[English] 日本語
Yorodumi
- PDB-9e7f: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9e7f
TitleCryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri
Components
  • (Large ribosomal subunit protein ...) x 31
  • (SSU ribosomal protein ...) x 3
  • (Small ribosomal subunit protein ...) x 24
  • 16S rRNA
  • 23S rRNA
  • 50S ribosomal protein L15e
  • 5S rRNA
  • DJ-1/PfpI domain-containing protein
  • LSU ribosomal protein L38E
  • PaREP1 domain containing protein
  • Putative signal-transduction protein with CBS domains
  • Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein
  • aS35
  • eL42
KeywordsRIBOSOME / Translation / Hibernation / RNA
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / ribosome biogenesis / large ribosomal subunit / ribosomal small subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / ribosome biogenesis / large ribosomal subunit / ribosomal small subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S 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 / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L14e / : / : / Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein L40e, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal ...Ribosomal protein L14e / : / : / Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein L40e, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / : / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S14, type Z, archaeal / Ribosomal protein S8e, archaeal / Ribosomal protein L19e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L32e, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / : / DJ-1/PfpI / DJ-1/PfpI family / Ribosomal protein L7Ae, archaea / Domain in cystathionine beta-synthase and other proteins. / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / CBS domain superfamily / Ribosomal L15/L27a, N-terminal / CBS domain / CBS domain / CBS domain profile. / Ribosomal protein L23 / : / Class I glutamine amidotransferase-like / metallochaperone-like domain / TRASH domain / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein S27e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / : / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein S19A/S15e
Similarity search - Domain/homology
SPERMINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL2 ...SPERMINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / SSU ribosomal protein S30E / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL22 / DJ-1/PfpI domain-containing protein / Large ribosomal subunit protein eL13 / LSU ribosomal protein L38E / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL15 / SSU ribosomal protein S25E / SSU ribosomal protein S26E / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / 50S ribosomal protein L15e / PaREP1 domain containing protein / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Putative signal-transduction protein with CBS domains / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL40 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL13 / Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein / Large ribosomal subunit protein eL37 / Small ribosomal subunit protein eS28
Similarity search - Component
Biological speciesPyrobaculum calidifontis JCM 11548 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsNissley, A.J. / Cate, J.H.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2002182 United States
CitationJournal: To Be Published
Title: Structure of an Archaeal Ribosome with a Divergent Active Site
Authors: Nissley, A.J. / Shulgina, Y. / Kivimae, R.W. / Downing, B.E. / Penev, P.I. / Banfield, J.F. / Nayak, D.D. / Cate, J.H.D.
History
DepositionNov 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
2: 5S rRNA
3: Putative signal-transduction protein with CBS domains
1: 23S rRNA
4: 16S rRNA
AA: Large ribosomal subunit protein uL2
AB: Large ribosomal subunit protein uL3
AC: Large ribosomal subunit protein uL4
AD: Large ribosomal subunit protein uL5
AE: Large ribosomal subunit protein uL6
AF: Large ribosomal subunit protein eL8
AG: Large ribosomal subunit protein uL13
AH: Large ribosomal subunit protein eL13
AI: Large ribosomal subunit protein uL14
AJ: Large ribosomal subunit protein eL14
AK: Large ribosomal subunit protein eL14
AL: Large ribosomal subunit protein uL15
AM: 50S ribosomal protein L15e
AN: Large ribosomal subunit protein uL16
AO: Large ribosomal subunit protein uL18
AP: Large ribosomal subunit protein eL18
AQ: Large ribosomal subunit protein eL19
AR: Large ribosomal subunit protein eL20
AS: Large ribosomal subunit protein eL21
AT: Large ribosomal subunit protein uL22
AU: Large ribosomal subunit protein uL23
AV: Large ribosomal subunit protein uL24
AW: Large ribosomal subunit protein eL24
AX: Large ribosomal subunit protein uL29
AY: Large ribosomal subunit protein uL30
AZ: Large ribosomal subunit protein eL30
Aa: Large ribosomal subunit protein eL31
Ab: Large ribosomal subunit protein eL32
Ac: Large ribosomal subunit protein eL34
Ad: Large ribosomal subunit protein eL37
Ae: LSU ribosomal protein L38E
Af: Large ribosomal subunit protein eL39
Ag: Large ribosomal subunit protein eL40
Ah: eL42
Ai: Large ribosomal subunit protein eL43
Aj: DJ-1/PfpI domain-containing protein
Ak: PaREP1 domain containing protein
BA: Small ribosomal subunit protein eS1
BB: Small ribosomal subunit protein uS2
BC: Small ribosomal subunit protein uS3
BD: Small ribosomal subunit protein uS4
BE: Small ribosomal subunit protein eS4
BF: Small ribosomal subunit protein uS5
BG: Small ribosomal subunit protein eS6
BH: Small ribosomal subunit protein uS7
BI: Small ribosomal subunit protein uS8
BJ: Small ribosomal subunit protein eS8
BK: Small ribosomal subunit protein uS9
BL: Small ribosomal subunit protein uS10
BM: Small ribosomal subunit protein uS11
BN: Small ribosomal subunit protein uS12
BO: Small ribosomal subunit protein uS13
BP: Small ribosomal subunit protein uS14
BQ: Small ribosomal subunit protein uS15
BR: Small ribosomal subunit protein uS17
BS: Small ribosomal subunit protein eS17
BT: Small ribosomal subunit protein uS19
BU: Small ribosomal subunit protein eS19
BV: Small ribosomal subunit protein eS24
BW: SSU ribosomal protein S25E
BX: SSU ribosomal protein S26E
BY: Small ribosomal subunit protein eS27
BZ: Small ribosomal subunit protein eS28
Ba: SSU ribosomal protein S30E
Bb: aS35
Bc: Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,631,374396
Polymers2,611,60570
Non-polymers19,770326
Water115,0626387
1


