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- PDB-5ot7: Elongation factor G-ribosome complex captures in the absence of i... -

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Entry
Database: PDB / ID: 5ot7
TitleElongation factor G-ribosome complex captures in the absence of inhibitors.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • (Ribosomal protein ...) x 3
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • Elongation factor GEF-G
  • mRNAMessenger RNA
  • tRNA-Phe
KeywordsRIBOSOME / Elongation factor G / Translation / Translocation
Function / homology
Function and homology information


translation elongation factor activity / regulation of translation / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / tRNA binding / ribosome / rRNA binding ...translation elongation factor activity / regulation of translation / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
: / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L1, bacterial-type / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV ...: / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L1, bacterial-type / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Elongation factor Tu domain 2 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L31 type A / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / 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 L25p family / Ribosomal protein L25 / 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 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 L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 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 L14P, bacterial-type / Ribosomal protein S4, 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
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 ...GUANOSINE-5'-DIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Elongation factor G / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMace, K. / Giudice, E. / Chat, S. / Gillet, R.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-14-ASTR-0001 France
GENCIi2015037391 France
CitationJournal: Nucleic Acids Res / Year: 2018
Title: The structure of an elongation factor G-ribosome complex captured in the absence of inhibitors.
Authors: Kevin Macé / Emmanuel Giudice / Sophie Chat / Reynald Gillet /
Abstract: During translation's elongation cycle, elongation factor G (EF-G) promotes messenger and transfer RNA translocation through the ribosome. Until now, the structures reported for EF-G-ribosome ...During translation's elongation cycle, elongation factor G (EF-G) promotes messenger and transfer RNA translocation through the ribosome. Until now, the structures reported for EF-G-ribosome complexes have been obtained by trapping EF-G in the ribosome. These results were based on use of non-hydrolyzable guanosine 5'-triphosphate (GTP) analogs, specific inhibitors or a mutated EF-G form. Here, we present the first cryo-electron microscopy structure of EF-G bound to ribosome in the absence of an inhibitor. The structure reveals a natural conformation of EF-G·GDP in the ribosome, with a previously unseen conformation of its third domain. These data show how EF-G must affect translocation, and suggest the molecular mechanism by which fusidic acid antibiotic prevents the release of EF-G after GTP hydrolysis.
History
DepositionAug 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 28, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
1: 16S Ribosomal RNA
2: tRNA-Phe
3: mRNA
4: 23S Ribosomal RNA
5: 5S Ribosomal RNA
6: 50S ribosomal protein L25
7: 50S ribosomal protein L9
A: 30S ribosomal protein S2
B: 30S ribosomal protein S3
C: 30S ribosomal protein S4
D: 30S ribosomal protein S5
E: 30S ribosomal protein S6
F: 30S ribosomal protein S7
G: 30S ribosomal protein S8
H: 30S ribosomal protein S9
I: 30S ribosomal protein S10
J: 30S ribosomal protein S11
K: 30S ribosomal protein S12
L: 30S ribosomal protein S13
M: 30S ribosomal protein S14 type Z
N: 30S ribosomal protein S15
O: 30S ribosomal protein S16
P: 30S ribosomal protein S17
Q: 30S ribosomal protein S18
R: 30S ribosomal protein S19
S: 30S ribosomal protein S20
T: 30S ribosomal protein Thx
U: Elongation factor G
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: 50S ribosomal protein L1
g: 50S ribosomal protein L2
h: 50S ribosomal protein L3
i: 50S ribosomal protein L4
j: 50S ribosomal protein L5
k: 50S ribosomal protein L6
l: Ribosomal protein uL10
m: Ribosomal protein uL11
n: Ribosomal protein bL12
o: 50S ribosomal protein L13
p: 50S ribosomal protein L14
q: 50S ribosomal protein L15
r: 50S ribosomal protein L16
s: 50S ribosomal protein L17
t: 50S ribosomal protein L18
u: 50S ribosomal protein L19
v: 50S ribosomal protein L20
w: 50S ribosomal protein L21
x: 50S ribosomal protein L22
y: 50S ribosomal protein L23
z: 50S ribosomal protein L24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,303,759525
Polymers2,291,89159
Non-polymers11,868466
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules 12345

