[English] 日本語
Yorodumi
- PDB-6v3a: Cryo-EM structure of the Acinetobacter baumannii Ribosome: 70S wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v3a
TitleCryo-EM structure of the Acinetobacter baumannii Ribosome: 70S with E-site tRNA
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • 16s Ribosomal RNA
  • 23s ribosomal RNA
  • 5s ribosomal RNA
  • mRNAMessenger RNA
  • tRNA-met
KeywordsRIBOSOME / Acinetobacter baumannii
Function / homology
Function and homology information


ribosomal large subunit assembly / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...ribosomal large subunit assembly / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L21, conserved site ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal 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 L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein 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 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 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS18 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS4 / 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 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / 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 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL20
Similarity search - Component
Biological speciesAcinetobacter sp. CIP 51.11 (bacteria)
Acinetobacter beijerinckii ANC 3835 (bacteria)
Acinetobacter baumannii (bacteria)
Acinetobacter sp. ANC 4470 (bacteria)
Acinetobacter baumannii AB0057 (bacteria)
Acinetobacter sp. NIPH 899 (bacteria)
Acinetobacter sp. 809848 (bacteria)
Acinetobacter rudis CIP 110305 (bacteria)
Acinetobacter sp. CIP 102082 (bacteria)
Acinetobacter sp. ANC 5600 (bacteria)
Acinetobacter sp. 263903-1 (bacteria)
Acinetobacter venetianus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsMorgan, C.E. / Yu, E.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: mBio / Year: 2020
Title: Cryo-electron Microscopy Structure of the Acinetobacter baumannii 70S Ribosome and Implications for New Antibiotic Development.
Authors: Christopher E Morgan / Wei Huang / Susan D Rudin / Derek J Taylor / James E Kirby / Robert A Bonomo / Edward W Yu /
Abstract: Antimicrobial resistance is a major health threat as it limits treatment options for infection. At the forefront of this serious issue is , a Gram-negative opportunistic pathogen that exhibits the ...Antimicrobial resistance is a major health threat as it limits treatment options for infection. At the forefront of this serious issue is , a Gram-negative opportunistic pathogen that exhibits the remarkable ability to resist antibiotics through multiple mechanisms. As bacterial ribosomes represent a target for multiple distinct classes of existing antimicrobial agents, we here use single-particle cryo-electron microscopy (cryo-EM) to elucidate five different structural states of the ribosome, including the 70S, 50S, and 30S forms. We also determined interparticle motions of the 70S ribosome in different tRNA bound states using three-dimensional (3D) variability analysis. Together, our structural data further our understanding of the ribosome from and other Gram-negative pathogens and will enable structure-based drug discovery to combat antibiotic-resistant bacterial infections. is a severe nosocomial threat largely due to its intrinsic antibiotic resistance and remarkable ability to acquire new resistance determinants. The bacterial ribosome serves as a major target for modern antibiotics and the design of new therapeutics. Here, we present cryo-EM structures of the 70S ribosome, revealing several unique species-specific structural features that may facilitate future drug development to combat this recalcitrant bacterial pathogen.
History
DepositionNov 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-21031
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: 50S ribosomal protein L33
1: 50S ribosomal protein L34
2: 50S ribosomal protein L35
3: 50S ribosomal protein L36
AN1: 23s ribosomal RNA
B: 5s ribosomal RNA
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
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: 50S ribosomal protein L18
O: 50S ribosomal protein L19
P: 50S ribosomal protein L20
Q: 50S ribosomal protein L21
R: 50S ribosomal protein L22
S: 50S ribosomal protein L23
T: 50S ribosomal protein L24
U: 50S ribosomal protein L25
V: 50S ribosomal protein L27
W: 50S ribosomal protein L28
X: 50S ribosomal protein L29
Y: 50S ribosomal protein L30
Z: 50S ribosomal protein L32
sN1: 16s Ribosomal RNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
u: 30S ribosomal protein S21
v: tRNA-met
w: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,163,128148
Polymers2,160,77953
Non-polymers2,34995
Water9,368520
1


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

-
Components

+
50S ribosomal protein ... , 28 types, 28 molecules 0123CDEFGHIJKLMNOPQRSTUVWXYZ

#1: Protein 50S ribosomal protein L33 /


Mass: 6105.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. CIP 51.11 (bacteria) / References: UniProt: N9PPR9
#2: Protein/peptide 50S ribosomal protein L34 /


Mass: 5192.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter beijerinckii ANC 3835 (bacteria)
References: UniProt: N9DYI8
#3: Protein 50S ribosomal protein L35 /


Mass: 7424.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I693
#4: Protein/peptide 50S ribosomal protein L36 /


Mass: 4276.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. ANC 4470 (bacteria) / References: UniProt: A0A1Y3CHB1
#7: Protein 50S ribosomal protein L2 /


Mass: 30346.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA36
#8: Protein 50S ribosomal protein L3 /


Mass: 22512.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA39
#9: Protein 50S ribosomal protein L4 /


Mass: 21583.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA38
#10: Protein 50S ribosomal protein L5 /


Mass: 20051.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA27
#11: Protein 50S ribosomal protein L6 /


Mass: 19126.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA24
#12: Protein 50S ribosomal protein L9 /


Mass: 15800.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IBC3
#13: Protein 50S ribosomal protein L13 /


