[English] 日本語
Yorodumi
- PDB-9smd: Ribosome-dome complex including the Sec-translocon (SecYEG-SecA-S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9smd
TitleRibosome-dome complex including the Sec-translocon (SecYEG-SecA-SecDF) from antibiotics treated Mycoplasma pneumoniae cells (Combined)
Components
  • (16S ribosomal ...) x 2
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 26
  • (Large ribosomal subunit protein ...) x 3
  • (Protein translocase subunit ...) x 2
  • (Uncharacterized lipoprotein ...) x 4
  • (mRNA) x 2
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Nascent peptide
  • Probable protein-export membrane protein SecG
  • SecDF
  • SecE
  • Small ribosomal subunit protein uS9
  • tRNA-Asp (P-site)
  • tRNA-Lys (A-site)
KeywordsTRANSLATION / Ribosome / Translocation / Chaperone / Antibiotics
Function / homology
Function and homology information


cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / intracellular protein transmembrane transport / protein transport by the Sec complex / protein-transporting ATPase activity / protein import / protein secretion / transmembrane protein transporter activity / protein targeting ...cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / intracellular protein transmembrane transport / protein transport by the Sec complex / protein-transporting ATPase activity / protein import / protein secretion / transmembrane protein transporter activity / protein targeting / transferase activity / large ribosomal subunit / ribosomal small subunit assembly / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / translation / ribonucleoprotein complex / structural constituent of ribosome / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Family of unknown function (DUF6856) / Protein of unknown function DUF3713 / Protein of unknown function (DUF3713) / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain ...: / Family of unknown function (DUF6856) / Protein of unknown function DUF3713 / Protein of unknown function (DUF3713) / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily / SecA, preprotein cross-linking domain superfamily / SecA, C-terminal helicase domain / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA P-loop domain / SecA family signature. / SecA family profile. / SecA DEAD-like domain / SecA preprotein cross-linking domain / Protein translocase subunit SecY / Protein secY signature 1. / Protein secY signature 2. / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / Ribosomal protein uL10 C-terminal region / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / : / : / Ribosomal protein uL15, N-terminal region / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein S21 / Ribosomal protein L9 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L6, conserved site / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L6 signature 1. / Ribosomal protein L9, C-terminal domain superfamily / : / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / 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, RNA binding domain / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal protein L36 signature. / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / : / Ribosomal protein S19, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type
Similarity search - Domain/homology
: / 1,4-DIAMINOBUTANE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL16 ...: / 1,4-DIAMINOBUTANE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein bS21 / Uncharacterized protein MG055 homolog / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL10 / Uncharacterized lipoprotein MG348 homolog / Uncharacterized lipoprotein MG338 homolog / Uncharacterized lipoprotein MG309 homolog / Uncharacterized lipoprotein MG307 homolog / Uncharacterized protein MG277 homolog / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein uL11 / Protein translocase subunit SecA / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17 / Protein translocase subunit SecY / Probable protein-export membrane protein SecG
Similarity search - Component
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.4 Å
AuthorsXue, L. / Jensen, R.K. / Mahamid, J.
Funding support United States, Germany, China, Denmark, 4items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative2021-234620 United States
German Research Foundation (DFG)426290502 Germany
Ministry of Science and Technology (MoST, China)2024YFA1306200 China
Independent Research Fund Denmark - Medical Sciences0164-00010A Denmark
CitationJournal: To Be Published
Title: In-cell discovery and characterization of a non-canonical bacterial protein translocation-folding complex
Authors: Jensen, R. / Xue, L. / Marotta, F. / Somody, J.C. / Selkrig, J. / Lenz, S. / Rappsilber, J. / Savitski, M.M. / Kosinski, J. / Typas, A. / Zimmermann-Kogadeeva, M. / Bork, P. / Mahamid, J.
History
DepositionSep 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: Large ribosomal subunit protein bL34
1: 50S ribosomal protein L35
10: Protein translocase subunit SecY
11: Probable protein-export membrane protein SecG
12: SecE
17: SecDF
2: 50S ribosomal protein L36
3: 23S ribosomal RNA
4: 5S ribosomal RNA
5: 16S ribosomal RNA
6: 16S ribosomal RNA
7: tRNA-Asp (P-site)
8: tRNA-Lys (A-site)
9: Protein translocase subunit SecA
A: 30S ribosomal protein S2
AA: 30S ribosomal protein S5
AB: mRNA
AC: 50S ribosomal protein L31
C: 30S ribosomal protein S4
E: 30S ribosomal protein S6
F: 30S ribosomal protein S7
G: 30S ribosomal protein S8
H: Small ribosomal subunit protein uS9
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 S21
W: 30S ribosomal protein S3
Y: mRNA
Z: Nascent peptide
a: 50S ribosomal protein L2
b: 50S ribosomal protein L3
c: 50S ribosomal protein L4
d: 50S ribosomal protein L5
e: 50S ribosomal protein L6
f: 50S ribosomal protein L9
g: 50S ribosomal protein L10
h: 50S ribosomal protein L11
i: 50S ribosomal protein L13
j: 50S ribosomal protein L14
k: 50S ribosomal protein L15
l: 50S ribosomal protein L16
m: 50S ribosomal protein L17
n: Large ribosomal subunit protein uL18
o: 50S ribosomal protein L19
p: 50S ribosomal protein L20
q: 50S ribosomal protein L21
r: 50S ribosomal protein L22
s: Large ribosomal subunit protein uL23
t: 50S ribosomal protein L24
u: 50S ribosomal protein L27
v: 50S ribosomal protein L28
w: 50S ribosomal protein L29
x: 50S ribosomal protein L31
y: 50S ribosomal protein L32
z: 50S ribosomal protein L33 1
13: Uncharacterized lipoprotein MG307 homolog
14: Uncharacterized lipoprotein MG309 homolog
15: Uncharacterized lipoprotein MG338 homolog
18: Uncharacterized lipoprotein MG348 homolog
16: Uncharacterized lipoprotein MG348 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,552,719406
Polymers3,543,45969
Non-polymers9,259337
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, The assembly is supported by in-cell cross-linking mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