#1: RNA chain 16S Ribosomal RNA /


Mass: 489331.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: GenBank: 55771382
#2: RNA chain tRNA-Phe


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1319589919
#3: RNA chain mRNA / Messenger RNA


Mass: 4889.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: RNA chain 23S Ribosomal RNA /


Mass: 943515.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: GenBank: 55771382
#5: RNA chain 5S Ribosomal RNA /


Mass: 38553.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: GenBank: 55771382

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50S ribosomal protein ... , 30 types, 30 molecules 67VWXYZabcdefghijkopqrstuvwxyz

#6: Protein 50S ribosomal protein L25 / / TL5


Mass: 20107.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHZ1
#7: Protein 50S ribosomal protein L9 /


Mass: 16164.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLQ1
#29: Protein 50S ribosomal protein L27 /


Mass: 8760.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60493
#30: Protein 50S ribosomal protein L28 /


Mass: 10559.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60494
#31: Protein 50S ribosomal protein L29 /


Mass: 8539.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP6
#32: Protein 50S ribosomal protein L30 /


Mass: 6799.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ6
#33: Protein 50S ribosomal protein L31 /


Mass: 8300.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SJE1
#34: Protein 50S ribosomal protein L32 /


Mass: 6590.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80339
#35: Protein/peptide 50S ribosomal protein L33 /


Mass: 6214.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P35871
#36: Protein/peptide 50S ribosomal protein L34 /


Mass: 5975.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80340
#37: Protein 50S ribosomal protein L35 /


Mass: 7374.981 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SKU1
#38: Protein/peptide 50S ribosomal protein L36 / / Ribosomal protein B


Mass: 4435.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHR2
#39: Protein 50S ribosomal protein L1 /


Mass: 24644.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLP7
#40: Protein 50S ribosomal protein L2 /


Mass: 30401.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60405
#41: Protein 50S ribosomal protein L3 /


Mass: 22321.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN8
#42: Protein 50S ribosomal protein L4 / / L1e


Mass: 23071.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN9
#43: Protein 50S ribosomal protein L5 /


Mass: 20720.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ0
#44: Protein 50S ribosomal protein L6 /


Mass: 19182.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P0DOY8
#48: Protein 50S ribosomal protein L13 /


Mass: 15828.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60488
#49: Protein 50S ribosomal protein L14 /


Mass: 13323.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP8
#50: Protein 50S ribosomal protein L15 /


Mass: 16319.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ7
#51: Protein 50S ribosomal protein L16 /


Mass: 15993.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60489
#52: Protein 50S ribosomal protein L17 /


Mass: 13750.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q9Z9H5
#53: Protein 50S ribosomal protein L18 / / TL24


Mass: 10998.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ4
#54: Protein 50S ribosomal protein L19 /


Mass: 16289.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60490
#55: Protein 50S ribosomal protein L20 /


Mass: 13648.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60491
#56: Protein 50S ribosomal protein L21 /


Mass: 11069.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60492
#57: Protein 50S ribosomal protein L22 /


Mass: 12808.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP3
#58: Protein 50S ribosomal protein L23 /


Mass: 10386.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP0
#59: Protein 50S ribosomal protein L24 /


Mass: 11181.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP9

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30S ribosomal protein ... , 20 types, 20 molecules ABCDEFGHIJKLMNOPQRST

#8: Protein 30S ribosomal protein S2 /


Mass: 27116.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80371
#9: Protein 30S ribosomal protein S3 /


Mass: 22975.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80372
#10: Protein 30S ribosomal protein S4 /


Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80373
#11: Protein 30S ribosomal protein S5 /


Mass: 16460.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ5
#12: Protein 30S ribosomal protein S6 / / TS9


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLP8
#13: Protein 30S ribosomal protein S7 /


Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P17291
#14: Protein 30S ribosomal protein S8 /


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P0DOY9
#15: Protein 30S ribosomal protein S9 /


Mass: 14279.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80374
#16: Protein 30S ribosomal protein S10 /


Mass: 11398.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN7
#17: Protein 30S ribosomal protein S11 /


