[English] 日本語
Yorodumi
- PDB-7uph: Structure of a ribosome with tethered subunits -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uph
TitleStructure of a ribosome with tethered subunits
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 27
  • 5S rRNA5S ribosomal RNA
  • Tethered rRNA
KeywordsRIBOSOME / Engineered / Tethered / Synthetic
Function / homology
Function and homology information


DnaA-L2 complex / : / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / ribosomal large subunit assembly ...DnaA-L2 complex / : / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L16 signature 1. ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal protein S15, bacterial-type / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein S2 signature 2. / Ribosomal L32p protein family / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein S12, bacterial-type
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / 50S ribosomal protein L33 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL36 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / 50S ribosomal protein L33 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL18 / 30S ribosomal protein S3 / Large ribosomal subunit protein uL5 / 30S ribosomal protein S21 / 50S ribosomal protein L30 / 50S ribosomal protein L4 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL17 / 30S ribosomal protein S14 / 50S ribosomal protein L24 / Large ribosomal subunit protein uL6 / : / : / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein uS15 / 50S ribosomal protein L29 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS12 / 30S ribosomal protein S4 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsKim, D.S. / Watkins, A. / Bidstrup, E. / Lee, J. / Topkar, V.V. / Kofman, C. / Schwarz, K.J. / Liu, Y. / Pintilie, G. / Roney, E. ...Kim, D.S. / Watkins, A. / Bidstrup, E. / Lee, J. / Topkar, V.V. / Kofman, C. / Schwarz, K.J. / Liu, Y. / Pintilie, G. / Roney, E. / Das, R. / Jewett, M.C.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1716766 United States
Other privateRGP0015/2017
Other privateW911NF-16-1-0372
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122579 United States
Citation
Journal: Nat Chem Biol / Year: 2022
Title: Three-dimensional structure-guided evolution of a ribosome with tethered subunits.
Authors: Do Soon Kim / Andrew Watkins / Erik Bidstrup / Joongoo Lee / Ved Topkar / Camila Kofman / Kevin J Schwarz / Yan Liu / Grigore Pintilie / Emily Roney / Rhiju Das / Michael C Jewett /
Abstract: RNA-based macromolecular machines, such as the ribosome, have functional parts reliant on structural interactions spanning sequence-distant regions. These features limit evolutionary exploration of ...RNA-based macromolecular machines, such as the ribosome, have functional parts reliant on structural interactions spanning sequence-distant regions. These features limit evolutionary exploration of mutant libraries and confound three-dimensional structure-guided design. To address these challenges, we describe Evolink (evolution and linkage), a method that enables high-throughput evolution of sequence-distant regions in large macromolecular machines, and library design guided by computational RNA modeling to enable exploration of structurally stable designs. Using Evolink, we evolved a tethered ribosome with a 58% increased activity in orthogonal protein translation and a 97% improvement in doubling times in SQ171 cells compared to a previously developed tethered ribosome, and reveal new permissible sequences in a pair of ribosomal helices with previously explored biological function. The Evolink approach may enable enhanced engineering of macromolecular machines for new and improved functions for synthetic biology.
#1: Journal: Protein Sci / Year: 2021
Title: UCSF ChimeraX: Structure visualization for researchers, educators, and developers.
Authors: Pettersen, E.F. / Goddard, T.D. / Huang, C.C. / Meng, E.C. / Couch, G.S. / Croll, T.I. / Morris, J.H. / Ferrin, T.E.
#2: Journal: Nat Methods / Year: 2017
Title: cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Authors: Punjani, A. / Rubinstein, J.L. / Fleet, D.J. / Brubaker, M.A.
#3: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 30S ribosomal protein S14
B: 30S ribosomal protein S15
C: 30S ribosomal protein S16
D: 30S ribosomal protein S17
E: 30S ribosomal protein S18
F: 30S ribosomal protein S19
G: 30S ribosomal protein S20
H: 30S ribosomal protein S21
I: Tethered rRNA
J: 5S rRNA
K: 50S ribosomal protein L2
L: 50S ribosomal protein L3
M: 50S ribosomal protein L4
N: 50S ribosomal protein L5
O: 50S ribosomal protein L6
R: 50S ribosomal protein L13
S: 50S ribosomal protein L14
T: 50S ribosomal protein L15
U: 50S ribosomal protein L16
V: 50S ribosomal protein L17
W: 30S ribosomal protein S2
X: 30S ribosomal protein S3
Y: 30S ribosomal protein S4
Z: 30S ribosomal protein S5
a: 30S ribosomal protein S6
b: 30S ribosomal protein S7
c: 30S ribosomal protein S8
d: 30S ribosomal protein S9
e: 30S ribosomal protein S10
f: 30S ribosomal protein S11
g: 30S ribosomal protein S12
h: 30S ribosomal protein S13
i: 50S ribosomal protein L32
j: 50S ribosomal protein L33
k: 50S ribosomal protein L34
l: 50S ribosomal protein L35
m: 50S ribosomal protein L36
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


Theoretical massNumber of molelcules
Total (without water)2,085,07449
Polymers2,085,07449
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

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

#1: 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, EC2875150_5460 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A829E173
#2: 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, HMPREF9536_02433 / Production host: Escherichia coli (E. coli) / References: UniProt: D7XN21
#3: 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
#4: 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, AC28_3826 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A080IK26
#5: Protein 30S ribosomal protein S18 /


Mass: 6466.477 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: W1EY92
#6: Protein 30S ribosomal protein S19 /


Mass: 9057.626 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsS, ECKIH15140_04691 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9LGZ0
#7: Protein 30S ribosomal protein S20 /


Mass: 9506.190 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: C3TRH7
#8: Protein 30S ribosomal protein S21 /