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

-
Components

-
RNA chain , 3 types, 3 molecules 214

#1: RNA chain 5S rRNA


Mass: 41803.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: GenBank: 126248349
#3: RNA chain 23S rRNA


Mass: 984007.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
#4: RNA chain 16S rRNA


Mass: 487519.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: GenBank: 343200235

-
Protein , 8 types, 8 molecules 3AMAeAhAjAkBbBc

#2: Protein Putative signal-transduction protein with CBS domains


Mass: 72127.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MX58
#16: Protein 50S ribosomal protein L15e


Mass: 22623.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWR6
#34: Protein LSU ribosomal protein L38E


Mass: 7954.435 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTT1
#37: Protein eL42


Mass: 10603.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
#39: Protein DJ-1/PfpI domain-containing protein


Mass: 20956.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTM7
#40: Protein PaREP1 domain containing protein


Mass: 10938.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWU0
#68: Protein aS35


Mass: 7856.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
#69: Protein Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein


Mass: 6956.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MY11

+
Large ribosomal subunit protein ... , 31 types, 32 molecules AAABACADAEAFAGAHAIAJAKALANAOAPAQARASATAUAVAWAXAYAZAaAbAcAdAfAgAi

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


Mass: 26240.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MS41
#6: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 37240.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWI4
#7: Protein Large ribosomal subunit protein uL4


Mass: 31602.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWI5
#8: Protein Large ribosomal subunit protein uL5


Mass: 20156.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MXP8
#9: Protein Large ribosomal subunit protein uL6


Mass: 21663.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWV5
#10: Protein Large ribosomal subunit protein eL8 / 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 16013.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTA9
#11: Protein Large ribosomal subunit protein uL13


Mass: 21736.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MXZ7
#12: Protein Large ribosomal subunit protein eL13


Mass: 17939.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTP8
#13: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 15768.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MX34
#14: Protein Large ribosomal subunit protein eL14 / 50S ribosomal protein L14e


Mass: 11470.542 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MS76
#15: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 17525.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MUZ1
#17: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L10e


Mass: 19893.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MXP3
#18: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 23424.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MSJ3
#19: Protein Large ribosomal subunit protein eL18


Mass: 13224.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MXZ6
#20: Protein Large ribosomal subunit protein eL19


Mass: 17414.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MSJ4
#21: Protein Large ribosomal subunit protein eL20 / 50S ribosomal protein L18Ae / 50S ribosomal protein L20e / 50S ribosomal protein LX


Mass: 8929.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MX77
#22: Protein Large ribosomal subunit protein eL21 / 50S ribosomal protein L21e


Mass: 11319.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWX9
#23: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 21309.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTL6
#24: Protein Large ribosomal subunit protein uL23


Mass: 9307.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWI6
#25: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 14588.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWZ8
#26: Protein Large ribosomal subunit protein eL24 / 50S ribosomal protein L24e


Mass: 7102.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTA8
#27: Protein Large ribosomal subunit protein uL29


Mass: 9158.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTL2
#28: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 20287.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MU87
#29: Protein Large ribosomal subunit protein eL30 / 50S ribosomal protein L30e


