[English] 日本語
Yorodumi
- PDB-5mgp: Structural basis for ArfA-RF2 mediated translation termination on... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5mgp
TitleStructural basis for ArfA-RF2 mediated translation termination on stop-codon lacking mRNAs
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Alternative ribosome-rescue factor A
  • P-site tRNA
  • Peptide chain release factor 2
  • mRNAMessenger RNA
KeywordsRIBOSOME / Cryo-Em / Ribosome / Termination / alternative rescue factor A
Function / homologyRibosomal protein L13, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L15 ...Ribosomal protein L13, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L15 / Ribosomal L18e/L15P superfamily / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L31 type A / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein L28/L24 / Ribosomal protein S16 domain superfamily / L21-like superfamily / Ribosomal protein L17 superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein S21 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S19, superfamily / Ribosomal protein L19 superfamily / Ribosomal protein S13, bacterial-type / Ribosomal protein L9, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25, short-form / Ribosomal protein L6, alpha-beta domain / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S16, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein L35 / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L18e/L15P / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L34, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L16, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein L33 superfamily / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L16 signature 1. / PCRF domain / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / KH domain / Ribosomal protein L9, C-terminal domain / Ribosomal Proteins L2, C-terminal domain / Domain of unknown function / Ribosomal protein S5, C-terminal domain / Ribosomal L32p protein family / Ribosomal protein S7 signature. / Ribosomal protein S20 / Ribosomal protein L35 / S4 domain / Ribosomal L25p family / Ribosomal protein L9, N-terminal domain / Ribosomal protein S6
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.1 Å resolution
AuthorsHuter, P. / Mueller, C. / Beckert, B. / Arenz, S. / Berninghausen, O. / Beckmann, R. / Wilson, N.D.
CitationJournal: Nature / Year: 2017
Title: Structural basis for ArfA-RF2-mediated translation termination on mRNAs lacking stop codons.
Authors: Paul Huter / Claudia Müller / Bertrand Beckert / Stefan Arenz / Otto Berninghausen / Roland Beckmann / Daniel N Wilson
Abstract: In bacteria, ribosomes stalled on truncated mRNAs that lack a stop codon are rescued by the transfer-messenger RNA (tmRNA), alternative rescue factor A (ArfA) or ArfB systems. Although tmRNA-ribosome ...In bacteria, ribosomes stalled on truncated mRNAs that lack a stop codon are rescued by the transfer-messenger RNA (tmRNA), alternative rescue factor A (ArfA) or ArfB systems. Although tmRNA-ribosome and ArfB-ribosome structures have been determined, how ArfA recognizes the presence of truncated mRNAs and recruits the canonical termination release factor RF2 to rescue the stalled ribosomes is unclear. Here we present a cryo-electron microscopy reconstruction of the Escherichia coli 70S ribosome stalled on a truncated mRNA in the presence of ArfA and RF2. The structure shows that the C terminus of ArfA binds within the mRNA entry channel on the small ribosomal subunit, and explains how ArfA distinguishes between ribosomes that bear truncated or full-length mRNAs. The N terminus of ArfA establishes several interactions with the decoding domain of RF2, and this finding illustrates how ArfA recruits RF2 to the stalled ribosome. Furthermore, ArfA is shown to stabilize a unique conformation of the switch loop of RF2, which mimics the canonical translation termination state by directing the catalytically important GGQ motif within domain 3 of RF2 towards the peptidyl-transferase centre of the ribosome. Thus, our structure reveals not only how ArfA recruits RF2 to the ribosome but also how it promotes an active conformation of RF2 to enable translation termination in the absence of a stop codon.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 21, 2016 / Release: Dec 14, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 14, 2016Structure modelrepositoryInitial release
1.1Feb 8, 2017Structure modelDatabase references
1.2Aug 30, 2017Structure modelAuthor supporting evidence / Data collection / Derived calculationsem_image_scans / em_software / pdbx_audit_support / struct_conn_em_software.name / _pdbx_audit_support.funding_organization

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3508
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-3508
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 23S ribosomal RNA
B: 5S ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
6: 50S ribosomal protein L31
a: 16S ribosomal RNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
u: 30S ribosomal protein S21
v: mRNA
w: Alternative ribosome-rescue factor A
x: P-site tRNA
z: Peptide chain release factor 2


Theoretical massNumber of molelcules
Total (without water)2,184,50556
Polyers2,184,50556
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)267710
ΔGint (kcal/M)-2270
Surface area (Å2)794370
MethodPISA

-
Components

-
RNA chain , 5 types, 5 molecules ABavx

#1: RNA chain 23S ribosomal RNA /


Mass: 941305.250 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank:802133627
#2: RNA chain 5S ribosomal RNA /


Mass: 38813.133 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank:1028480521
#32: RNA chain 16S ribosomal RNA /


Mass: 498725.406 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank:802133627
#53: RNA chain mRNA / Messenger RNA


Mass: 1866.181 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#55: RNA chain P-site tRNA


Mass: 24846.746 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: GenBank:1052521625

+
50S ribosomal protein ... , 29 types, 29 molecules CDEFGHJKLMNOPQRSTUVWXYZ012346

#3: Protein/peptide 50S ribosomal protein L2 /


Mass: 29663.244 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P60422
#4: Protein/peptide 50S ribosomal protein L3 /


