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- PDB-7bl5: pre-50S-ObgE particle -

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Basic information

Entry
Database: PDB / ID: 7bl5
Titlepre-50S-ObgE particle
Components
  • (50S ribosomal protein ...) x 29
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • GTPase ObgE/CgtA
  • Ribosomal large subunit pseudouridine synthase D
  • Ribosomal silencing factor RsfS
  • UPF0307 protein YjgA
KeywordsRIBOSOME / pre-50S / ribosome biogenesis / ribosome assembly
Function / homology
Function and homology information


23S rRNA pseudouridine1911/1915/1917 synthase / guanyl ribonucleotide binding / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / dormancy process / pseudouridine synthase activity / negative regulation of ribosome biogenesis / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response ...23S rRNA pseudouridine1911/1915/1917 synthase / guanyl ribonucleotide binding / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / dormancy process / pseudouridine synthase activity / negative regulation of ribosome biogenesis / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / translational initiation / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / chromosome segregation / regulation of cell growth / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / response to radiation / mRNA 5'-UTR binding / ribosomal large subunit assembly / GDP binding / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / GTPase activity / negative regulation of DNA-templated transcription / GTP binding / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosome-associated, YjgA / PSPTO4464-like domain superfamily / Protein of unknown function (DUF615) / Pseudouridine synthase, RluC/RluD / Pseudouridine synthase, RluA-like, conserved site / Rlu family of pseudouridine synthase signature. / GTP1/OBG, conserved site / GTP1/OBG family signature. / OBG-type GTPase / Pseudouridine synthase, RsuA/RluA-like ...Ribosome-associated, YjgA / PSPTO4464-like domain superfamily / Protein of unknown function (DUF615) / Pseudouridine synthase, RluC/RluD / Pseudouridine synthase, RluA-like, conserved site / Rlu family of pseudouridine synthase signature. / GTP1/OBG, conserved site / GTP1/OBG family signature. / OBG-type GTPase / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / GTP1/OBG / Obg domain profile. / Ribosomal silencing factor during starvation / Protein Iojap/ribosomal silencing factor RsfS / Pseudouridine synthase, catalytic domain superfamily / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein L25, short-form / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Nucleotidyltransferase superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 signature. / 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 L11, N-terminal / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / 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 L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / 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 L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / 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 / L28p-like
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 ...GUANOSINE-5'-DIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL9 / UPF0307 protein YjgA / Large ribosomal subunit protein uL13 / Ribosomal silencing factor RsfS / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Ribosomal large subunit pseudouridine synthase D / GTPase ObgE/CgtA / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHilal, T. / Nikolay, R. / Spahn, C.M.T. / Schmidt, S.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR1805 Germany
German Research Foundation (DFG)SFB740 Germany
Human Frontier Science Program (HFSP)RPG0008/2014 Germany
CitationJournal: Mol Cell / Year: 2021
Title: Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization.
Authors: Rainer Nikolay / Tarek Hilal / Sabine Schmidt / Bo Qin / David Schwefel / Carlos H Vieira-Vieira / Thorsten Mielke / Jörg Bürger / Justus Loerke / Kazuaki Amikura / Timo Flügel / Takuya ...Authors: Rainer Nikolay / Tarek Hilal / Sabine Schmidt / Bo Qin / David Schwefel / Carlos H Vieira-Vieira / Thorsten Mielke / Jörg Bürger / Justus Loerke / Kazuaki Amikura / Timo Flügel / Takuya Ueda / Matthias Selbach / Elke Deuerling / Christian M T Spahn /
Abstract: Ribosome biogenesis is a fundamental multi-step cellular process that culminates in the formation of ribosomal subunits, whose production and modification are regulated by numerous biogenesis factors. ...Ribosome biogenesis is a fundamental multi-step cellular process that culminates in the formation of ribosomal subunits, whose production and modification are regulated by numerous biogenesis factors. In this study, we analyze physiologic prokaryotic ribosome biogenesis by isolating bona fide pre-50S subunits from an Escherichia coli strain with the biogenesis factor ObgE, affinity tagged at its native gene locus. Our integrative structural approach reveals a network of interacting biogenesis factors consisting of YjgA, RluD, RsfS, and ObgE on the immature pre-50S subunit. In addition, our study provides mechanistic insight into how the GTPase ObgE, in concert with other biogenesis factors, facilitates the maturation of the 50S functional core and reveals both conserved and divergent evolutionary features of ribosome biogenesis between prokaryotes and eukaryotes.
History
DepositionJan 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
G: 50S ribosomal protein L6
J: 50S ribosomal protein L13
L: 50S ribosomal protein L15
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
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
B: 5S ribosomal RNA
I: 50S ribosomal protein L11
K: 50S ribosomal protein L14
P: 50S ribosomal protein L19
6: Ribosomal silencing factor RsfS
7: Ribosomal large subunit pseudouridine synthase D
8: UPF0307 protein YjgA
9: GTPase ObgE/CgtA
M: 50S ribosomal protein L16
A: 23S ribosomal RNA
H: 50S ribosomal protein L9
e: 50S ribosomal protein L10
F: 50S ribosomal protein L5
b: 50S ribosomal protein L31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,490,38039
Polymers1,489,82235
Non-polymers5574
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area170280 Å2
ΔGint-1415 kcal/mol
Surface area548840 Å2
MethodPISA

