[English] 日本語
Yorodumi
- PDB-6qdw: Cryo-EM structure of the 50S ribosomal subunit at 2.83 Angstroms ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qdw
TitleCryo-EM structure of the 50S ribosomal subunit at 2.83 Angstroms with modeled GBC SecM peptide
Components
  • (50S ribosomal protein ...) x 28
  • 23S rRNA
  • 5S rRNA
  • Gamma-crystallin B
  • glycine-tRNA glyT
KeywordsRIBOSOME / Translation / 50S ribosome / Nascent peptide chain
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation ...structural constituent of eye lens / lens development in camera-type eye / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / visual perception / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / : / Beta/Gamma crystallin / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Crystallins beta and gamma 'Greek key' motif profile. ...Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / : / Beta/Gamma crystallin / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Ribosomal Protein L25; Chain P / Gamma-crystallin-like / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Aldehyde Oxidoreductase; domain 3 / Rubrerythrin, domain 2 / RRM (RNA recognition motif) domain / Ribosomal protein L25, short-form / Single Sheet / Nucleic acid-binding proteins / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 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 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 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 L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / 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 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 L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / 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 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 protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / : / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L21 / Ribosomal protein L19
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL27 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL15 / Gamma-crystallin B / 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 bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / 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 / 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 speciesBos taurus (cattle)
Escherichia coli (E. coli)
Escherichia coli BL21 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsSchulte, L. / Reitz, J. / Hodirnau, V.V. / Kudlinzki, D. / Mao, J. / Glaubitz, C. / Frangakis, A. / Schwalbe, H.
CitationJournal: Nat Commun / Year: 2020
Title: Cysteine oxidation and disulfide formation in the ribosomal exit tunnel.
Authors: Linda Schulte / Jiafei Mao / Julian Reitz / Sridhar Sreeramulu / Denis Kudlinzki / Victor-Valentin Hodirnau / Jakob Meier-Credo / Krishna Saxena / Florian Buhr / Julian D Langer / Martin ...Authors: Linda Schulte / Jiafei Mao / Julian Reitz / Sridhar Sreeramulu / Denis Kudlinzki / Victor-Valentin Hodirnau / Jakob Meier-Credo / Krishna Saxena / Florian Buhr / Julian D Langer / Martin Blackledge / Achilleas S Frangakis / Clemens Glaubitz / Harald Schwalbe /
Abstract: Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide ...Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.
History
DepositionJan 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4531
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: 50S ribosomal protein L28
1: 50S ribosomal protein L29
2: 50S ribosomal protein L30
3: 50S ribosomal protein L32
4: 50S ribosomal protein L33
6: 50S ribosomal protein L34
7: 50S ribosomal protein L35
8: 50S ribosomal protein L36
a: 5S rRNA
b: 23S rRNA
c: 50S ribosomal protein L2
d: 50S ribosomal protein L3
e: 50S ribosomal protein L4
f: 50S ribosomal protein L5
g: 50S ribosomal protein L6
h: 50S ribosomal protein L9
j: 50S ribosomal protein L13
k: 50S ribosomal protein L14
l: 50S ribosomal protein L15
m: 50S ribosomal protein L16
n: 50S ribosomal protein L17
o: 50S ribosomal protein L18
p: 50S ribosomal protein L19
q: 50S ribosomal protein L20
r: 50S ribosomal protein L21
s: 50S ribosomal protein L22
t: 50S ribosomal protein L23
u: 50S ribosomal protein L24
v: glycine-tRNA glyT
w: 50S ribosomal protein L25
y: 50S ribosomal protein L27
z: Gamma-crystallin B


Theoretical massNumber of molelcules
Total (without water)1,374,47232
Polymers1,374,47232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area154880 Å2
ΔGint-1328 kcal/mol
Surface area479240 Å2
MethodPISA

-
Components

+
50S ribosomal protein ... , 28 types, 28 molecules 01234678cdefghjklmnopqrstuwy