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P60438
#5: Protein/peptide 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P60723
#6: Protein/peptide 50S ribosomal protein L5 /


Mass: 20073.234 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P62399
#7: Protein/peptide 50S ribosomal protein L6 /


Mass: 18801.598 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0AG55
#8: Protein/peptide 50S ribosomal protein L9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7R1
#9: Protein/peptide 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0AA10
#10: Protein/peptide 50S ribosomal protein L14 /


Mass: 13451.910 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0ADY3
#11: Protein/peptide 50S ribosomal protein L15 /


Mass: 14877.273 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P02413
#12: Protein/peptide 50S ribosomal protein L16 /


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0ADY7
#13: Protein/peptide 50S ribosomal protein L17 /


Mass: 13721.938 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0AG44
#14: Protein/peptide 50S ribosomal protein L18 /


Mass: 12663.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0C018
#15: Protein/peptide 50S ribosomal protein L19 /


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7K6
#16: Protein/peptide 50S ribosomal protein L20 /


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7L3
#17: Protein/peptide 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0AG48
#18: Protein/peptide 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P61175
#19: Protein/peptide 50S ribosomal protein L23 /


Mass: 10546.472 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0ADZ0
#20: Protein/peptide 50S ribosomal protein L24 /


Mass: 11078.874 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P60624
#21: Protein/peptide 50S ribosomal protein L25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P68919
#22: Protein/peptide 50S ribosomal protein L27 /


Mass: 8174.394 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7L8
#23: Protein/peptide 50S ribosomal protein L28 /


Mass: 8896.354 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7M2
#24: Protein/peptide 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7M6
#25: Protein/peptide 50S ribosomal protein L30 /


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0AG51
#26: Protein/peptide 50S ribosomal protein L32 /


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7N4
#27: Protein/peptide 50S ribosomal protein L33 /


Mass: 5814.842 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7N9
#28: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7P5
#29: Protein/peptide 50S ribosomal protein L35 / / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7Q1
#30: Protein/peptide 50S ribosomal protein L36 / / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7Q6
#31: Protein/peptide 50S ribosomal protein L31 /


Mass: 7516.693 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7M9

+
30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu

#33: Protein/peptide 30S ribosomal protein S2 /


Mass: 24253.943 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7V0
#34: Protein/peptide 30S ribosomal protein S3 /


Mass: 23078.785 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7V3
#35: Protein/peptide 30S ribosomal protein S4 /


Mass: 23383.002 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7V8
#36: Protein/peptide 30S ribosomal protein S5 /


Mass: 16532.088 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7W1
#37: Protein/peptide 30S ribosomal protein S6 /


Mass: 11669.371 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P02358
#38: Protein/peptide 30S ribosomal protein S7 /


Mass: 16861.523 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P02359
#39: Protein/peptide 30S ribosomal protein S8 /


Mass: 14015.361 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7W7
#40: Protein/peptide 30S ribosomal protein S9 /


Mass: 14554.882 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7X3
#41: Protein/peptide 30S ribosomal protein S10 /


Mass: 11196.988 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7R5
#42: Protein/peptide 30S ribosomal protein S11 /


Mass: 12388.068 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7R9
#43: Protein/peptide 30S ribosomal protein S12 /


Mass: 13636.961 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7S3
#44: Protein/peptide 30S ribosomal protein S13 /


Mass: 12625.753 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7S9
#45: Protein/peptide 30S ribosomal protein S14 /


Mass: 11546.442 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0AG59
#46: Protein/peptide 30S ribosomal protein S15 /


Mass: 10159.621 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0ADZ4
#47: Protein/peptide 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7T3
#48: Protein/peptide 30S ribosomal protein S17 /


Mass: 9263.946 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0AG63
#49: Protein/peptide 30S ribosomal protein S18 /


Mass: 7606.768 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7T7
#50: Protein/peptide 30S ribosomal protein S19 /


Mass: 9057.626 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7U3
#51: Protein/peptide 30S ribosomal protein S20 /


Mass: 9506.190 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P0A7U7
#52: Protein/peptide 30S ribosomal protein S21 /


Mass: 7763.073 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt:P68679

-
Protein/peptide , 2 types, 2 molecules wz

#54: Protein/peptide Alternative ribosome-rescue factor A /


Mass: 5265.089 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: arfA, yhdL, b4550, JW3253 / Production host: Escherichia coli (E. coli) / References: UniProt:P36675
#56: Protein/peptide Peptide chain release factor 2 / RF-2


Mass: 40566.781 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: prfB, supK, b2891, JW5847 / Production host: Escherichia coli (E. coli) / References: UniProt:P07012

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Structural basis for ArfA-RF2 mediated translation termination 1 on stop-codon lacking mRNAsRIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 560MULTIPLE SOURCES
2ribosomeRIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 551NATURAL
3mRNA, tRNA, Peptide chain release factor 2RIBOSOME53, 54, 561RECOMBINANT
Molecular weightValue: 2.5 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
11562Escherichia coli (E. coli)
22562Escherichia coli (E. coli)
33562Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2
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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 302 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

EM softwareName: FREALIGN / Version: 9.11 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 69089 / Symmetry type: POINT

+
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.
  • All the functionalities will be ported from the levgacy version.
  • 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