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- PDB-9hc4: Cryo-EM structure of P. urativorans 70S ribosome with 2 copies of... -

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Basic information

Entry
Database: PDB / ID: 9hc4
TitleCryo-EM structure of P. urativorans 70S ribosome with 2 copies of bS20.
Components
  • (Large ribosomal subunit protein ...) x 29
  • (Small ribosomal subunit protein ...) x 20
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
KeywordsRIBOSOME / ribosome heterogeneity / functionally specialized ribosomes / polysome
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / 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 / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / 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 L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / 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 L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 / 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 L9 signature. / : / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / 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 L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / 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 S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / 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 L28/L24 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 domain superfamily / Ribosomal protein S16
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL31B / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL21
Similarity search - Component
Biological speciesPsychrobacter urativorans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHelena-Bueno, K. / Hill, C.H. / Melnikov, S.V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal SocietyRGS/R2/202003 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Structurally heterogeneous ribosomes cooperate in protein synthesis in bacterial cells.
Authors: Karla Helena-Bueno / Sophie Kopetschke / Sebastian Filbeck / Lewis I Chan / Sonia Birsan / Arnaud Baslé / Maisie Hudson / Stefan Pfeffer / Chris H Hill / Sergey V Melnikov /
Abstract: Ribosome heterogeneity is a paradigm in biology, pertaining to the existence of structurally distinct populations of ribosomes within a single organism or cell. This concept suggests that ...Ribosome heterogeneity is a paradigm in biology, pertaining to the existence of structurally distinct populations of ribosomes within a single organism or cell. This concept suggests that structurally distinct pools of ribosomes have different functional properties and may be used to translate specific mRNAs. However, it is unknown to what extent structural heterogeneity reflects genuine functional specialization rather than stochastic variations in ribosome assembly. Here, we address this question by combining cryo-electron microscopy and tomography to observe individual structurally heterogeneous ribosomes in bacterial cells. We show that 70% of ribosomes in Psychrobacter urativorans contain a second copy of the ribosomal protein bS20 at a previously unknown binding site on the large ribosomal subunit. We then determine that this second bS20 copy appears to be functionally neutral. This demonstrates that ribosome heterogeneity does not necessarily lead to functional specialization, even when it involves significant variations such as the presence or absence of a ribosomal protein. Instead, we show that heterogeneous ribosomes can cooperate in general protein synthesis rather than specialize in translating discrete populations of mRNA.
History
DepositionNov 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Small ribosomal subunit protein uS9
C1: Large ribosomal subunit protein bL9
R3: Small ribosomal subunit protein bS18
A4: Small ribosomal subunit protein uS2
E5: Small ribosomal subunit protein uS5
L6: Small ribosomal subunit protein uS12
F7: Large ribosomal subunit protein uL5
E9: Large ribosomal subunit protein uL4
aA: Large ribosomal subunit protein bL32
MB: Large ribosomal subunit protein bL17
UC: Large ribosomal subunit protein bL25
WD: Large ribosomal subunit protein bL28
XE: Large ribosomal subunit protein uL29
RF: Large ribosomal subunit protein uL22
FG: Small ribosomal subunit protein bS6
VH: Large ribosomal subunit protein bL27
TI: Large ribosomal subunit protein uL24
fJ: Large ribosomal subunit protein bL31B
HK: Small ribosomal subunit protein uS14
OL: Small ribosomal subunit protein uS15
MM: Small ribosomal subunit protein uS13
PO: Large ribosomal subunit protein bL20
SP: Small ribosomal subunit protein uS19
BQ: Small ribosomal subunit protein uS8
GR: Large ribosomal subunit protein uL6
GS: Small ribosomal subunit protein uS7
CT: Small ribosomal subunit protein uS3
KU: Small ribosomal subunit protein uS11
NV: Small ribosomal subunit protein bS21
YW: Large ribosomal subunit protein uL30
IX: Large ribosomal subunit protein uL13
JY: Small ribosomal subunit protein uS10
QZ: Small ribosomal subunit protein uS17
Ba: Large ribosomal subunit protein bL34
Qb: Large ribosomal subunit protein bL21
Nc: Large ribosomal subunit protein uL18
Kd: Large ribosomal subunit protein uL15
Je: Large ribosomal subunit protein uL14
Af: Large ribosomal subunit protein uL3
Lg: Large ribosomal subunit protein uL16
dh: Large ribosomal subunit protein bL35
Oi: Large ribosomal subunit protein bL19
Pj: Small ribosomal subunit protein bS16
bk: Large ribosomal subunit protein bL33
Cl: Large ribosomal subunit protein uL2
Dm: Small ribosomal subunit protein uS4
Sn: Large ribosomal subunit protein uL23
To: Small ribosomal subunit protein bS20
ep: Large ribosomal subunit protein bL36
A: Small ribosomal subunit protein bS20
D8: 5S rRNA
iN: 16S rRNA
Z2: 23S rRNA


Theoretical massNumber of molelcules
Total (without water)2,180,73453
Polymers2,180,73453
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Small ribosomal subunit protein ... , 20 types, 21 molecules FR3A4E5L6FGHKOLMMSPBQGSCTKUNVJYQZPjDmToA

