[English] 日本語
Yorodumi
- PDB-7oif: CspA-27 cotranslational folding intermediate 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7oif
TitleCspA-27 cotranslational folding intermediate 2
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • CspA transcriptional activator
  • mRNAMessenger RNA
  • tRNA-Ser
KeywordsRIBOSOME / cotranslational folding / CspA27-2
Function / homology
Function and homology information


endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / polysomal ribosome / ribosome assembly / DNA-templated transcription, termination / ribosomal small subunit assembly / large ribosomal subunit rRNA binding ...endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / polysomal ribosome / ribosome assembly / DNA-templated transcription, termination / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / response to radiation / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / negative regulation of transcription, DNA-templated / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein L31 type A / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 superfamily ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein L31 type A / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L31 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L28 / Ribosomal protein L9 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19 signature. / Ribosomal protein L34 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L36 / Ribosomal protein S2 signature 2. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6 signature. / Ribosomal protein S6, conserved site / Ribosomal protein S3, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S13, bacterial-type / Ribosomal L28 family / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S4, bacterial-type / Ribosomal protein L33 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L18 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L16 / L28p-like / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal L32p protein family / Ribosomal protein S15, bacterial-type / Ribosomal protein L30, bacterial-type / Ribosomal protein L34 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L34 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L21 / Ribosomal protein L19 superfamily / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein S6
Similarity search - Domain/homology
50S ribosomal protein L14 / 50S ribosomal protein L27 / 50S ribosomal protein L29 / 30S ribosomal protein S13 / 50S ribosomal protein L19 / 30S ribosomal protein S20 / 30S ribosomal protein S7 / 50S ribosomal protein L15 / 50S ribosomal protein L34 / 50S ribosomal protein L36 ...50S ribosomal protein L14 / 50S ribosomal protein L27 / 50S ribosomal protein L29 / 30S ribosomal protein S13 / 50S ribosomal protein L19 / 30S ribosomal protein S20 / 30S ribosomal protein S7 / 50S ribosomal protein L15 / 50S ribosomal protein L34 / 50S ribosomal protein L36 / 50S ribosomal protein L9 / 50S ribosomal protein L13 / 30S ribosomal protein S4 / 50S ribosomal protein L16 / 50S ribosomal protein L21 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L25 / 50S ribosomal protein L23 / : / 30S ribosomal protein S8 / 30S ribosomal protein S5 / 30S ribosomal protein S17 / 30S ribosomal protein S12 / 30S ribosomal protein S18 / : / 50S ribosomal protein L32 / 30S ribosomal protein S2 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S10 / 50S ribosomal protein L17 / 50S ribosomal protein L33 / 50S ribosomal protein L30 / 30S ribosomal protein S14 / 30S ribosomal protein S3 / 50S ribosomal protein L31 / 50S ribosomal protein L5 / 50S ribosomal protein L28 / 30S ribosomal protein S11 / 30S ribosomal protein S9 / : / 30S ribosomal protein S6 / 30S ribosomal protein S16 / 30S ribosomal protein S21 / 30S ribosomal protein S15 / 50S ribosomal protein L18 / 50S ribosomal protein L24 / 30S ribosomal protein S19 / : / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli LAU-EC10 (bacteria)
Escherichia coli M114 (bacteria)
Escherichia coli KTE73 (bacteria)
