[English] 日本語
Yorodumi
- PDB-5jpq: Cryo-EM structure of the 90S pre-ribosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jpq
TitleCryo-EM structure of the 90S pre-ribosome
Components
  • (WD40 domain proteins) x 2
  • 18S ribosomal RNA
  • Bms1
  • Emg1
  • Imp3
  • KRR1 small subunit processome component
  • Kre33
  • Nop1
  • Pre mRNA splicing protein
  • Putative U3 small nucleolar ribonucleoprotein
  • Rcl1
  • Snu13NHP2L1
  • U3 RNA
  • U3 small nucleolar RNA-associated protein 21
  • UTP-A oligomerization domain
  • UTP-B oligomerisation domain
  • UTP10
  • UTP6
  • Utp24
  • Utp30
  • eS1
  • eS24
  • eS28
  • eS4
  • eS6
  • eS7
  • eS8
  • rrp9
  • uS11
  • uS15
  • uS17
  • uS4
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / nuclear RNP
Function / homology
Function and homology information


tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / nuclear microtubule / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA modification / box C/D sno(s)RNA 3'-end processing ...tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / nuclear microtubule / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA modification / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / rRNA base methylation / rRNA primary transcript binding / ribonuclease P activity / tRNA 5'-leader removal / N-acetyltransferase activity / rRNA methylation / U3 snoRNA binding / : / tRNA processing / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / enzyme activator activity / 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) / regulation of translational fidelity / RNA nuclease activity / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA endonuclease activity / Transferases; Transferring one-carbon groups; Methyltransferases / nuclear periphery / small-subunit processome / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / rRNA processing / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome biogenesis / small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / GTPase activity / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Archaeal Nop5/56-rel, N-terminal domain / : / : / : / KRR1 small subunit processome component, second KH domain / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain ...: / : / Archaeal Nop5/56-rel, N-terminal domain / : / : / : / KRR1 small subunit processome component, second KH domain / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / Helicase / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / Ribosomal RNA assembly KRR1 / rRNA-processing protein Fcf1, PIN domain / Ribosomal RNA-processing protein Rrp9-like / rRNA-processing protein Fcf1/Utp23 / Fcf1 / BP28, C-terminal domain / RNA 3'-terminal phosphate cyclase-like, conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosome biogenesis protein Bms1, N-terminal / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / RNA 3'-terminal phosphate cyclase signature. / BP28CT (NUC211) domain / Small-subunit processome, Utp21 / RNA 3'-terminal phosphate cyclase type 2 / Utp21 specific WD40 associated putative domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Nucleolar protein Nop56/Nop58 / Krr1, KH1 domain / Krr1 KH1 domain / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / U3 snoRNP protein/Ribosome production factor 1 / Large family of predicted nucleotide-binding domains / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / AARP2CN (NUC121) domain / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN (NUC121) domain / Protein of unknown function (DUF663) / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / PIN domain / Ribosomal protein L7Ae, archaea / Brix domain / Brix domain / Brix domain profile. / Brix / Anaphase-promoting complex subunit 4, WD40 domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Anaphase-promoting complex subunit 4 WD40 domain / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / K Homology domain, type 1 superfamily / PIN-like domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S3Ae, conserved site / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / Ribosomal protein S8e
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / C/D box methylation guide ribonucleoprotein complex aNOP56 subunit / 40S ribosomal protein S6 / RNA cytidine acetyltransferase / KRR1 small subunit processome component / U3 small nucleolar RNA-associated protein 10 / Uncharacterized protein ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / C/D box methylation guide ribonucleoprotein complex aNOP56 subunit / 40S ribosomal protein S6 / RNA cytidine acetyltransferase / KRR1 small subunit processome component / U3 small nucleolar RNA-associated protein 10 / Uncharacterized protein / Uncharacterized protein / PIN domain-containing protein / U3 small nucleolar ribonucleoprotein protein IMP4 / 40S ribosomal protein S24 / 40S ribosomal protein S7 / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein eL8 / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / RNA 3'-terminal phosphate cyclase-like protein / Ribosome biogenesis protein BMS1 / 40S ribosomal protein S8 / 40S ribosomal protein S11, putative / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS28A
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsTurk, M. / Cheng, J. / Berninghausen, O. / Kornprobst, M. / Flemming, D. / Kos-Braun, I.C. / Kos, M. / Thoms, M. / Hurt, E. / Beckmann, R.
CitationJournal: Cell / Year: 2016
Title: Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome.
Authors: Markus Kornprobst / Martin Turk / Nikola Kellner / Jingdong Cheng / Dirk Flemming / Isabelle Koš-Braun / Martin Koš / Matthias Thoms / Otto Berninghausen / Roland Beckmann / Ed Hurt /
Abstract: The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that ...The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome, revealing how a network of biogenesis factors including 19 β-propellers and large α-solenoid proteins engulfs the pre-rRNA. Within the 90S pre-ribosome, we identify the UTP-A, UTP-B, Mpp10-Imp3-Imp4, Bms1-Rcl1, and U3 snoRNP modules, which are organized around 5'-ETS and partially folded 18S rRNA. The U3 snoRNP is strategically positioned at the center of the 90S particle to perform its multiple tasks during pre-rRNA folding and processing. The architecture of the elusive 90S pre-ribosome gives unprecedented structural insight into the early steps of pre-rRNA maturation. Nascent rRNA that is co-transcriptionally folded and given a particular shape by encapsulation within a dedicated mold-like structure is reminiscent of how polypeptides use chaperone chambers for their protein folding.
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Other
Revision 1.2Jul 5, 2017Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: em_image_scans / ndb_struct_na_base_pair ...em_image_scans / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.4Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.5Jan 23, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact ...pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.6Mar 11, 2020Group: Source and taxonomy / Category: entity_src_nat / Item: _entity_src_nat.pdbx_ncbi_taxonomy_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-8143
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8143
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: WD40 domain proteins
B: WD40 domain proteins
C: WD40 domain proteins
D: WD40 domain proteins
E: WD40 domain proteins
F: WD40 domain proteins
G: UTP10
H: UTP-A oligomerization domain
I: U3 small nucleolar RNA-associated protein 21
J: WD40 domain proteins
K: WD40 domain proteins
L: WD40 domain proteins
M: WD40 domain proteins
N: WD40 domain proteins
O: WD40 domain proteins
P: WD40 domain proteins
Q: UTP6
R: UTP-B oligomerisation domain
S: Pre mRNA splicing protein
T: Pre mRNA splicing protein
U: Snu13
V: Snu13
W: Nop1
X: Nop1
Y: rrp9
Z: Rcl1
a: Bms1
b: Imp3
c: Putative U3 small nucleolar ribonucleoprotein
d: Utp24
e: Emg1
f: Emg1
g: KRR1 small subunit processome component
h: KRR1 small subunit processome component
i: Kre33
j: Kre33
k: Utp30
l: WD40 domain proteins
m: WD40 domain proteins
n: WD40 domain proteins
o: eS1
p: eS4
q: uS7
r: eS6
s: eS7
t: eS8
u: uS4
v: uS15
w: uS11
x: uS9
y: uS17
z: uS8
0: eS24
1: eS28
2: 18S ribosomal RNA
3: U3 RNA


