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- PDB-9e7f: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in... -

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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 / cytosolic ribosome / ribosomal large subunit biogenesis / large ribosomal subunit / ribosome biogenesis / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / small ribosomal subunit ...ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / ribosomal large subunit biogenesis / large ribosomal subunit / ribosome biogenesis / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
: / 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 L14e / : / Ribosomal protein L40e, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal ...: / 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 L14e / : / 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 / Ribosomal protein L7Ae, archaea / DJ-1/PfpI / DJ-1/PfpI family / Ribosomal protein L24e / 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 S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L24e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L24e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S3, eukaryotic/archaeal / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S27e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein S19A/S15e / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein L34Ae
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

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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

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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

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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

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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

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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

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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

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Details

Has ligand of interestN
Has protein modificationY

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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

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

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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

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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

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