Escherichia coli H736 (bacteria)
Escherichia coli 2.3916 (bacteria)
Escherichia coli O145:NM (bacteria)
Escherichia coli DEC1D (bacteria)
Escherichia coli TA447 (bacteria)
Escherichia coli 99.0741 (bacteria)
Escherichia coli UMEA 3718-1 (bacteria)
Escherichia coli 2-427-07_S4_C3 (bacteria)
Escherichia coli H591 (bacteria)
Escherichia coli DEC1B (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsAgirrezabala, X. / Samatova, E. / Macher, M. / Liutkute, M. / Gil-Carton, D. / Novacek, J. / Valle, M. / Rodnina, M.V.
Funding support Spain, European Union, 3items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)CTQ2015-73560-JIN Spain
European Research Council (ERC)787926European Union
Ministry of Economy and Competitiveness (MINECO)PGC2018-098996-B-I00 Spain
CitationJournal: EMBO J / Year: 2022
Title: A switch from α-helical to β-strand conformation during co-translational protein folding.
Authors: Xabier Agirrezabala / Ekaterina Samatova / Meline Macher / Marija Liutkute / Manisankar Maiti / David Gil-Carton / Jiri Novacek / Mikel Valle / Marina V Rodnina /
Abstract: Cellular proteins begin to fold as they emerge from the ribosome. The folding landscape of nascent chains is not only shaped by their amino acid sequence but also by the interactions with the ...Cellular proteins begin to fold as they emerge from the ribosome. The folding landscape of nascent chains is not only shaped by their amino acid sequence but also by the interactions with the ribosome. Here, we combine biophysical methods with cryo-EM structure determination to show that folding of a β-barrel protein begins with formation of a dynamic α-helix inside the ribosome. As the growing peptide reaches the end of the tunnel, the N-terminal part of the nascent chain refolds to a β-hairpin structure that remains dynamic until its release from the ribosome. Contacts with the ribosome and structure of the peptidyl transferase center depend on nascent chain conformation. These results indicate that proteins may start out as α-helices inside the tunnel and switch into their native folds only as they emerge from the ribosome. Moreover, the correlation of nascent chain conformations with reorientation of key residues of the ribosomal peptidyl-transferase center suggest that protein folding could modulate ribosome activity.
History
DepositionMay 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-12928
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: 23S rRNA
2: 16S rRNA
3: 5S rRNA
4: mRNA
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
I: 50S ribosomal protein L13
J: 50S ribosomal protein L14
K: 50S ribosomal protein L15
L: 50S ribosomal protein L16
M: 50S ribosomal protein L17
N: 50S ribosomal protein L18
O: 50S ribosomal protein L19
P: 50S ribosomal protein L20
Q: 50S ribosomal protein L21
R: 50S ribosomal protein L22
S: 50S ribosomal protein L23
T: 50S ribosomal protein L24
U: 50S ribosomal protein L25
V: 50S ribosomal protein L27
W: 50S ribosomal protein L28
X: 50S ribosomal protein L29
Y: 50S ribosomal protein L30
Z: 50S ribosomal protein L31
a: 50S ribosomal protein L32
b: 50S ribosomal protein L33
c: 50S ribosomal protein L34
d: 50S ribosomal protein L35
e: 50S ribosomal protein L36
f: 30S ribosomal protein S2
g: 30S ribosomal protein S3
h: 30S ribosomal protein S4
i: 30S ribosomal protein S5
j: 30S ribosomal protein S6
k: 30S ribosomal protein S7
l: 30S ribosomal protein S8
m: 30S ribosomal protein S9
n: 30S ribosomal protein S10
o: 30S ribosomal protein S11
p: 30S ribosomal protein S12
q: 30S ribosomal protein S13
r: 30S ribosomal protein S14
s: 30S ribosomal protein S15
t: 30S ribosomal protein S16
u: 30S ribosomal protein S17
v: 30S ribosomal protein S18
w: 30S ribosomal protein S19
x: 30S ribosomal protein S20
y: 30S ribosomal protein S21
z: tRNA-Ser
B: CspA transcriptional activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,158,020473
Polymers2,147,77955
Non-polymers10,242418
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
RNA chain , 5 types, 5 molecules 1234z