#1: Protein 50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: SRVCQVTGK RPVTGNNRSH ALNATKRRFL PNLHSHRFWV ESEKRFVTLRVSAKGMRVID KKGIDTVLAE LRARGEKY
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N3L9, UniProt: P0A7M2*PLUS
#2: Protein 50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N7F5, UniProt: P0A7M6*PLUS
#3: Protein 50S ribosomal protein L30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N7G4, UniProt: P0AG51*PLUS
#4: Protein 50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140NAZ2, UniProt: P0A7N4*PLUS
#5: Protein 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N5Z7, UniProt: P0A7N9*PLUS
#6: Protein/peptide 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140NHV0, UniProt: P0A7P5*PLUS
#7: Protein 50S ribosomal protein L35


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N9E3, UniProt: P0A7Q1*PLUS
#8: Protein/peptide 50S ribosomal protein L36


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N5M6, UniProt: P0A7Q6*PLUS
#11: Protein 50S ribosomal protein L2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N7J1, UniProt: P60422*PLUS
#12: Protein 50S ribosomal protein L3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N3G7, UniProt: P60438*PLUS
#13: Protein 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N5K8, UniProt: P60723*PLUS
#14: Protein 50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N5A3, UniProt: P62399*PLUS
#15: Protein 50S ribosomal protein L6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N2T1, UniProt: P0AG55*PLUS
#16: Protein 50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140NDV1, UniProt: P0A7R1*PLUS
#17: Protein 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N598, UniProt: P0AA10*PLUS
#18: Protein 50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: Delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N3H4, UniProt: P0ADY3*PLUS
#19: Protein 50S ribosomal protein L15


Mass: 14994.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N711, UniProt: P02413*PLUS
#20: Protein 50S ribosomal protein L16


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N6Z2, UniProt: P0ADY7*PLUS
#21: Protein 50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N4M0, UniProt: P0AG44*PLUS
#22: Protein 50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N4L0, UniProt: P0C018*PLUS
#23: Protein 50S ribosomal protein L19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N6T7, UniProt: P0A7K6*PLUS
#24: Protein 50S ribosomal protein L20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140NBS1, UniProt: P0A7L3*PLUS
#25: Protein 50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N5D7, UniProt: P0AG48*PLUS
#26: Protein 50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N2S3, UniProt: P61175*PLUS
#27: Protein 50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: C6EGE8
#28: Protein 50S ribosomal protein L24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N5L7, UniProt: P60624*PLUS
#30: Protein 50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N846, UniProt: P68919*PLUS
#31: Protein 50S ribosomal protein L27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / Strain: B / BL21-DE3 / References: UniProt: A0A140N340, UniProt: P0A7L8*PLUS

-
RNA chain , 3 types, 3 molecules abv

#9: RNA chain 5S rRNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / References: GenBank: 1706539273
#10: RNA chain 23S rRNA


Mass: 942342.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Variant: delta tig / References: GenBank: 296142109
#29: RNA chain glycine-tRNA glyT


Mass: 23935.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli (strain B / BL21-DE3) (bacteria)
Variant: delta tig / References: GenBank: 1730024484

-
Protein , 1 types, 1 molecules z

#32: Protein Gamma-crystallin B / Gamma-B-crystallin / Gamma-crystallin II


Mass: 7157.970 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CRYGB / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): delta tig / References: UniProt: P02526

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
150S ribosomal + GBC SecM peptide complexRIBOSOMEall0MULTIPLE SOURCES
2GBC SecM peptideCOMPLEX#321RECOMBINANT
350 ribosomal subunitRIBOSOME#1-#311NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Bos taurus (cattle)9913
33Escherichia coli BL21(DE3) (bacteria)469008
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5 / Details: Tico Buffer
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESC8H18N2O4S1
230 mMAmmonium chlorideNH4CL1
312 mMMagnesium ChlorideMgCl21
41 mMEthylenediaminetetraacetic acid (EDTA)C10H16N2O81
SpecimenConc.: 0.12 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 IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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 FIELD / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 1.66 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3
EM imaging opticsEnergyfilter name: GIF Quantum SE
Image scansMovie frames/image: 36

-
Processing

SoftwareName: PHENIX / Version: dev_3318: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
7Cootmodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196254 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 3JBU

3jbu

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01398979
ELECTRON MICROSCOPYf_angle_d1.098148813
ELECTRON MICROSCOPYf_dihedral_angle_d17.69252269
ELECTRON MICROSCOPYf_chiral_restr0.06219154
ELECTRON MICROSCOPYf_plane_restr0.0077378

+
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