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- PDB-9znf: Cryo-EM structure of the Methanosarcina acetivorans 70S ribosome ... -

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Basic information

Entry
Database: PDB / ID: 9znf
TitleCryo-EM structure of the Methanosarcina acetivorans 70S ribosome in complex with SriA and SriB
Components
  • (CBS domain-containing ...) x 2
  • (Large ribosomal subunit protein ...) x 30
  • (Small ribosomal subunit protein ...) x 24
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • DUF5350 family protein
  • E-site tRNA
  • Putative zinc finger domain-containing protein
KeywordsRIBOSOME / Hibernation / Archaea
Function / homology
Function and homology information


: / ribonuclease P activity / tRNA 5'-leader removal / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / transferase activity / ribosomal small subunit biogenesis ...: / ribonuclease P activity / tRNA 5'-leader removal / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / 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 / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Protein of unknown function DUF5350 / Family of unknown function (DUF5350) / : / 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 L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein S9, archaeal ...Protein of unknown function DUF5350 / Family of unknown function (DUF5350) / : / 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 L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein S9, 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 L15e, 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 L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L32e, archaeal / : / Ribosomal protein L7Ae, archaea / : / : / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / : / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L10e / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal L40e family / Ribosomal protein L44e / Ribosomal protein L44 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L30e signature 2. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L30e, conserved site / Ribosomal protein S3, eukaryotic/archaeal / 60S ribosomal protein L19 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L18e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / DUF1610 domain-containing protein / CBS domain-containing protein / CBS domain-containing protein ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / DUF1610 domain-containing protein / CBS domain-containing protein / CBS domain-containing protein / DUF5350 family protein / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL40 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein eL24 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS17A / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL16
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.03 Å
AuthorsNissley, A.J. / Cate, J.H.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Biorxiv / Year: 2026
Title: A family of archaeal hibernation factors that bind in tandem and protect ribosomes in dormant cells
Authors: Nissley, A.J. / Williams, M.C. / Shulgina, Y. / Kivimae, R.W. / Nayak, D.D. / Cate, J.H.D.
History
DepositionDec 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: 23S rRNA
2: 5S rRNA
3: 16S rRNA
5: CBS domain-containing protein
4: CBS domain-containing protein
8: E-site tRNA
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 uL14
AI: Large ribosomal subunit protein uL15
AJ: Large ribosomal subunit protein eL15
AK: Large ribosomal subunit protein uL16
AL: Large ribosomal subunit protein uL18
AM: Large ribosomal subunit protein eL18
AN: Large ribosomal subunit protein eL19
AO: Large ribosomal subunit protein eL20
AP: Large ribosomal subunit protein eL21
AQ: Large ribosomal subunit protein uL22
AR: Large ribosomal subunit protein uL23
AS: Large ribosomal subunit protein uL24
AT: Large ribosomal subunit protein eL24
AU: Large ribosomal subunit protein uL29
AV: Large ribosomal subunit protein uL30
AW: Large ribosomal subunit protein eL30
AX: Large ribosomal subunit protein eL31
AY: Large ribosomal subunit protein eL32
AZ: Large ribosomal subunit protein eL37
Aa: Large ribosomal subunit protein eL39
Ab: Large ribosomal subunit protein eL40
Ac: Large ribosomal subunit protein eL42
Ad: Large ribosomal subunit protein eL43
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 uS9
BK: Small ribosomal subunit protein eS8
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 uS17A
BS: Small ribosomal subunit protein eS17
BT: Small ribosomal subunit protein uS19
BU: Small ribosomal subunit protein eS19
BV: Putative zinc finger domain-containing protein
BW: Small ribosomal subunit protein eS24
BX: Small ribosomal subunit protein eS27
BY: Small ribosomal subunit protein eS28
BZ: DUF5350 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,410,814378
Polymers2,402,68262
Non-polymers8,133316
Water157,4518740
1


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

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Components

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RNA chain , 4 types, 4 molecules 1238

#1: RNA chain 23S rRNA


Mass: 939362.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: GenBank: 470469544
#2: RNA chain 5S rRNA


Mass: 42646.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: GenBank: 19918815
#3: RNA chain 16S rRNA


Mass: 478458.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: GenBank: 470466243
#6: RNA chain E-site tRNA


Mass: 24249.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea)

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CBS domain-containing ... , 2 types, 2 molecules 54

#4: Protein CBS domain-containing protein


Mass: 37446.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Gene: HA338_08680 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A832S9K2
#5: Protein CBS domain-containing protein


Mass: 30268.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Gene: HA338_08675 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A832SJD6

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Large ribosomal subunit protein ... , 30 types, 30 molecules AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAd

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


Mass: 25738.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU4
#8: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 36949.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU7
#9: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 27516.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU6
#10: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 18398.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT4
#11: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19530.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT1
#12: Protein Large ribosomal subunit protein eL8 / 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 12741.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TQL9
#13: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16085.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TT43
#14: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 14356.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT7
#15: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15129.009 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRS5
#16: Protein Large ribosomal subunit protein eL15 / 50S ribosomal protein L15e