+
Large ribosomal subunit protein ... , 3 types, 3 molecules 0ns

#1: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5616.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P78006
#52: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 13073.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50302
#57: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 21139.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75578

+
50S ribosomal protein ... , 26 types, 27 molecules 12ACxabcdefghijklmopqrtuvwyz

#2: Protein 50S ribosomal protein L35


Mass: 6793.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75447
#7: Protein/peptide 50S ribosomal protein L36


Mass: 4400.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P52864
#18: Protein 50S ribosomal protein L31


Mass: 10980.657 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P78020
#39: Protein 50S ribosomal protein L2


Mass: 31966.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75577
#40: Protein 50S ribosomal protein L3


Mass: 31298.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75580
#41: Protein 50S ribosomal protein L4


Mass: 23632.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75579
#42: Protein 50S ribosomal protein L5


Mass: 20270.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50306
#43: Protein 50S ribosomal protein L6


Mass: 20624.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50303
#44: Protein 50S ribosomal protein L9


Mass: 17185.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75540
#45: Protein 50S ribosomal protein L10


Mass: 17645.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75240
#46: Protein 50S ribosomal protein L11


Mass: 14803.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75550
#47: Protein 50S ribosomal protein L13


Mass: 16821.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75178
#48: Protein 50S ribosomal protein L14


Mass: 13478.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50308
#49: Protein 50S ribosomal protein L15


Mass: 16768.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50300
#50: Protein 50S ribosomal protein L16


Mass: 15646.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P41204
#51: Protein 50S ribosomal protein L17


Mass: 14270.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q59547
#53: Protein 50S ribosomal protein L19


Mass: 13870.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75133
#54: Protein 50S ribosomal protein L20


Mass: 14742.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P78023
#55: Protein 50S ribosomal protein L21


Mass: 11664.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P78026
#56: Protein 50S ribosomal protein L22


Mass: 17355.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75575
#58: Protein 50S ribosomal protein L24


Mass: 12461.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50307
#59: Protein 50S ribosomal protein L27


Mass: 11527.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75458
#60: Protein 50S ribosomal protein L28


Mass: 7549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75171
#61: Protein 50S ribosomal protein L29


Mass: 13003.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50310
#62: Protein 50S ribosomal protein L32


Mass: 6641.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75238
#63: Protein 50S ribosomal protein L33 1


Mass: 6298.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P78015

+
Protein translocase subunit ... , 2 types, 2 molecules 109

#3: Protein Protein translocase subunit SecY


Mass: 52003.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q59548
#14: Protein Protein translocase subunit SecA


Mass: 91942.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75559, protein-secreting ATPase

+
Protein , 4 types, 4 molecules 111217H

#4: Protein Probable protein-export membrane protein SecG


Mass: 8352.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q9EXD0
#5: Protein SecE


Mass: 14489.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75048
#6: Protein SecDF


Mass: 108345.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75387
#23: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 15158.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75179

+
RNA chain , 6 types, 6 molecules 3478ABY

#8: RNA chain 23S ribosomal RNA


Mass: 940911.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: GenBank: 26117688
#9: RNA chain 5S ribosomal RNA


Mass: 34796.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: GenBank: 3042778399
#12: RNA chain tRNA-Asp (P-site)


Mass: 24731.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria)
#13: RNA chain tRNA-Lys (A-site)


Mass: 24697.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria)
#17: RNA chain mRNA


Mass: 6617.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria)
#37: RNA chain mRNA


Mass: 6698.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria)

+
16S ribosomal ... , 2 types, 2 molecules 56

#10: RNA chain 16S ribosomal RNA


Mass: 492302.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: GenBank: 26117688
#11: RNA chain 16S ribosomal RNA


Mass: 492303.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: GenBank: 26117688

+
30S ribosomal protein ... , 19 types, 19 molecules AAACEFGIJKLMNOPQRSTW

#15: Protein 30S ribosomal protein S2


Mass: 33468.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75560
#16: Protein 30S ribosomal protein S5


