4V4N

Structure of the Methanococcus jannaschii ribosome-SecYEBeta channel complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the SecY channel during initiation of protein translocation.

Park, E.Menetret, J.F.Gumbart, J.C.Ludtke, S.J.Li, W.Whynot, A.Rapoport, T.A.Akey, C.W.

(2013) Nature 506: 102-106

  • DOI: 10.1038/nature12720
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic SecY or eukaryotic Sec61 complexes, and are translocated across the membrane during their synthesis. Crystal structures of the inactive ch ...

    Many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic SecY or eukaryotic Sec61 complexes, and are translocated across the membrane during their synthesis. Crystal structures of the inactive channel show that the SecY subunit of the heterotrimeric complex consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces the lipid phase. The closed channel has an empty cytoplasmic funnel and an extracellular funnel that is filled with a small helical domain, called the plug. During initiation of translocation, a ribosome-nascent chain complex binds to the SecY (or Sec61) complex, resulting in insertion of the nascent chain. However, the mechanism of channel opening during translocation is unclear. Here we have addressed this question by determining structures of inactive and active ribosome-channel complexes with cryo-electron microscopy. Non-translating ribosome-SecY channel complexes derived from Methanocaldococcus jannaschii or Escherichia coli show the channel in its closed state, and indicate that ribosome binding per se causes only minor changes. The structure of an active E. coli ribosome-channel complex demonstrates that the nascent chain opens the channel, causing mostly rigid body movements of the amino- and carboxy-terminal halves of SecY. In this early translocation intermediate, the polypeptide inserts as a loop into the SecY channel with the hydrophobic signal sequence intercalated into the open lateral gate. The nascent chain also forms a loop on the cytoplasmic surface of SecY rather than entering the channel directly.


    Organizational Affiliation

    Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, Massachusetts 02118-2526, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase subunit SecE
A7
67Methanocaldococcus jannaschiiMutation(s): 0 
Find proteins for Q57817 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q57817

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase subunit SecG
A8
52Methanocaldococcus jannaschiiMutation(s): 0 
Find proteins for P60460 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  P60460

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L39E
Af
51Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19E
AQ
150Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22P
AS
150Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23P
AT
84Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24P
AU
121Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29P
AW
72Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecY
AX
436Methanocaldococcus jannaschiiMutation(s): 0 
Find proteins for Q60175 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q60175

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein L7AE
AG, B3
123Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3AE
BA
190Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2P
BB
202Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3P
BC
186Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4P
BD
172Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4E
BE
241Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5P
BF
217Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6E
BG
125Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7P
BH
215Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8P
BI
129Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8E
BJ
127Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10P
BL
102Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11P
BM
133Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13P
BO
148Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14P
BP
56Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15P/S13E
BQ
158Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17P
BR
113Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17E
BS
67Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19P
BT
111Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19E
BU
144Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S24E
BV
99Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S27E
BW
63Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S28E
BX
71Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S27AE
BY
50Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1P
AA
216Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31E
Aa
92Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
AB
239Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32E
Ab
127Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3P
AC
365Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4P
AD
255Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34E
Ad
89Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5P
AE
186Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37E
Ae
62Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6P
AF
184Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11P
AH
134Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L41E
Ah
24Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13P
AI
142Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14P
AJ
132Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L44E
Aj
94Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein P0/L10E
Ak
212Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15P
AL
147Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15E
AM
194Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10E/L16
AN
168Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21E
AR
95Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24E
AV
66Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30P
AY
155Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30E
AZ
99Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9P
BK
135Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12P
BN
145Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14E
A5, AK
81Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L40E
Ag
45Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37AE
Ai
78Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18P
AO
197Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18E
AP
120Methanocaldococcus jannaschiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 10
MoleculeChainsLengthOrganism
E-tRNAB177Methanocaldococcus jannaschii

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Entity ID: 11
MoleculeChainsLengthOrganism
16S ribosomal RNAB21495Methanocaldococcus jannaschii

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Entity ID: 38
MoleculeChainsLengthOrganism
23S ribosomal RNAA13049Methanocaldococcus jannaschii

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Entity ID: 39
MoleculeChainsLengthOrganism
5S ribosomal RNAA3126Methanocaldococcus jannaschii
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-03-18
    Changes: Other
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-12-18
    Changes: Other