Mass: 22650.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TPX0
#17: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L10e


Mass: 19409.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TU90
#18: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 19233.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRS8
#19: Protein Large ribosomal subunit protein eL18 / 50S ribosomal protein L18e


Mass: 13714.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TT44
#20: Protein Large ribosomal subunit protein eL19


Mass: 17061.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832W9G6
#21: Protein Large ribosomal subunit protein eL20 / 50S ribosomal protein L18Ae / 50S ribosomal protein L20e / 50S ribosomal protein LX


Mass: 6972.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TIN5
#22: Protein Large ribosomal subunit protein eL21 / 50S ribosomal protein L21e


Mass: 11063.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TQU3
#23: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 16764.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU2
#24: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 9447.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU5
#25: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 13075.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT6
#26: Protein Large ribosomal subunit protein eL24 / 50S ribosomal protein L24e


Mass: 7204.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TQL7
#27: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7622.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU0
#28: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 17627.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRS6
#29: Protein Large ribosomal subunit protein eL30 / 50S ribosomal protein L30e


Mass: 10316.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRB9
#30: Protein Large ribosomal subunit protein eL31 / 50S ribosomal protein L31e


Mass: 10331.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TIN3
#31: Protein Large ribosomal subunit protein eL32 / 50S ribosomal protein L32e


Mass: 14335.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT0
#32: Protein Large ribosomal subunit protein eL37 / 50S ribosomal protein L37e


Mass: 6456.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TL48
#33: Protein Large ribosomal subunit protein eL39 / 50S ribosomal protein L39e


Mass: 6257.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TIN2
#34: Protein/peptide Large ribosomal subunit protein eL40 / 50S ribosomal protein L40e


Mass: 5602.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TJ19
#35: Protein Large ribosomal subunit protein eL42


Mass: 10872.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832W9V9
#36: Protein Large ribosomal subunit protein eL43


Mass: 10557.483 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832SMV9

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Small ribosomal subunit protein ... , 24 types, 24 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBWBXBY

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


Mass: 22938.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TKI9
#38: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 24807.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TT39
#39: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 34780.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU1
#40: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 24559.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRR1
#41: Protein Small ribosomal subunit protein eS4 / 30S ribosomal protein S4e


Mass: 26301.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT5
#42: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 22732.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRS7
#43: Protein Small ribosomal subunit protein eS6 / 30S ribosomal protein S6e


Mass: 14474.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TQL4
#44: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 21062.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRC2
#45: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14085.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT2
#46: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14512.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TT42
#47: Protein Small ribosomal subunit protein eS8 / 30S ribosomal protein S8e


Mass: 13801.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TS82
#48: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11380.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: P61929
#49: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13324.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRR0
#50: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 15540.140 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRC1
#51: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 18315.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRR2
#52: Protein/peptide Small ribosomal subunit protein uS14 / 30S ribosomal protein S14 type Z


Mass: 5971.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT3
#53: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 17503.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TS56
#54: Protein Small ribosomal subunit protein uS17A / 30S ribosomal protein S17 1


Mass: 12184.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT8
#55: Protein Small ribosomal subunit protein eS17 / 30S ribosomal protein S17e


Mass: 7477.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8THP2
#56: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 15467.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU3
#57: Protein Small ribosomal subunit protein eS19


Mass: 16563.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832W9Q0
#59: Protein Small ribosomal subunit protein eS24 / 30S ribosomal protein S24e


Mass: 11620.263 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TJT2
#60: Protein Small ribosomal subunit protein eS27 / 30S ribosomal protein S27e


Mass: 6955.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: P61931
#61: Protein Small ribosomal subunit protein eS28 / 30S ribosomal protein S28e


Mass: 8268.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TQL8

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Protein , 2 types, 2 molecules BVBZ

#58: Protein Putative zinc finger domain-containing protein


Mass: 6162.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832S8D7
#62: Protein DUF5350 family protein


Mass: 6434.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832SMB7

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Non-polymers , 3 types, 9056 molecules

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


Mass: 24.305 Da / Num. of mol.: 305 / Source method: obtained synthetically / Formula: Mg
#64: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 8740 / 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-#620MULTIPLE SOURCES
250S subunitCOMPLEX#1-#2, #4-#361NATURAL
330S subunitCOMPLEX#3, #37-#621NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Methanosarcina acetivorans (archaea)2214
32Methanosarcina acetivorans (archaea)2214
43Methanosarcina acetivorans (archaea)2214
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
250 mMpotassium chlorideKCl1
310 mMMagnesium chlorideMgCl21
42 mMDTTC4H10O2S21
SpecimenConc.: 0.42 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: 9090

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2488798
3D reconstructionResolution: 2.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95430 / Symmetry type: POINT
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: other
RefinementHighest resolution: 2.03 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004142123
ELECTRON MICROSCOPYf_angle_d0.6210883
ELECTRON MICROSCOPYf_dihedral_angle_d12.73153131
ELECTRON MICROSCOPYf_chiral_restr0.0426718
ELECTRON MICROSCOPYf_plane_restr0.00512439

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