Mass: 10886.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MXZ2
#30: Protein Large ribosomal subunit protein eL31 / 50S ribosomal protein L31e


Mass: 10668.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MX75
#31: Protein Large ribosomal subunit protein eL32


Mass: 18172.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MSJ5
#32: Protein Large ribosomal subunit protein eL34 / 50S ribosomal protein L34e


Mass: 9373.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MV68
#33: Protein Large ribosomal subunit protein eL37


Mass: 6174.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MY38
#35: Protein Large ribosomal subunit protein eL39 / 50S ribosomal protein L39e


Mass: 6030.298 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MUU4
#36: Protein Large ribosomal subunit protein eL40 / 50S ribosomal protein L40e


Mass: 6356.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MX99
#38: Protein Large ribosomal subunit protein eL43


Mass: 11387.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MUM7

+
Small ribosomal subunit protein ... , 24 types, 24 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBYBZ

#41: Protein Small ribosomal subunit protein eS1 / 30S ribosomal protein S3Ae / Ribosomal protein S1e


Mass: 24740.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MVE0
#42: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 23829.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MS50
#43: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 24688.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTL3
#44: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 18516.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MUS9
#45: Protein Small ribosomal subunit protein eS4 / 30S ribosomal protein S4e


Mass: 26774.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWZ7
#46: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 22153.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MU88
#47: Protein Small ribosomal subunit protein eS6 / 30S ribosomal protein S6e


Mass: 16248.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MUD0
#48: Protein Small ribosomal subunit protein uS7


Mass: 25515.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MS29
#49: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14836.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MSJ6
#50: Protein Small ribosomal subunit protein eS8 / 30S ribosomal protein S8e


Mass: 14446.925 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MWY2
#51: Protein Small ribosomal subunit protein uS9


Mass: 16146.151 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
#52: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 12221.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MT22
#53: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 14984.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MX63
#54: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 16477.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MXZ4
#55: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 16758.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MUT0
#56: Protein Small ribosomal subunit protein uS14


Mass: 6429.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MSJ7
#57: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 17587.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MVD1
#58: Protein Small ribosomal subunit protein uS17


Mass: 16986.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MTT7
#59: Protein Small ribosomal subunit protein eS17 / 30S ribosomal protein S17e


Mass: 8082.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MS42
#60: Protein Small ribosomal subunit protein uS19


Mass: 18182.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A0A831L0N9
#61: Protein Small ribosomal subunit protein eS19


Mass: 17770.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MUU6
#62: Protein Small ribosomal subunit protein eS24


Mass: 14855.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MSX4
#65: Protein Small ribosomal subunit protein eS27 / 30S ribosomal protein S27e


Mass: 7446.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MUV2
#66: Protein Small ribosomal subunit protein eS28 / 30S ribosomal protein S28e


Mass: 8575.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: B1Y9V2

-
SSU ribosomal protein ... , 3 types, 3 molecules BWBXBa

#63: Protein SSU ribosomal protein S25E


Mass: 12477.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MV37
#64: Protein SSU ribosomal protein S26E


Mass: 11571.864 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MV49
#67: Protein SSU ribosomal protein S30E


Mass: 6113.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrobaculum calidifontis JCM 11548 (archaea)
References: UniProt: A3MSW3

-
Non-polymers , 4 types, 6713 molecules

#70: Chemical...
ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C10H26N4
#71: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 251 / Source method: obtained synthetically / Formula: Mg
#72: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#73: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6387 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
170S ribosomeRIBOSOME#1-#690NATURAL
250S SubunitCOMPLEX#1, #3, #5-#401NATURAL
330S subunitCOMPLEX#4, #41-#691NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
31
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Pyrobaculum calidifontis JCM 11548 (archaea)410359
32Pyrobaculum calidifontis JCM 11548 (archaea)410359
43Pyrobaculum calidifontis JCM 11548 (archaea)410359
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
210 mMPotassium ChlorideKCl1
320 mMMagnesium AcetateMg(CH3COO)21
43 mMSpermineC10H26N41
52 mMDTTC4H10O2S21
SpecimenConc.: 0.12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7318

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4particle selection
2SerialEMimage acquisition
4cryoSPARC4.4CTF correction
7UCSF ChimeraXmodel fitting
9Cootmodel refinement
10PHENIXmodel refinement
11cryoSPARC4.4initial Euler assignment
12cryoSPARC4.4final Euler assignment
14cryoSPARC4.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2360632
3D reconstructionResolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72157 / Details: Global resolution / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

+
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