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- PDB-9l96: State D of archaeal pre-50S ribosome -

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Basic information

Entry
Database: PDB / ID: 9l96
TitleState D of archaeal pre-50S ribosome
Components
  • (Large ribosomal subunit protein ...) x 27
  • 23S RNA
  • 5S RNA
  • CBS domain-containing protein
KeywordsRIBOSOME / State D of archaeal pre-50S ribosome
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) / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / nucleotide binding / DNA repair / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
: / : / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein L19e, archaeal / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal ...: / : / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein L19e, archaeal / Ribosomal protein L15e, 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 / DNA repair Rad51/transcription factor NusA, alpha-helical / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / SAM-like Helix-hairpin-helix tandem / CBS domain / CBS domain / CBS domain profile. / : / : / Ribosomal protein L23 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribosomal protein L2, archaeal-type / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L10e / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / : / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L19 / Ribosomal protein L13, eukaryotic/archaeal / : / Ribosomal protein L18e / : / : / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L15e, conserved site / Ribosomal protein L15e signature. / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal_L15e / Ribosomal protein L32e / Ribosomal protein L37ae/L37e / Ribosomal protein L32e superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL20 ...ADENOSINE-5'-DIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL18 / Signal transduction protein / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL18
Similarity search - Component
Biological speciesHaloferax mediterranei ATCC 33500 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsLi, Z.Q. / Yang, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32301015 China
CitationJournal: To Be Published
Title: State D of archaeal pre-50S ribosome
Authors: Li, Z.Q. / Yang, X.Y.
History
DepositionDec 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 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
0: 23S RNA
9: 5S RNA
a: CBS domain-containing protein
E: Large ribosomal subunit protein eL8
F: Large ribosomal subunit protein uL16
G: Large ribosomal subunit protein eL15
H: Large ribosomal subunit protein eL18
I: Large ribosomal subunit protein uL18
J: Large ribosomal subunit protein eL19
K: Large ribosomal subunit protein eL21
L: Large ribosomal subunit protein uL22
M: Large ribosomal subunit protein eL24
N: Large ribosomal subunit protein uL24
O: Large ribosomal subunit protein uL30
P: Large ribosomal subunit protein eL31
Q: Large ribosomal subunit protein eL32
R: Large ribosomal subunit protein eL43
S: Large ribosomal subunit protein eL37
T: Large ribosomal subunit protein eL42
U: Large ribosomal subunit protein uL2
V: Large ribosomal subunit protein uL3
W: Large ribosomal subunit protein uL4
X: Large ribosomal subunit protein uL5
Y: Large ribosomal subunit protein uL6
b: Large ribosomal subunit protein uL13
f: Large ribosomal subunit protein uL14
d: Large ribosomal subunit protein uL29
c: Large ribosomal subunit protein uL23
A: Large ribosomal subunit protein eL39
e: Large ribosomal subunit protein eL20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,457,812266
Polymers1,451,18830
Non-polymers6,624236
Water00
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 , 2 types, 2 molecules 09

#1: RNA chain 23S RNA


Mass: 944066.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: GenBank: 640913992
#2: RNA chain 5S RNA


Mass: 39188.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: GenBank: 631803440

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Protein , 1 types, 1 molecules a

#3: Protein CBS domain-containing protein / Putative signal transduction protein


Mass: 44531.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: M0INN0

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Large ribosomal subunit protein ... , 27 types, 27 molecules EFGHIJKLMNOPQRSTUVWXYbfdcAe

#4: Protein Large ribosomal subunit protein eL8


Mass: 12659.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R865
#5: Protein Large ribosomal subunit protein uL16


Mass: 19814.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R1S5
#6: Protein Large ribosomal subunit protein eL15


Mass: 22703.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R1Z8
#7: Protein Large ribosomal subunit protein eL18


Mass: 12754.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R8A5
#8: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18 / HmeL18


Mass: 20208.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: P50561
#9: Protein Large ribosomal subunit protein eL19


Mass: 17291.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R7P1
#10: Protein Large ribosomal subunit protein eL21


Mass: 10606.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R877
#11: Protein Large ribosomal subunit protein uL22


Mass: 16975.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R7Q4
#12: Protein Large ribosomal subunit protein eL24


Mass: 7658.405 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R867
#13: Protein Large ribosomal subunit protein uL24


Mass: 13361.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R7P8
#14: Protein Large ribosomal subunit protein uL30


Mass: 17112.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R7N8
#15: Protein Large ribosomal subunit protein eL31


Mass: 10593.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R0V9
#16: Protein Large ribosomal subunit protein eL32 / 50S ribosomal protein L32e


Mass: 25889.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R7P2
#17: Protein Large ribosomal subunit protein eL43


Mass: 9832.003 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R290
#18: Protein Large ribosomal subunit protein eL37


Mass: 6442.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R849
#19: Protein Large ribosomal subunit protein eL42


Mass: 10698.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R2C4
#20: Protein Large ribosomal subunit protein uL2


Mass: 25707.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R7Q6
#21: Protein Large ribosomal subunit protein uL3


Mass: 37409.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R7Q9
#22: Protein Large ribosomal subunit protein uL4


Mass: 27023.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R7Q8
#23: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5 / HmeL5


Mass: 19145.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: P50557
#24: Protein Large ribosomal subunit protein uL6


Mass: 19543.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R7P3
#25: Protein Large ribosomal subunit protein uL13


Mass: 16199.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R8A4
#26: Protein Large ribosomal subunit protein uL14


Mass: 14272.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R7P9
#27: Protein Large ribosomal subunit protein uL29


Mass: 7690.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R7Q2
#28: Protein Large ribosomal subunit protein uL23


Mass: 9441.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R7Q7
#29: Protein/peptide Large ribosomal subunit protein eL39


Mass: 6058.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R0V8
#30: Protein Large ribosomal subunit protein eL20


Mass: 6308.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloferax mediterranei ATCC 33500 (archaea)
References: UniProt: I3R0W1

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Non-polymers , 3 types, 236 molecules

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


Mass: 24.305 Da / Num. of mol.: 232 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#33: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: State D of archaeal pre-50S ribosome / Type: RIBOSOME / Entity ID: #1-#30 / Source: NATURAL
Source (natural)Organism: Haloferax mediterranei ATCC 33500 (archaea)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 918876 / Symmetry type: POINT
RefinementCross valid method: NONE

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