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Components

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50S ribosomal protein ... , 29 types, 29 molecules CDEGJLNOQRSTUVWXYZ012IKPMHeFb

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


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P60422
#2: Protein 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P60438
#3: Protein 50S ribosomal protein L4 / / Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P60723
#4: Protein 50S ribosomal protein L6 / / Large ribosomal subunit protein uL6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0AG55
#5: Protein 50S ribosomal protein L13 / / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0AA10
#6: Protein 50S ribosomal protein L15 / / Large ribosomal subunit protein uL15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P02413
#7: Protein 50S ribosomal protein L17 / / Large ribosomal subunit protein bL17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0AG44
#8: Protein 50S ribosomal protein L18 / / Large ribosomal subunit protein uL18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0C018
#9: Protein 50S ribosomal protein L20 / / Large ribosomal subunit protein bL20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0A7L3
#10: Protein 50S ribosomal protein L21 / / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0AG48
#11: Protein 50S ribosomal protein L22 / / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P61175
#12: Protein 50S ribosomal protein L23 / / Large ribosomal subunit protein uL23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0ADZ0
#13: Protein 50S ribosomal protein L24 / / Large ribosomal subunit protein uL24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P60624
#14: Protein 50S ribosomal protein L25 / / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P68919
#15: Protein 50S ribosomal protein L27 / / Large ribosomal subunit protein bL27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0A7L8
#16: Protein 50S ribosomal protein L28 / / Large ribosomal subunit protein bL28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0A7M2
#17: Protein 50S ribosomal protein L29 / / Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0A7M6
#18: Protein 50S ribosomal protein L30 / / Large ribosomal subunit protein uL30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0AG51
#19: Protein 50S ribosomal protein L32 / / Large ribosomal subunit protein bL32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0A7N4
#20: Protein 50S ribosomal protein L33 / / Large ribosomal subunit protein bL33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0A7N9
#21: Protein/peptide 50S ribosomal protein L34 / / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0A7P5
#23: Protein 50S ribosomal protein L11 / / Large ribosomal subunit protein uL11


Mass: 14894.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0A7J7
#24: Protein 50S ribosomal protein L14 / / Large ribosomal subunit protein uL14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0ADY3
#25: Protein 50S ribosomal protein L19 / / Large ribosomal subunit protein bL19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0A7K6
#30: Protein 50S ribosomal protein L16 / / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0ADY7
#32: Protein 50S ribosomal protein L9 / / Large ribosomal subunit protein bL9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0A7R1
#33: Protein 50S ribosomal protein L10 / / 50S ribosomal protein L8 / Large ribosomal subunit protein uL10


Mass: 17736.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0A7J3
#34: Protein 50S ribosomal protein L5 / / Large ribosomal subunit protein uL5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P62399
#35: Protein 50S ribosomal protein L31 / / Large ribosomal subunit protein bL31-A


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0A7M9

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RNA chain , 2 types, 2 molecules BA

#22: RNA chain 5S ribosomal RNA /


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
#31: RNA chain 23S ribosomal RNA /


Mass: 946433.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)

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Protein , 4 types, 4 molecules 6789

#26: Protein Ribosomal silencing factor RsfS


Mass: 11594.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0AAT6
#27: Protein Ribosomal large subunit pseudouridine synthase D / / 23S rRNA pseudouridine(1911/1915/1917) synthase / rRNA pseudouridylate synthase D / rRNA-uridine isomerase D


Mass: 37180.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P33643, 23S rRNA pseudouridine1911/1915/1917 synthase
#28: Protein UPF0307 protein YjgA / x96 protein


Mass: 21395.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P0A8X0
#29: Protein GTPase ObgE/CgtA / GTP-binding protein Obg


Mass: 43340.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: P42641, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

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Non-polymers , 4 types, 31 molecules

#36: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#37: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#38: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#39: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Assembly intermediate complex 3 / Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL
Molecular weightValue: 1.5 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 36000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 900 nm / Cs: 2 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 5 sec. / Electron dose: 25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 8468

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874+SVNrefinement
PHENIX1.18.2_3874+SVNrefinement
EM software
IDNameVersionCategory
2Leginon3.3image acquisition
4CTFFIND4CTF correction
10cryoSPARCinitial Euler assignment
11cisTEMfinal Euler assignment
12cisTEMclassification
13cisTEM3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 287576
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22282 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 130.13 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0017107189
ELECTRON MICROSCOPYf_angle_d0.4339159792
ELECTRON MICROSCOPYf_chiral_restr0.026720348
ELECTRON MICROSCOPYf_plane_restr0.0039010
ELECTRON MICROSCOPYf_dihedral_angle_d17.2241173

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