Mass: 24138.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50301
#19: Protein 30S ribosomal protein S4


Mass: 23817.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P46775
#20: Protein 30S ribosomal protein S6


Mass: 25430.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75543
#21: Protein 30S ribosomal protein S7


Mass: 17897.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75545
#22: Protein 30S ribosomal protein S8


Mass: 15903.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50304
#24: Protein 30S ribosomal protein S10


Mass: 12226.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75581
#25: Protein 30S ribosomal protein S11


Mass: 12709.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50296
#26: Protein 30S ribosomal protein S12


Mass: 15666.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75546
#27: Protein 30S ribosomal protein S13


Mass: 14209.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50297
#28: Protein 30S ribosomal protein S14 type Z


Mass: 6901.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50305
#29: Protein 30S ribosomal protein S15


Mass: 9921.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75173
#30: Protein 30S ribosomal protein S16


Mass: 10806.921 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: A0A0H3DLS7
#31: Protein 30S ribosomal protein S17


Mass: 9859.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50309
#32: Protein 30S ribosomal protein S18


Mass: 12411.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75541
#33: Protein 30S ribosomal protein S19


Mass: 10057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75576
#34: Protein 30S ribosomal protein S20


Mass: 9993.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75237
#35: Protein 30S ribosomal protein S21


Mass: 7539.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P57079
#36: Protein 30S ribosomal protein S3


Mass: 30657.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P41205

+
Protein/peptide , 1 types, 1 molecules Z

#38: Protein/peptide Nascent peptide


Mass: 3127.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria)

+
Uncharacterized lipoprotein ... , 4 types, 5 molecules 1314151816

#64: Protein Uncharacterized lipoprotein MG307 homolog


Mass: 136216.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75342
#65: Protein Uncharacterized lipoprotein MG309 homolog


Mass: 143385.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75334
#66: Protein Uncharacterized lipoprotein MG338 homolog


Mass: 140427.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75296
#67: Protein Uncharacterized lipoprotein MG348 homolog


Mass: 30410.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75255

+
Non-polymers , 5 types, 356 molecules

#68: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#69: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 317 / Source method: obtained synthetically / Formula: Mg
#70: Chemical
ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H12N2
#71: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#72: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

+
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: pooled Ribosome-Sec translocon-Dome supercomplexes from four antibiotic treated Mycoplasma pneumoniae datasets(chloramphenicol treated & on K2 camera; puseudoridimycin treated; spectinomycin ...Name: pooled Ribosome-Sec translocon-Dome supercomplexes from four antibiotic treated Mycoplasma pneumoniae datasets(chloramphenicol treated & on K2 camera; puseudoridimycin treated; spectinomycin treated; chloramphenicol treated & on K3 camera)
Type: CELL / Source: NATURAL
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Buffer solutionpH: 7.4
Details: Modified Hayflick medium: 14.7g/l Difco PPLO(Becton Dickinson), 20% (v/v) Gibco horse serum (New Zealand origin), 100 mM HEPES-Na; pH 7.4, 1% (w/w) glucose, 0.002% (w/w) phenol red, 1000 U/ml penicillin G.
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Mycoplasma pneumoniae M129 cells were grown on gold Quantifoil grids at 37 Celsius in modified Hayflick medium. Treatment with different antibiotics for 15-20 minutes before plunge freezing.
Specimen supportGrid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: Back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental control chamber.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDElectron dose (e/Å2)Avg electron dose per subtomogram (e/Å2)Detector modeFilm or detector model
113.2130COUNTINGGATAN K2 SUMMIT (4k x 4k)
213.34137GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
1PyTomvolume selection
2Warp1.0.9volume selection
3SerialEMimage acquisition
5Warp1.0.9CTF correction
12RELION3.0.8final Euler assignment
13RELION3.0.8classification
14RELION3.0.83D reconstruction
Image processingDetails: Data collected on both GATAN K2 and K3 camera were combined for averaging
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2304 / Symmetry type: POINT
EM volume selectionDetails: Ribosome-Sec translocon-Dome supercomplex in chloramphenicol treated Mycoplasma pneumoniae cells by K2 camera: 18957 sub-tomograms from 65 tomograms Ribosome-Sec translocon-Dome supercomplex ...Details: Ribosome-Sec translocon-Dome supercomplex in chloramphenicol treated Mycoplasma pneumoniae cells by K2 camera: 18957 sub-tomograms from 65 tomograms Ribosome-Sec translocon-Dome supercomplex in puseudoridimycin treated Mycoplasma pneumoniae cells : 15314 sub-tomograms from 86 tomograms ribosome-cage supercomplexs in spectinomycin-treated Mycoplasma pneumoniae cells: 12935 sub-tomograms from 70 tomograms; ribosome-cage supercomplexs in chlooramphenicol-treated Mycoplasma pneumoniae cells by K3 camera: 30774 sub-tomograms from 139 tomograms
Num. of tomograms: 360 / Num. of volumes extracted: 77980

+
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