Mass: 6629.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsU, FWK02_18995 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C9AJ78
#21: Protein 30S ribosomal protein S2 / / Small ribosomal subunit protein uS2


Mass: 24971.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsB, b0169, JW0164 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V0
#22: Protein 30S ribosomal protein S3 /


Mass: 23078.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsC, NCTC9094_00425 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A376HTV6
#23: 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, A1UM_03988 / Production host: Escherichia coli (E. coli) / References: UniProt: L3PZ69
#24: Protein 30S ribosomal protein S5 /


Mass: 15804.282 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsE, ECJG_02962 / Production host: Escherichia coli (E. coli) / References: UniProt: F4TL26
#25: Protein 30S ribosomal protein S6 /


Mass: 11669.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsF, b4200, JW4158 / Production host: Escherichia coli (E. coli) / References: UniProt: P02358
#26: 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, b3341, JW3303 / Production host: Escherichia coli (E. coli) / References: UniProt: P02359
#27: 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, ECDEC2D_3910 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A828U358
#28: 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, HMPREF1599_00992 / Production host: Escherichia coli (E. coli) / References: UniProt: V0A2W7
#29: Protein 30S ribosomal protein S10 /


Mass: 11196.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsJ, NRG857_16455 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3EQD3
#30: Protein 30S ribosomal protein S11 / / Small ribosomal subunit protein uS11


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, b3297, JW3259 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R9
#31: 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 (E. coli) / Gene: rpsL, EC40522_4581 / Production host: Escherichia coli (E. coli) / References: UniProt: I2UHF1
#32: Protein 30S ribosomal protein S13 /


Mass: 12625.753 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsM, A13A_03621 / Production host: Escherichia coli (E. coli) / References: UniProt: S1P5F8

-
RNA chain , 2 types, 2 molecules IJ

#9: RNA chain Tethered rRNA


Mass: 1439279.875 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)
#10: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38177.762 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: 1266940032

+
50S ribosomal protein ... , 27 types, 27 molecules KLMNORSTUVijklmnopqrstuvwxy

#11: 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, b3317, JW3279 / Production host: Escherichia coli (E. coli) / References: UniProt: P60422
#12: Protein 50S ribosomal protein L3 / / Large ribosomal subunit 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) / Gene: rplC, b3320, JW3282 / Production host: Escherichia coli (E. coli) / References: UniProt: P60438
#13: Protein 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplD, ECMG_02584 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9FY55
#14: 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, CCU01_002520 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P8BX24
#15: Protein 50S ribosomal protein L6 /


Mass: 18801.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: G736_03813 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8E0IYC4
#16: Protein 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplM, A1UI_03510 / Production host: Escherichia coli (E. coli) / References: UniProt: S1EW51
#17: Protein 50S ribosomal protein L14 /


Mass: 13451.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplN, A13A_03633 / Production host: Escherichia coli (E. coli) / References: UniProt: S1NW45
#18: Protein 50S ribosomal protein L15 /


Mass: 15008.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplO / Production host: Escherichia coli (E. coli) / References: UniProt: A0A037Y8L6
#19: Protein 50S ribosomal protein L16 /


Mass: 15327.261 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplP, b3313, JW3275 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADY7
#20: Protein 50S ribosomal protein L17 /


Mass: 13721.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplQ, ECMP0215528_3804 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A829CNM8
#33: 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 (E. coli) / Gene: rpmF, ECDEC2D_1303 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A828UBL8
#34: Protein/peptide 50S ribosomal protein L33 /


Mass: 5814.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmG, AC28_4219 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A080IDV9
#35: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmH / Production host: Escherichia coli (E. coli) / References: UniProt: B7MGC4
#36: 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 (E. coli) / Gene: rpmI, ERFG_01622 / Production host: Escherichia coli (E. coli) / References: UniProt: E9XJC8
#37: Protein/peptide 50S ribosomal protein L36 /


Mass: 4377.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmJ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2L017
#38: 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, EAVG_03042 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3KXD9
#39: 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, A13A_02795 / Production host: Escherichia coli (E. coli) / References: UniProt: S1PSA3
#40: 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, A311_02335 / Production host: Escherichia coli (E. coli) / References: UniProt: L4J8J1
#41: Protein 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplU, V415_03715 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8E0K7J3
#42: Protein 50S ribosomal protein L22 / / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli / Gene: rplV, eryB, b3315, JW3277 / Production host: Escherichia coli (E. coli) / References: UniProt: P61175
#43: Protein 50S ribosomal protein L23 /


Mass: 10546.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplW, V415_19135 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8E0K1Q0
#44: Protein 50S ribosomal protein L24 /


Mass: 11078.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplX, EC90111_1965 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8E0FZY0
#45: Protein 50S ribosomal protein L25 /


Mass: 10713.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplY / Production host: Escherichia coli (E. coli) / References: UniProt: D7XH79
#46: Protein 50S ribosomal protein L27 /


Mass: 8174.394 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmA, ECVG_02038 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3JCC7
#47: 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, G925_03874 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2KZD0
#48: 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 (E. coli) / Gene: rpmC, HMPREF9540_02078 / Production host: Escherichia coli (E. coli) / References: UniProt: D7Y3D2
#49: 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, ECLG_01671 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9B9V2

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Ribosome with tethered subunits / Type: RIBOSOME / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingAverage exposure time: 1.35 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: UCSF ChimeraX / Version: 1.3/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM software
IDNameVersionCategory
1cryoSPARC3.1particle selection
2EPU2.8image acquisition
7UCSF Chimera1.16model fitting
11cryoSPARC3.1classification
12cryoSPARC3.13D reconstruction
19PHENIX1.20.1model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 102279
3D reconstructionResolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34852 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 4YBB

4ybb

+
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