#1: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 941526.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: RNA chain 16S rRNA


Mass: 497404.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1108570162
#3: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38790.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: CP035706.1
#4: RNA chain mRNA / Messenger RNA


Mass: 1868.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#54: RNA chain tRNA-Ser


Mass: 28464.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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

#5: Protein 50S ribosomal protein L2 / / Large ribosomal subunit protein uL2


Mass: 29663.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplB / Production host: Escherichia coli (E. coli) / References: UniProt: P60422
#6: Protein 50S ribosomal protein L3 / / ribosomal protein uL3


Mass: 22277.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P60438
#7: Protein 50S ribosomal protein L4 / / ribosomal protein uL4


Mass: 22121.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P60723
#8: Protein 50S ribosomal protein L5 /


Mass: 20073.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplE / Production host: Escherichia coli (E. coli) / References: UniProt: H4IXW7
#9: Protein 50S ribosomal protein L6 /


Mass: 18672.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli LAU-EC10 (bacteria) / Gene: rplF, V415_19070 / Production host: Escherichia coli (E. coli) / References: UniProt: V8K235
#10: Protein 50S ribosomal protein L9 / / ribosomal protein bL9


Mass: 15789.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R1
#11: Protein 50S ribosomal protein L13 / / ribosomal protein uL13


Mass: 16050.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA10
#12: Protein 50S ribosomal protein L14 / / ribosomal protein uL14


Mass: 13565.067 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADY3
#13: Protein 50S ribosomal protein L15 / / ribosomal protein uL15


Mass: 15008.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P02413
#14: Protein 50S ribosomal protein L16 / / ribosomal protein uL16


Mass: 15312.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADY7
#15: Protein 50S ribosomal protein L17 /


Mass: 13592.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli M114 (bacteria) / Gene: rplQ, ERYG_01882 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K9TEC5
#16: Protein 50S ribosomal protein L18 /


Mass: 12663.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplR / Production host: Escherichia coli (E. coli) / References: UniProt: F4SQ31
#17: Protein 50S ribosomal protein L19 /


Mass: 13028.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplS / Production host: Escherichia coli (E. coli) / References: UniProt: I2XAW2
#18: Protein 50S ribosomal protein L20 /


Mass: 13396.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplT / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7B6WTL0
#19: Protein 50S ribosomal protein L21 / / ribosomal protein bL21


Mass: 11586.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG48
#20: Protein 50S ribosomal protein L22 / / ribosomal protein uL22


Mass: 12253.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P61175
#21: Protein 50S ribosomal protein L23 /


Mass: 10661.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli KTE73 (bacteria) / Gene: rplW, A1UI_03591 / Production host: Escherichia coli (E. coli) / References: UniProt: S1EUY1
#22: Protein 50S ribosomal protein L24 /


Mass: 11208.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli H736 (bacteria) / Gene: rplX, ECHG_03175 / Production host: Escherichia coli (E. coli) / References: UniProt: F4SQ36
#23: Protein 50S ribosomal protein L25 / / ribosomal protein bL25


Mass: 10713.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P68919
#24: Protein 50S ribosomal protein L27 /


Mass: 8547.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 2.3916 (bacteria) / Gene: rpmA, EC23916_1043 / Production host: Escherichia coli (E. coli) / References: UniProt: I2X5R7
#25: Protein 50S ribosomal protein L28 /


Mass: 8896.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B7P765
#26: Protein 50S ribosomal protein L29 /


Mass: 7155.267 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 2.3916 (bacteria) / Gene: rpmC, EC23916_1173 / Production host: Escherichia coli (E. coli) / References: UniProt: I2X6R6
#27: Protein 50S ribosomal protein L30 /


Mass: 6423.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3K2S4
#28: Protein 50S ribosomal protein L31 /


Mass: 7516.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O145:NM (bacteria) / Gene: rpmE, CCU01_028900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P8CB21
#29: Protein 50S ribosomal protein L32 /


Mass: 6332.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DEC1D (bacteria) / Gene: rpmF, ECDEC1D_1598 / Production host: Escherichia coli (E. coli) / References: UniProt: H4J6G2
#30: Protein 50S ribosomal protein L33 /


Mass: 6057.179 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli TA447 (bacteria) / Gene: rpmG, ECXG_02476 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3IVN5
#31: Protein/peptide 50S ribosomal protein L34 / / ribosomal protein bL34


Mass: 5397.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7P5
#32: Protein 50S ribosomal protein L35 /


Mass: 7181.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 99.0741 (bacteria) / Gene: rpmI, EC970259_2017 / Production host: Escherichia coli (E. coli) / References: UniProt: V6FQE4
#33: Protein/peptide 50S ribosomal protein L36 / / Ribosomal protein B / ribosomal protein bL36


Mass: 4377.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Q6

-
30S ribosomal protein ... , 20 types, 20 molecules fghijklmnopqrstuvwxy

#34: Protein 30S ribosomal protein S2 /


Mass: 25072.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsB, D9J46_02895 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3K3SDJ5
#35: Protein 30S ribosomal protein S3 /


Mass: 23248.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsC, G4V09_06545, NCTC9094_00425 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A376HTV6
#36: Protein 30S ribosomal protein S4 /


