[English] 日本語
Yorodumi
- PDB-9b24: WT strain gidB mutant mycobacterial ribosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9b24
TitleWT strain gidB mutant mycobacterial ribosome
Components
  • (Large ribosomal subunit protein ...) x 28
  • (Small ribosomal subunit protein ...) x 18
  • 23S rRNA
  • 23S rRNA part
  • 50S ribosomal protein L36
  • 5S rRNA
  • RNA (1528-MER)
KeywordsRIBOSOME / mycobacteria
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / : / Ribosomal protein S14, type Z ...Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / : / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / 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 L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein L28/L24 / Ribosomal protein S18 signature. / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / :
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL33A ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / 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 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bS18B / Large ribosomal subunit protein bL34
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsYoung, I.D. / Chen, Y. / Javid, B. / Fraser, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM133129 United States
CitationJournal: To be published
Title: Ribosomal RNA methylation by GidB is a capacitor for discrimination of mischarged tRNA
Authors: Chen, Y. / Young, I.D. / Fraser, J.S. / Javid, B.
History
DepositionMar 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (1528-MER)
C: Small ribosomal subunit protein uS3
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: Small ribosomal subunit protein bS6
G: Small ribosomal subunit protein uS7
H: Small ribosomal subunit protein uS8
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
M: Small ribosomal subunit protein uS13
N: Small ribosomal subunit protein uS14B
O: Small ribosomal subunit protein uS15
P: Small ribosomal subunit protein bS16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18B
T: Small ribosomal subunit protein bS20
V: Small ribosomal subunit protein uS2
Y: 23S rRNA
U: 5S rRNA
Z: Large ribosomal subunit protein uL2
a: Large ribosomal subunit protein uL3
b: Large ribosomal subunit protein uL4
c: Large ribosomal subunit protein uL5
d: Large ribosomal subunit protein uL6
e: Large ribosomal subunit protein uL11
f: Large ribosomal subunit protein uL13
g: Large ribosomal subunit protein uL14
h: Large ribosomal subunit protein uL15
i: Large ribosomal subunit protein uL16
j: Large ribosomal subunit protein bL17
k: Large ribosomal subunit protein uL18
l: Large ribosomal subunit protein bL19
m: Large ribosomal subunit protein bL20
n: Large ribosomal subunit protein bL21
o: Large ribosomal subunit protein uL22
p: Large ribosomal subunit protein uL23
q: Large ribosomal subunit protein uL24
r: Large ribosomal subunit protein bL25
s: Large ribosomal subunit protein bL27
t: Large ribosomal subunit protein bL28
u: Large ribosomal subunit protein uL29
v: Large ribosomal subunit protein uL10
w: Large ribosomal subunit protein uL30
x: Large ribosomal subunit protein bL32
y: Large ribosomal subunit protein bL33A
z: Large ribosomal subunit protein bL34
1: Large ribosomal subunit protein bL35
2: 50S ribosomal protein L36
4: 23S rRNA part
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,279,854680
Polymers2,264,36051
Non-polymers15,493629
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
RNA chain , 4 types, 4 molecules AYU4

#1: RNA chain RNA (1528-MER)


Mass: 495373.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: GenBank: 2093960070
#20: RNA chain 23S rRNA


Mass: 1012140.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: GenBank: 2198294598
#21: RNA chain 5S rRNA


Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: GenBank: 967054
#51: RNA chain 23S rRNA part


Mass: 26249.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: GenBank: 4586628

-
Small ribosomal subunit protein ... , 18 types, 18 molecules CDEFGHIJKLMNOPQRTV

#2: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 30191.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSD7
#3: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23415.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSL7
#4: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 21946.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSG6
#5: Protein Small ribosomal subunit protein bS6


Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0A2U9Q0X2
#6: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 17660.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QS97
#7: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14492.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSG3
#8: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 16794.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSP9
#9: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11454.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSD0
#10: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 14671.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSL6
#11: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13896.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QS96
#12: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 14249.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSL5
#13: Protein Small ribosomal subunit protein uS14B / 30S ribosomal protein S14 type Z


Mass: 6976.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSG2
#14: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10368.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QVQ3
#15: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 16795.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QV37
#16: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 11127.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSE0
#17: Protein Small ribosomal subunit protein bS18B / 30S ribosomal protein S18 2


Mass: 9524.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0R7F7
#18: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9556.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0R102
#19: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 30145.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QVB8

+
Large ribosomal subunit protein ... , 28 types, 28 molecules Zabcdefghijklmnopqrstuvwxyz1

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


Mass: 30425.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSD4
#23: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 23011.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSD1
#24: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22920.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSD2
#25: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 21152.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSG1
#26: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19483.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSG4
#27: Protein Large ribosomal subunit protein uL11 / 50S ribosomal protein L11


Mass: 15023.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QS45
#28: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16146.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSP8
#29: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13400.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSF9
#30: Protein Large ribosomal subunit protein uL15


Mass: 15602.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSG8
#31: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15774.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSD8
#32: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 21892.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSL9
#33: Protein Large ribosomal subunit protein uL18


Mass: 13711.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSG5
#34: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 12892.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QV42
#35: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 14494.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QYU6
#36: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11055.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0R151
#37: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 16353.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSD6
#38: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 11047.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSD3
#39: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11228.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSG0
#40: Protein Large ribosomal subunit protein bL25 / General stress protein CTC


Mass: 22571.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0R3D2
#41: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 9249.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0R150
#42: Protein Large ribosomal subunit protein bL28


Mass: 6891.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QV03
#43: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 8790.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSD9
#44: Protein Large ribosomal subunit protein uL10 / 50S ribosomal protein L10


Mass: 18035.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QS62
#45: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 7022.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSG7
#46: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6467.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0R3I9
#47: Protein Large ribosomal subunit protein bL33A / 50S ribosomal protein L33 1


Mass: 6468.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QS39
#48: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5522.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0R7K0
#49: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7298.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QYU7

-
Protein/peptide , 1 types, 1 molecules 2

#50: Protein/peptide 50S ribosomal protein L36


Mass: 4341.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Variant: gidB mutant / Strain: WT / References: UniProt: A0QSL4

-
Non-polymers , 2 types, 629 molecules

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


Mass: 24.305 Da / Num. of mol.: 624 / Source method: obtained synthetically / Formula: Mg
#53: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mycobacterium smegmatis ribosome, WT strain, gidB mutant
Type: RIBOSOME / Entity ID: #1-#51 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: HWS19
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA positive charge / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.2 K

-
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 magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / C2 aperture diameter: 150 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 901.165 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9030

-
Processing

EM software
IDNameVersionCategory
1cisTEMdevelopmentparticle selection
2SerialEMimage acquisition
3cisTEMdevelopmentCTF correction
4UCSF ChimeraXmodel fitting
5ISOLDEmodel fitting
6Cootmodel fitting
7PyMOLmodel fitting
12PHENIX1.19.2_4158model refinement
13ISOLDEmodel refinement
14cisTEMdevelopmentinitial Euler assignment
15cisTEMdevelopmentfinal Euler assignment
16cisTEMdevelopmentclassification
17cisTEMdevelopment3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1466881 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15o60

5o60

15o601PDBexperimental model
25o5j

5o5j

15o5j2PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004159110
ELECTRON MICROSCOPYf_angle_d0.652238404
ELECTRON MICROSCOPYf_dihedral_angle_d16.08963142
ELECTRON MICROSCOPYf_chiral_restr0.0430574
ELECTRON MICROSCOPYf_plane_restr0.00612621

+
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