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- PDB-4v4n: Structure of the Methanococcus jannaschii ribosome-SecYEBeta chan... -

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Basic information

Entry
Database: PDB / ID: 4v4n
TitleStructure of the Methanococcus jannaschii ribosome-SecYEBeta channel complex
Components
  • (30S ribosomal protein ...) x 26
  • (50S ribosomal protein ...) x 34
  • (Preprotein translocase subunit ...) x 2
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • E-tRNA
  • Protein translocase subunit SecY
KeywordsRIBOSOME/PROTEIN TRANSPORT / archaea / archaeal / ribosomal / 50S / protein synthesis / RNA / large subunit / co-translational translocation / protein conducting channel / RIBOSOME-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting / protein transport / plasma membrane
Similarity search - Function
Preprotein translocase subunit SecG / Protein translocase subunit SecY / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secY signature 1. / Protein secY signature 2. ...Preprotein translocase subunit SecG / Protein translocase subunit SecY / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Preprotein translocase subunit SecG / Protein translocase subunit SecE / Protein translocase subunit SecY
Similarity search - Component
Biological speciesMethanococcus jannaschii (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsMenetret, J.F. / Park, E. / Gumbart, J.C. / Ludtke, S.J. / Li, W. / Whynot, A. / Rapoport, T.A. / Akey, C.W.
CitationJournal: Nature / Year: 2014
Title: Structure of the SecY channel during initiation of protein translocation.
Authors: Eunyong Park / Jean-François Ménétret / James C Gumbart / Steven J Ludtke / Weikai Li / Andrew Whynot / Tom A Rapoport / Christopher W Akey /
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 ...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.
History
DepositionJun 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3J43, 3J44, 1VVK
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 18, 2015Group: Other
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.4Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A7: Preprotein translocase subunit SecE
A8: Preprotein translocase subunit SecG
Af: 50S ribosomal protein L39E
AQ: 50S ribosomal protein L19E
AS: 50S ribosomal protein L22P
AT: 50S ribosomal protein L23P
AU: 50S ribosomal protein L24P
AW: 50S ribosomal protein L29P
AX: Protein translocase subunit SecY
B1: E-tRNA
B2: 16S ribosomal RNA
B3: 30S ribosomal protein L7AE
BA: 30S ribosomal protein S3AE
BB: 30S ribosomal protein S2P
BC: 30S ribosomal protein S3P
BD: 30S ribosomal protein S4P
BE: 30S ribosomal protein S4E
BF: 30S ribosomal protein S5P
BG: 30S ribosomal protein S6E
BH: 30S ribosomal protein S7P
BI: 30S ribosomal protein S8P
BJ: 30S ribosomal protein S8E
BK: 30S ribosomal protein S9P
BL: 30S ribosomal protein S10P
BM: 30S ribosomal protein S11P
BN: 30S ribosomal protein S12P
BO: 30S ribosomal protein S13P
BP: 30S ribosomal protein S14P
BQ: 30S ribosomal protein S15P/S13E
BR: 30S ribosomal protein S17P
BS: 30S ribosomal protein S17E
BT: 30S ribosomal protein S19P
BU: 30S ribosomal protein S19E
BV: 30S ribosomal protein S24E
BW: 30S ribosomal protein S27E
BX: 30S ribosomal protein S28E
BY: 30S ribosomal protein S27AE
A1: 23S ribosomal RNA
A3: 5S ribosomal RNA
A5: 50S ribosomal protein L14E
AA: 50S ribosomal protein L1P
Aa: 50S ribosomal protein L31E
AB: 50S ribosomal protein L2
Ab: 50S ribosomal protein L32E
AC: 50S ribosomal protein L3P
AD: 50S ribosomal protein L4P
Ad: 50S ribosomal protein L34E
AE: 50S ribosomal protein L5P
Ae: 50S ribosomal protein L37E
AF: 50S ribosomal protein L6P
AG: 30S ribosomal protein L7AE
Ag: 50S ribosomal protein L40E
AH: 50S ribosomal protein L11P
Ah: 50S ribosomal protein L41E
AI: 50S ribosomal protein L13P
Ai: 50S ribosomal protein L37AE
AJ: 50S ribosomal protein L14P
Aj: 50S ribosomal protein L44E
AK: 50S ribosomal protein L14E
Ak: 50S ribosomal protein P0/L10E
AL: 50S ribosomal protein L15P
AM: 50S ribosomal protein L15E
AN: 50S ribosomal protein L10E/L16
AO: 50S ribosomal protein L18P
AP: 50S ribosomal protein L18E
AR: 50S ribosomal protein L21E
AV: 50S ribosomal protein L24E
AY: 50S ribosomal protein L30P
AZ: 50S ribosomal protein L30E


Theoretical massNumber of molelcules
Total (without water)2,556,27269
Polymers2,556,27269
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Preprotein translocase subunit ... , 2 types, 2 molecules A7A8

#1: Protein Preprotein translocase subunit SecE / SECE/SECgamma


Mass: 7701.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus jannaschii (archaea) / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q57817
#2: Protein Preprotein translocase subunit SecG / SECbeta


Mass: 5853.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus jannaschii (archaea) / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P60460

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50S ribosomal protein ... , 34 types, 35 molecules AfAQASATAUAWA5AKAAAaABAbACADAdAEAeAFAgAHAhAIAiAJAjAkALAMANAO...