Mass: 23383.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsD / Production host: Escherichia coli (E. coli) / References: UniProt: V0YKB3
#37: Protein 30S ribosomal protein S5 /


Mass: 16475.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli UMEA 3718-1 (bacteria)
Gene: rpsE, G994_03521 / Production host: Escherichia coli (E. coli) / References: UniProt: T9SGC3
#38: Protein 30S ribosomal protein S6 /


Mass: 12125.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: D9J60_11985 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J9U446
#39: Protein 30S ribosomal protein S7 / / Small ribosomal subunit protein uS7


Mass: 16861.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsG / Production host: Escherichia coli (E. coli) / References: UniProt: P02359
#40: Protein 30S ribosomal protein S8 /


Mass: 14015.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsH / Production host: Escherichia coli (E. coli) / References: UniProt: H4JDM0
#41: Protein 30S ribosomal protein S9 /


Mass: 14554.882 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsI / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L7FQ03
#42: Protein 30S ribosomal protein S10 /


Mass: 11254.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 2-427-07_S4_C3 (bacteria)
Gene: rpsJ, AD31_3986 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A073G203
#43: Protein 30S ribosomal protein S11 /


Mass: 12487.200 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsK / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5I5F5V9
#44: Protein 30S ribosomal protein S12 /


Mass: 13683.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 99.0741 (bacteria) / Gene: rpsL, EC970259_3994 / Production host: Escherichia coli (E. coli) / References: UniProt: V6FZ95
#45: Protein 30S ribosomal protein S13 /


Mass: 12868.091 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 2.3916 (bacteria) / Gene: rpsM, EC23916_1158 / Production host: Escherichia coli (E. coli) / References: UniProt: I2X719
#46: Protein 30S ribosomal protein S14 /


Mass: 11475.364 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsN / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3K3H0
#47: Protein 30S ribosomal protein S15 /


Mass: 10159.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsO / Production host: Escherichia coli (E. coli) / References: UniProt: E9YUR8
#48: Protein 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsP / Production host: Escherichia coli (E. coli) / References: UniProt: C3SYP2
#49: Protein 30S ribosomal protein S17 /


Mass: 9263.946 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsQ / Production host: Escherichia coli (E. coli) / References: UniProt: T6LV72
#50: Protein 30S ribosomal protein S18 /


Mass: 7734.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsR / Production host: Escherichia coli (E. coli) / References: UniProt: I2SQR9
#51: Protein 30S ribosomal protein S19 /


Mass: 9421.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli H591 (bacteria) / Gene: rpsS, ECPG_02636 / Production host: Escherichia coli (E. coli) / References: UniProt: F4VJV7
#52: Protein 30S ribosomal protein S20 /


Mass: 9577.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsT / Production host: Escherichia coli (E. coli) / References: UniProt: I4T5W9
#53: Protein 30S ribosomal protein S21 /


Mass: 8392.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsU / Production host: Escherichia coli (E. coli) / References: UniProt: E9TH65

-
Protein/peptide , 1 types, 1 molecules B

#55: Protein/peptide CspA transcriptional activator


Mass: 2938.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DEC1B (bacteria) / Gene: cspA, ECDEC1B_4216 / Production host: Escherichia coli (E. coli) / References: UniProt: H4IHP6

-
Non-polymers , 2 types, 418 molecules

#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 416 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 70S-CspA27-2 / Type: RIBOSOME / Entity ID: #1-#55 / Source: MULTIPLE SOURCES
Molecular weightValue: 2.5 MDa / Experimental value: NO
Buffer solutionpH: 7.5
Details: 50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 8 mM putrescine, 0.5 mM spermidine, 1 mM DTT, 1 mM GTP, pH 7.5
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 278 K

-
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2.2 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1Gautomatch0.53particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
5RELION3.07CTF correction
8UCSF Chimera1.13.1model fitting
9Coot0.9model fitting
11RELION3.07initial Euler assignment
12RELION3.07final Euler assignment
13RELION3.07classification
14RELION3.073D reconstruction
15PHENIX1.18model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44182 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: The software LocScale for model-based local density sharpening was used as implemented in the CCP-EM suite, version 1.3.0
Atomic model buildingPDB-ID: 6ORE

+
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