RLP7
s: Ribosome biogenesis protein RLP7


Theoretical massNumber of molelcules
Total (without water)2,240,93348
Polyers2,240,93348
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
RNA chain , 3 types, 3 molecules 123

#1: RNA chain 25S ribosomal RNA /


Mass: 1097493.875 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#2: RNA chain 5.8S ribosomal RNA /


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#3: RNA chain 5S ribosomal RNA /


Mass: 38951.105 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)

+
60S ribosomal protein ... , 37 types, 37 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#4: Protein/peptide 60S ribosomal protein L1 / / L10a


Mass: 24524.799 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX43
#5: Protein/peptide 60S ribosomal protein L2 / / L5 / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX45
#6: Protein/peptide 60S ribosomal protein L3 / / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14126
#7: Protein/peptide 60S ribosomal protein L4 / / L2 / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P10664
#8: Protein/peptide 60S ribosomal protein L11 / / L16 / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C0W9
#9: Protein/peptide 60S ribosomal protein L9 / / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05738
#10: Protein/peptide 60S ribosomal protein L6 / / L17 / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02326
#11: Protein/peptide 60S ribosomal protein L8 / / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P17076
#12: Protein/peptide 60S ribosomal protein L12 / / L15 / YL23


Mass: 17850.621 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX53
#13: Protein/peptide 60S ribosomal protein L16 / / L13a / L21 / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26784
#14: Protein/peptide 60S ribosomal protein L13 /


Mass: 22604.164 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12690
#15: Protein/peptide 60S ribosomal protein L23 / / L17a / YL32


Mass: 14493.950 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX41
#16: Protein/peptide 60S ribosomal protein L14 /


Mass: 15195.066 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36105
#17: Protein/peptide 60S ribosomal protein L28 / / L27a / L29 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02406
#18: Protein/peptide 60S ribosomal protein L15 / / L13 / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05748
#19: Protein/peptide 60S ribosomal protein L5 / / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3


Mass: 33764.828 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26321
#20: Protein/peptide 60S ribosomal protein L18 / / RP28


Mass: 20609.252 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX49
#21: Protein/peptide 60S ribosomal protein L19 / / L23 / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX82
#22: Protein/peptide 60S ribosomal protein L20 / / L18a


Mass: 20478.852 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX23
#23: Protein/peptide 60S ribosomal protein L21 /


Mass: 18279.266 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02753
#24: Protein/peptide 60S ribosomal protein L17 / / L20A / YL17


Mass: 20589.518 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05740
#25: Protein/peptide 60S ribosomal protein L22 / / L1c / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05749
#26: Protein/peptide 60S ribosomal protein L25 / / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04456
#27: Protein/peptide 60S ribosomal protein L26 / / L33 / YL33


Mass: 14265.784 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05743
#28: Protein/peptide 60S ribosomal protein L27 /


Mass: 15568.360 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H6
#29: Protein/peptide 60S ribosomal protein L35 /


Mass: 13942.640 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX84
#30: Protein/peptide 60S ribosomal protein L7 / / L6 / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05737
#31: Protein/peptide 60S ribosomal protein L30 / / L32 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14120
#32: Protein/peptide 60S ribosomal protein L31 / / L34 / YL28


Mass: 12980.158 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H8
#33: Protein/peptide 60S ribosomal protein L32 /


Mass: 14809.441 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38061
#34: Protein/peptide 60S ribosomal protein L33 / / L37 / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05744
#35: Protein/peptide 60S ribosomal protein L34 /


Mass: 13673.196 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P87262
#36: Protein/peptide 60S ribosomal protein L36 / / L39 / YL39


Mass: 11151.259 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05745
#37: Protein/peptide 60S ribosomal protein L37 / / L43 / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49166
#38: Protein/peptide 60S ribosomal protein L38 /


Mass: 8845.561 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49167
#39: Protein/peptide 60S ribosomal protein L39 / / L46 / YL40


Mass: 6358.640 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04650
#40: Protein/peptide 60S ribosomal protein L43 / / L37a / YL35


Mass: 10112.952 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX25

-
Protein/peptide , 5 types, 5 molecules lmnoq

#41: Protein/peptide metalloprotease ARX1 / Associated with ribosomal export complex protein 1


Mass: 65290.336 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q03862, hydrolases
#42: Protein/peptide Eukaryotic translation initiation factor 6 / Tif6 / eIF-6


Mass: 26476.605 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12522
#43: Protein/peptide mRNA turnover protein 4 / Mrt4


Mass: 27098.012 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P33201
#44: Protein/peptide Nucleolar GTP-binding protein 1 / Nog1


Mass: 74531.227 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02892
#46: Protein/peptide Ribosome assembly protein 4 / Rsa4


Mass: 57106.781 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P25382

-
Ribosome biogenesis protein ... , 2 types, 3 molecules prs

#45: Protein/peptide Ribosome biogenesis protein RLP24 / / Ribosomal protein L24-like


Mass: 24027.650 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q07915
#47: Protein/peptide Ribosome biogenesis protein RLP7 / / Ribosomal protein L7-like


Mass: 36621.074 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40693

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeParent ID
1Arx1 pre-60S particleRIBOSOME0
2Arx1 pre-60S particleRIBOSOME1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Nov 12, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

SymmetryPoint symmetry: C1
3D reconstructionResolution: 8.7 Å / Number of particles: 75887 / Nominal pixel size: 1.0605 / Actual pixel size: 1.0605 / Symmetry type: POINT
Atomic model buildingPDB-ID: 3U5D
Number of atoms included #LASTProtein: 0 / Nucleic acid: 22036 / Ligand: 0 / Solvent: 0 / Total: 22036

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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