#3: Protein 50S ribosomal protein L39E / Ribosome


Mass: 6323.784 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#4: Protein 50S ribosomal protein L19E / Ribosome


Mass: 17920.600 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#5: Protein 50S ribosomal protein L22P / Ribosome


Mass: 17043.994 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#6: Protein 50S ribosomal protein L23P / Ribosome


Mass: 9647.393 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#7: Protein 50S ribosomal protein L24P / Ribosome


Mass: 14364.969 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#8: Protein 50S ribosomal protein L29P / Ribosome


Mass: 8549.290 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#40: Protein 50S ribosomal protein L14E / Ribosome


Mass: 8751.348 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#41: Protein 50S ribosomal protein L1P / Ribosome


Mass: 23893.088 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#42: Protein 50S ribosomal protein L31E / Ribosome


Mass: 10767.811 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#43: Protein 50S ribosomal protein L2 /


Mass: 26085.379 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#44: Protein 50S ribosomal protein L32E / Ribosome


Mass: 15231.212 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#45: Protein 50S ribosomal protein L3P / Ribosome


Mass: 41465.969 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#46: Protein 50S ribosomal protein L4P / Ribosome


Mass: 28765.779 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#47: Protein 50S ribosomal protein L34E / Ribosome


Mass: 10677.132 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#48: Protein 50S ribosomal protein L5P / Ribosome


Mass: 21269.877 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#49: Protein 50S ribosomal protein L37E / Ribosome


Mass: 7245.577 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#50: Protein 50S ribosomal protein L6P / Ribosome


Mass: 20891.189 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#51: Protein/peptide 50S ribosomal protein L40E / Ribosome


Mass: 5327.440 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#52: Protein 50S ribosomal protein L11P / Ribosome


Mass: 14160.834 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#53: Protein/peptide 50S ribosomal protein L41E / Ribosome


Mass: 3277.149 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#54: Protein 50S ribosomal protein L13P / Ribosome


Mass: 16345.384 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#55: Protein 50S ribosomal protein L37AE / Ribosome


Mass: 8451.080 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#56: Protein 50S ribosomal protein L14P / Ribosome


Mass: 14446.868 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#57: Protein 50S ribosomal protein L44E / Ribosome


Mass: 11234.449 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#58: Protein 50S ribosomal protein P0/L10E / Ribosome


Mass: 23257.232 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#59: Protein 50S ribosomal protein L15P / Ribosome


Mass: 16439.346 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#60: Protein 50S ribosomal protein L15E / Ribosome


Mass: 22644.896 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#61: Protein 50S ribosomal protein L10E/L16 / Ribosome


Mass: 19584.717 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#62: Protein 50S ribosomal protein L18P / Ribosome


Mass: 22633.268 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#63: Protein 50S ribosomal protein L18E / Ribosome


Mass: 13758.037 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#64: Protein 50S ribosomal protein L21E / Ribosome


Mass: 11141.122 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#65: Protein 50S ribosomal protein L24E / Ribosome


Mass: 7938.257 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#66: Protein 50S ribosomal protein L30P / Ribosome


Mass: 17745.029 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#67: Protein 50S ribosomal protein L30E / Ribosome


Mass: 10727.576 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)

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Protein , 1 types, 1 molecules AX

#9: Protein Protein translocase subunit SecY / SECY/SECalpha


Mass: 47482.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus jannaschii (archaea) / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q60175

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RNA chain , 4 types, 4 molecules B1B2A1A3

#10: RNA chain E-tRNA


Mass: 24880.865 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#11: RNA chain 16S ribosomal RNA /


Mass: 485455.500 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#38: RNA chain 23S ribosomal RNA /


Mass: 990820.375 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#39: RNA chain 5S ribosomal RNA /


Mass: 40689.262 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)

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30S ribosomal protein ... , 26 types, 27 molecules B3AGBABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBY

#12: Protein 30S ribosomal protein L7AE / Ribosome


Mass: 13414.664 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#13: Protein 30S ribosomal protein S3AE / Ribosome


Mass: 22151.090 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#14: Protein 30S ribosomal protein S2P / Ribosome


Mass: 23039.861 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#15: Protein 30S ribosomal protein S3P / Ribosome


Mass: 20742.381 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#16: Protein 30S ribosomal protein S4P / Ribosome


Mass: 20409.756 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#17: Protein 30S ribosomal protein S4E / Ribosome


Mass: 27994.748 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#18: Protein 30S ribosomal protein S5P / Ribosome


Mass: 24453.385 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#19: Protein 30S ribosomal protein S6E / Ribosome


Mass: 14002.330 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#20: Protein 30S ribosomal protein S7P / Ribosome


Mass: 24701.791 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#21: Protein 30S ribosomal protein S8P / Ribosome