#1: Protein Small ribosomal subunit protein uS9


Mass: 14278.470 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T6M9
#3: Protein Small ribosomal subunit protein bS18


Mass: 8973.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MK69
#4: Protein Small ribosomal subunit protein uS2


Mass: 29465.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TFJ4
#5: Protein Small ribosomal subunit protein uS5


Mass: 18192.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8J0
#6: Protein Small ribosomal subunit protein uS12


Mass: 13753.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U4C3
#15: Protein Small ribosomal subunit protein bS6


Mass: 15839.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U628
#19: Protein Small ribosomal subunit protein uS14


Mass: 11777.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8P8
#20: Protein Small ribosomal subunit protein uS15


Mass: 10218.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TF29
#21: Protein Small ribosomal subunit protein uS13


Mass: 13244.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MJL8
#23: Protein Small ribosomal subunit protein uS19


Mass: 10336.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TUJ8
#24: Protein Small ribosomal subunit protein uS8


Mass: 14086.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U618
#26: Protein Small ribosomal subunit protein uS7


Mass: 17760.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8N5
#27: Protein Small ribosomal subunit protein uS3


Mass: 27120.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T6V9
#28: Protein Small ribosomal subunit protein uS11


Mass: 13676.589 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8P6
#29: Protein Small ribosomal subunit protein bS21


Mass: 8548.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4SY21
#32: Protein Small ribosomal subunit protein uS10


Mass: 11635.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TE68
#33: Protein Small ribosomal subunit protein uS17


Mass: 10362.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U401
#43: Protein Small ribosomal subunit protein bS16


Mass: 9955.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T275
#46: Protein Small ribosomal subunit protein uS4


Mass: 24279.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TE52
#48: Protein Small ribosomal subunit protein bS20


Mass: 9980.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T3R2

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Large ribosomal subunit protein ... , 29 types, 29 molecules C1F7E9aAMBUCWDXERFVHTIfJPOGRYWIXBaQbNcKdJeAfLgdhOibkClSnep

#2: Protein Large ribosomal subunit protein bL9


Mass: 18195.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V9E8
#7: Protein Large ribosomal subunit protein uL5


Mass: 19841.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T1L5
#8: Protein Large ribosomal subunit protein uL4


Mass: 21971.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U627
#9: Protein Large ribosomal subunit protein bL32


Mass: 7169.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4SWQ6
#10: Protein Large ribosomal subunit protein bL17


Mass: 13635.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U611
#11: Protein Large ribosomal subunit protein bL25 / General stress protein CTC


Mass: 23887.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U726
#12: Protein Large ribosomal subunit protein bL28


Mass: 9168.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T6Y7
#13: Protein Large ribosomal subunit protein uL29


Mass: 7519.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TBX9
#14: Protein Large ribosomal subunit protein uL22


Mass: 11932.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4SWS6
#16: Protein Large ribosomal subunit protein bL27


Mass: 9119.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TUE5
#17: Protein Large ribosomal subunit protein uL24


Mass: 11465.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TE60
#18: Protein Large ribosomal subunit protein bL31B


Mass: 10708.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4SX87
#22: Protein Large ribosomal subunit protein bL20


Mass: 13539.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MJR6
#25: Protein Large ribosomal subunit protein uL6


Mass: 19536.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MKV2
#30: Protein Large ribosomal subunit protein uL30


Mass: 6615.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4SWR7
#31: Protein Large ribosomal subunit protein uL13


Mass: 15802.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TBP4
#34: Protein/peptide Large ribosomal subunit protein bL34


Mass: 5292.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TEZ6
#35: Protein Large ribosomal subunit protein bL21


Mass: 11773.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5TIS3
#36: Protein Large ribosomal subunit protein uL18


Mass: 12550.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TUJ2
#37: Protein Large ribosomal subunit protein uL15


Mass: 15448.876 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T6V1
#38: Protein Large ribosomal subunit protein uL14


Mass: 13417.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MJS2
#39: Protein Large ribosomal subunit protein uL3


Mass: 22236.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T1M3
#40: Protein Large ribosomal subunit protein uL16


Mass: 15626.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8J3
#41: Protein Large ribosomal subunit protein bL35


Mass: 7594.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U4I0
#42: Protein Large ribosomal subunit protein bL19


Mass: 14598.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TV08
#44: Protein Large ribosomal subunit protein bL33


Mass: 6053.298 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4SWV1
#45: Protein Large ribosomal subunit protein uL2


Mass: 30263.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8Q0
#47: Protein Large ribosomal subunit protein uL23


Mass: 12816.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MJH9
#49: Protein/peptide Large ribosomal subunit protein bL36


Mass: 4330.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U3Z5

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RNA chain , 3 types, 3 molecules D8iNZ2

#50: RNA chain 5S rRNA


Mass: 36948.945 Da / Num. of mol.: 1 / Mutation: insertion of 85, C89A / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: GenBank: 930356181
#51: RNA chain 16S rRNA


Mass: 514644.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria)
#52: RNA chain 23S rRNA


Mass: 933563.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: GenBank: 930356181

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Details

Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 70S ribosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Psychrobacter urativorans (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1250 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19576 / Symmetry type: POINT

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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

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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

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