Theoretical massNumber of molelcules
Total (without water)3,984,52656
Polymers3,984,52656
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
Protein , 34 types, 54 molecules ABCDEFJKLNPlnGHIMOmQRSTUVWXYZa...

#1: Protein
WD40 domain proteins


Mass: 109801.734 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)
#2: Protein UTP10


Mass: 198508.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S5L1
#3: Protein UTP-A oligomerization domain


Mass: 78313.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)
#4: Protein U3 small nucleolar RNA-associated protein 21 / U3 snoRNA-associated protein 21 / U three protein 21


Mass: 104927.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q06078
#5: Protein WD40 domain proteins


Mass: 74058.758 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)
#6: Protein UTP6 /


Mass: 38825.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)
#7: Protein UTP-B oligomerisation domain


Mass: 47676.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)
#8: Protein Pre mRNA splicing protein


Mass: 46765.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: A0A0E3MJI1*PLUS
#9: Protein Snu13 / NHP2L1


Mass: 14074.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P55858*PLUS
#10: Protein Nop1


Mass: 26455.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P58032*PLUS
#11: Protein rrp9 /


Mass: 65146.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q06506*PLUS
#12: Protein Rcl1 /


Mass: 40220.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q08096*PLUS
#13: Protein Bms1


Mass: 135792.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q08965*PLUS
#14: Protein Imp3 /


Mass: 21802.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SDL4
#15: Protein Putative U3 small nucleolar ribonucleoprotein


Mass: 34216.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum / References: UniProt: G0SE90
#16: Protein Utp24


Mass: 21103.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SE30
#17: Protein Emg1 /


Mass: 27936.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q06287*PLUS
#18: Protein KRR1 small subunit processome component / / KRR-R motif-containing protein 1


Mass: 37500.777 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S3V7
#19: Protein Kre33


Mass: 119795.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S273
#20: Protein Utp30


Mass: 43700.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S7X0
#21: Protein eS1


Mass: 29709.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q23DE3*PLUS
#22: Protein eS4


Mass: 29512.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P0C233*PLUS
#23: Protein uS7


Mass: 25072.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P26783*PLUS
#24: Protein eS6


Mass: 32614.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: A4VD76*PLUS
#25: Protein eS7


Mass: 23231.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: I7MD19*PLUS
#26: Protein eS8


Mass: 24250.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q22AV0*PLUS
#27: Protein uS4


Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: O13516*PLUS
#28: Protein uS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P05756*PLUS
#29: Protein uS11


Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P06367*PLUS
#30: Protein uS9


Mass: 15877.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P0CX51*PLUS
#31: Protein uS17


Mass: 18142.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q22B78*PLUS
#32: Protein uS8


Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P0C0W1*PLUS
#33: Protein eS24


Mass: 17128.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: I7MAL3*PLUS
#34: Protein eS28


Mass: 7605.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: Q3E7X9*PLUS

-
RNA chain , 2 types, 2 molecules 23

#35: RNA chain 18S ribosomal RNA /


Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)
#36: RNA chain U3 RNA


Mass: 87969.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: 90s pre-ribosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Chaetomium thermophilum (fungus)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 16 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43000 / Symmetry type: POINT

+
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