Mass: 14552.977 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#22: Protein 30S ribosomal protein S8E / Ribosome


Mass: 14293.733 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#23: Protein 30S ribosomal protein S9P / Ribosome


Mass: 15317.932 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#24: Protein 30S ribosomal protein S10P / Ribosome


Mass: 11769.689 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#25: Protein 30S ribosomal protein S11P / Ribosome


Mass: 14280.448 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#26: Protein 30S ribosomal protein S12P / Ribosome


Mass: 16249.310 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#27: Protein 30S ribosomal protein S13P / Ribosome


Mass: 16948.904 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#28: Protein 30S ribosomal protein S14P / Ribosome


Mass: 6634.046 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#29: Protein 30S ribosomal protein S15P/S13E / Ribosome


Mass: 18640.025 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#30: Protein 30S ribosomal protein S17P / Ribosome


Mass: 13296.521 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#31: Protein 30S ribosomal protein S17E / Ribosome


Mass: 7942.465 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#32: Protein 30S ribosomal protein S19P / Ribosome


Mass: 13177.785 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#33: Protein 30S ribosomal protein S19E / Ribosome


Mass: 16633.314 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#34: Protein 30S ribosomal protein S24E / Ribosome


Mass: 11698.564 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#35: Protein 30S ribosomal protein S27E / Ribosome


Mass: 6888.388 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#36: Protein 30S ribosomal protein S28E / Ribosome


Mass: 8116.332 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)
#37: Protein/peptide 30S ribosomal protein S27AE / Ribosome


Mass: 5864.958 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea)

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Details

Sequence detailsRIBOSOME COORDINATES HAVE BEEN MODELED USING PROTEIN SEQUENCES FROM PYROCOCCUS FURIOSIS.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY / Number of used crystals: 1
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsParent-ID
1Methanococcus jannaschii 70S ribosome-SecYEbeta complexRIBOSOMEThe sample was reconstituted from ribosomal subunits purified from M. jannaschii and from recombinant SecYEbeta.0
2non-translating 70S ribosome1
3SecYEbetaSecY channel1
4transfer RNA1
Molecular weightValue: 2.6 MDa / Experimental value: NO
Buffer solutionName: 100 mM NH4Cl, 30 mM MgCl2, 20 mM HEPES-KOH, 6 mM beta-mercaptoethanol, 0.1% DDM
pH: 7.5
Details: 100 mM NH4Cl, 30 mM MgCl2, 20 mM HEPES-KOH, 6 mM beta-mercaptoethanol, 0.1% DDM
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil 400 mesh 2/1 Cu grids, air glow discharged, and 400 mesh Cu grids with a thin continuous carbon foil
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temp: 77 K / Humidity: 100 %
Details: Blot 1-2 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Apr 10, 2008 / Details: Low dose imaging, data collected manually
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 51000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Oxford holder / Temperature: 93 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM / Details: Kodak SO163 film
Image scansNum. digital images: 217
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1MDFFmodel fitting
2UCSF Chimeramodel fitting
3EMAN13D reconstruction
4EMAN23D reconstruction
CTF correctionDetails: per micrograph
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: projection matching / Resolution: 9 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 37000 / Nominal pixel size: 2.73 Å / Actual pixel size: 2.73 Å
Details: Final map calculated as an average of 6 different refinements in EMAN2 with different parameters. Resolution method was FSC at 0.5 cut-off using a comparison between experimental map and a ...Details: Final map calculated as an average of 6 different refinements in EMAN2 with different parameters. Resolution method was FSC at 0.5 cut-off using a comparison between experimental map and a map of the docked ribosomal models calculated at 7 Angstrom resolution with EMAN.
Num. of class averages: 3800 / Symmetry type: POINT
Atomic model building
IDProtocolSpaceDetails
1FLEXIBLE FITREALREFINEMENT PROTOCOL--FLEXIBLE
2FLEXIBLE FITREALREFINEMENT PROTOCOL--FLEXIBLE DETAILS--Docked with Chimera and fit with MDFF. Chains omitted- 1(el 1-77), 6(L83-1), 4(L83-2), c(L33e). Chains truncated- a(L31e) 78-85, W(L29) 67-72, C(L3) 103-125.
3FLEXIBLE FITREALREFINEMENT PROTOCOL--FLEXIBLE DETAILS--Regions omitted- rRNA chain 1 [1-6, 3047-3049 5 and 3 ends 23S], 150-163, 750-756, 1311-1321, 2904-2942 (ES).
4FLEXIBLE FITREALREFINEMENT PROTOCOL--FLEXIBLE
Atomic model building

Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-ID 3D fitting-IDAccession codeInitial refinement model-ID
11RHZ

1rhz

A11RHZ1
21RHZ

1rhz

B11RHZ1
31RHZ

1rhz

C11RHZ1
43J21

3j21
PDB Unreleased entry

23J212
53J2L

3j2l
PDB Unreleased entry

33J2L3
63J20

3j20
PDB Unreleased entry

43J204
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms9227 0 0 0 9227

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