Mass: 12606.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80376
#18: Protein 30S ribosomal protein S12 /


Mass: 13875.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN3
#19: Protein 30S ribosomal protein S13 /


Mass: 13494.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80377
#20: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P0DOY6
#21: Protein 30S ribosomal protein S15 /


Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SJ76
#22: Protein 30S ribosomal protein S16 /


Mass: 9995.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SJH3
#23: Protein 30S ribosomal protein S17 /


Mass: 11880.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P0DOY7
#24: Protein 30S ribosomal protein S18 /


Mass: 8155.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLQ0
#25: Protein 30S ribosomal protein S19 /


Mass: 9961.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP2
#26: Protein 30S ribosomal protein S20 /


Mass: 10921.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80380
#27: Protein/peptide 30S ribosomal protein Thx / Ribosome / S31


Mass: 3089.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SIH3

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Protein , 1 types, 1 molecules U

#28: Protein Elongation factor G / EF-G / EF-G


Mass: 76547.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: fusA, fus, TTHA1695 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SHN5

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Ribosomal protein ... , 3 types, 3 molecules lmn

#45: Protein Ribosomal protein uL10 /


Mass: 11109.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
#46: Protein Ribosomal protein uL11 /


Mass: 11932.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
#47: Protein Ribosomal protein bL12 /


Mass: 6060.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Non-polymers , 3 types, 466 molecules

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


Mass: 24.305 Da / Num. of mol.: 462 / Source method: obtained synthetically / Formula: Mg
#61: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#62: 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

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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

Component
IDNameTypeEntity IDParent-IDSource
1EF-G bound to 70S ribosomeRIBOSOME#1-#590MULTIPLE SOURCES
270S ribosomeRibosomeRIBOSOME#1, #4-#27, #29-#591NATURAL
3tRNA PHECOMPLEX#21NATURAL
4Elongation factor GEF-GCOMPLEX#281RECOMBINANT
5mRNAMessenger RNACOMPLEX#31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Thermus thermophilus HB8 (bacteria)300852
23Escherichia coli (E. coli)562
34Thermus thermophilus (bacteria)300852
45Escherichia coli (E. coli)562
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
14Escherichia coli BL21(DE3) (bacteria)469008
25synthetic construct (others)32630
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
15 mMHEPES-KOH (pH 7.5)1
210 mMAmmonium chlorideNH4CL1
310 mMMgOAc1
450 mMpotassium chlorideKCl1
50.1 mMEthylenediaminetetraacetic acid (EDTA)C10H16N2O81
66 mMBeta-mercaptoethanol2-Mercaptoethanol1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 303 K

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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: 59000 X / Calibrated magnification: 120443 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 2700 nm / Cs: 0.0023 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 45 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 949
EM imaging opticsSpherical aberration corrector: CS-corrected
Image scansMovie frames/image: 7 / Used frames/image: 1-7

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2particle selectionEman2 e2boxer.py was used to automatically select particle images.
2EPUimage acquisition
4CTFFIND4CTF correctionused for phase calculation
5RELION1.4CTF correctionused for phase flipping and amplitude correction
8UCSF Chimera1.11.2model fitting
9Coot0.8.3 EL (ccp4)model fitting
11RELION1.4initial Euler assignment
12RELION1.4final Euler assignment
13RELION1.4classification
14RELION1.43D reconstruction
15PHENIX1.12rc1-2807model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 96509
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32383 / Algorithm: BACK PROJECTION
Details: Resolution : 5.36 Resolution (masked and sharpened) : 3.8
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: each ribosomal rna and protein was first rigid body fitted in the map using UCSF chimera. The missing componant (mRNA and bL9) were then added and fitted. the quality of the fitting was then ...Details: each ribosomal rna and protein was first rigid body fitted in the map using UCSF chimera. The missing componant (mRNA and bL9) were then added and fitted. the quality of the fitting was then assesed and adjust manually, residue per residue using coot. the RNA confomation were ajusted with the ERRASER modul (in Phenix). The final model was refined using phenix real space refinement procedure.
RefinementHighest resolution: 3.8 Å

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