Mass: 15981.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I9B0
#14: Protein 50S ribosomal protein L14 /


Mass: 13523.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. NIPH 899 (bacteria) / References: UniProt: N8WQT6
#15: Protein 50S ribosomal protein L15 /


Mass: 15509.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA20
#16: Protein 50S ribosomal protein L16 /


Mass: 15498.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA32
#17: Protein 50S ribosomal protein L17 /


Mass: 14022.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA13
#18: Protein 50S ribosomal protein L18 /


Mass: 12443.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA23
#19: Protein 50S ribosomal protein L19 /


Mass: 13619.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IAS9
#20: Protein 50S ribosomal protein L20 /


Mass: 13468.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: V5VGC9
#21: Protein 50S ribosomal protein L21 /


Mass: 11496.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I6V9
#22: Protein 50S ribosomal protein L22 /


Mass: 11828.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. 809848 (bacteria) / References: UniProt: A0A009QSN8
#23: Protein 50S ribosomal protein L23 /


Mass: 11607.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA37
#24: Protein 50S ribosomal protein L24 /


Mass: 11187.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA28
#25: Protein 50S ribosomal protein L25 /


Mass: 10942.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I7B6
#26: Protein 50S ribosomal protein L27 /


Mass: 9072.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I6V8
#27: Protein 50S ribosomal protein L28 /


Mass: 9125.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter rudis CIP 110305 (bacteria) / References: UniProt: S3NQR5
#28: Protein 50S ribosomal protein L29 /


Mass: 7449.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA31
#29: Protein 50S ribosomal protein L30 /


Mass: 6654.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. CIP 102082 (bacteria) / References: UniProt: N8V730
#30: Protein 50S ribosomal protein L32 /


Mass: 7096.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I7A4

-
RNA chain , 5 types, 5 molecules AN1BsN1vw

#5: RNA chain 23s ribosomal RNA /


Mass: 945299.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria)
#6: RNA chain 5s ribosomal RNA /


Mass: 36996.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: GenBank: 1360860747
#31: RNA chain 16s Ribosomal RNA /


Mass: 500297.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: GenBank: CP044356.1
#52: RNA chain tRNA-met


Mass: 24760.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria)
#53: RNA chain mRNA / Messenger RNA


Mass: 935.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria)

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

#32: Protein 30S ribosomal protein S2 /


Mass: 27680.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: V5VBC2
#33: Protein 30S ribosomal protein S3 /


Mass: 27972.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: V5V9N0
#34: Protein 30S ribosomal protein S4 /


Mass: 23311.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA15
#35: Protein 30S ribosomal protein S5 /


Mass: 17181.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA22
#36: Protein 30S ribosomal protein S6 /


Mass: 14986.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IBC1
#37: Protein 30S ribosomal protein S7 /


Mass: 17733.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I7S0
#38: Protein 30S ribosomal protein S8 /


Mass: 14250.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA25
#39: Protein 30S ribosomal protein S9 /


Mass: 14287.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: V5VBA5
#40: Protein 30S ribosomal protein S10 /


Mass: 11718.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. ANC 5600 (bacteria) / References: UniProt: A0A1T1GZ10
#41: Protein 30S ribosomal protein S11 /


Mass: 13558.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. 263903-1 (bacteria) / References: UniProt: A0A062C259
#42: Protein 30S ribosomal protein S12 /


Mass: 13797.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I7R9
#43: Protein 30S ribosomal protein S13 /


Mass: 13295.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA17
#44: Protein 30S ribosomal protein S14 /


Mass: 11438.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA26
#45: Protein 30S ribosomal protein S15 /


Mass: 10145.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I3U0
#46: Protein 30S ribosomal protein S16 /


Mass: 11223.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: A0A1V3DIZ9
#47: Protein 30S ribosomal protein S17 /


Mass: 9543.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA30
#48: Protein 30S ribosomal protein S18 /


Mass: 9009.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter venetianus (bacteria) / References: UniProt: A0A150HZL5
#49: Protein 30S ribosomal protein S19 /


Mass: 10206.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA35
#50: Protein 30S ribosomal protein S20 /


Mass: 9723.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I5N9
#51: Protein 30S ribosomal protein S21 /


Mass: 8474.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. 263903-1 (bacteria) / References: UniProt: A0A062C3F9

-
Non-polymers , 4 types, 615 molecules

#54: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#55: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 93 / Source method: obtained synthetically / Formula: Mg
#56: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#57: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Acinetobacter baumannii 70S ribosome with E-site tRNA bound
Type: RIBOSOME / Entity ID: #1-#53 / Source: NATURAL
Molecular weightValue: 2.3 MDa / Experimental value: NO
Source (natural)Organism: Acinetobacter baumannii AB0057 (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.15_3459refinement
PHENIX1.15_3459refinement
EM software
IDNameCategoryDetails
2Latitudeimage acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12RELIONclassificationFocused classification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90845 / Symmetry type: POINT
Atomic model buildingPDB-ID: 5AFI

5afi

RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0018153924
ELECTRON MICROSCOPYf_angle_d0.4586230685
ELECTRON MICROSCOPYf_chiral_restr0.029329560
ELECTRON MICROSCOPYf_plane_restr0.003412107
ELECTRON MICROSCOPYf_dihedral_angle_d15.49981889

+
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