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- PDB-4v6m: Structure of the ribosome-SecYE complex in the membrane environment -

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Basic information

Entry
Database: PDB / ID: 4v6m
TitleStructure of the ribosome-SecYE complex in the membrane environment
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • (Preprotein translocase ...) x 2
  • 16S RIBOSOMAL RNA
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • Apolipoprotein A-I
  • Cell division protein FtsQ
  • FtsQ nascent chain
  • mRNA
KeywordsRIBOSOME/RIBOSOMAL PROTEIN / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / TRANSLATION / ZINC-FINGER / 70S RIBOSOME / RIBOSOME / TRANSLOCON / SECYEG / NANODISC / RIBOSOME-RIBOSOMAL PROTEIN complex
Function / homology
Function and homology information


cell septum assembly / Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption ...cell septum assembly / Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport / blood vessel endothelial cell migration / cholesterol import / negative regulation of heterotypic cell-cell adhesion / high-density lipoprotein particle binding / ABC transporters in lipid homeostasis / apolipoprotein A-I receptor binding / apolipoprotein receptor binding / negative regulation of cell adhesion molecule production / protein transport by the Sec complex / negative regulation of cytokine production involved in immune response / intracellular protein transmembrane transport / HDL assembly / negative regulation of very-low-density lipoprotein particle remodeling / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / protein-transporting ATPase activity / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron remodeling / cellular response to lipoprotein particle stimulus / Chylomicron assembly / high-density lipoprotein particle clearance / phospholipid efflux / chylomicron / high-density lipoprotein particle remodeling / positive regulation of cholesterol metabolic process / reverse cholesterol transport / lipid storage / phospholipid homeostasis / high-density lipoprotein particle assembly / chemorepellent activity / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transfer activity / cholesterol transport / high-density lipoprotein particle / very-low-density lipoprotein particle / FtsZ-dependent cytokinesis / endothelial cell proliferation / regulation of Cdc42 protein signal transduction / HDL remodeling / cholesterol efflux / Scavenging by Class A Receptors / triglyceride homeostasis / adrenal gland development / negative regulation of interleukin-1 beta production / negative chemotaxis / cholesterol binding / cell division site / cholesterol biosynthetic process / amyloid-beta formation / positive regulation of Rho protein signal transduction / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / protein secretion / misfolded RNA binding / endocytic vesicle / Group I intron splicing / protein transmembrane transporter activity / RNA folding / positive regulation of cholesterol efflux / negative regulation of tumor necrosis factor-mediated signaling pathway / membrane => GO:0016020 / transcriptional attenuation / Scavenging of heme from plasma / protein targeting / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / cholesterol metabolic process / Retinoid metabolism and transport / translational termination / negative regulation of cytoplasmic translation / four-way junction DNA binding / positive regulation of stress fiber assembly / DnaA-L2 complex / heat shock protein binding / translation repressor activity / negative regulation of translational initiation / regulation of mRNA stability / endocytic vesicle lumen / negative regulation of DNA-templated DNA replication initiation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cholesterol homeostasis
Similarity search - Function
Cell division protein FtsQ / Cell division protein FtsQ, C-terminal / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / Apolipoprotein A/E ...Cell division protein FtsQ / Cell division protein FtsQ, C-terminal / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Protein secE/sec61-gamma signature. / 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 / POTRA domain / POTRA domain profile. / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 superfamily
Similarity search - Domain/homology
Chem-PEV / Chem-PGV / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Protein translocase subunit SecY / Protein translocase subunit SecE ...Chem-PEV / Chem-PGV / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Protein translocase subunit SecY / Protein translocase subunit SecE / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Apolipoprotein A-I / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25 / Protein translocase subunit SecE / Protein translocase subunit SecY / Cell division protein FtsQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli DH1 (bacteria)
Escherichia coli O157:H7 (bacteria)
Escherichia coli K-12 (bacteria)
Escherichia coli 536 (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsFrauenfeld, J. / Gumbart, J. / van der Sluis, E.O. / Funes, S. / Gartmann, M. / Beatrix, B. / Mielke, T. / Berninghausen, O. / Becker, T. / Schulten, K. / Beckmann, R.
CitationJournal: Nat Struct Mol Biol / Year: 2011
Title: Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
Authors: Jens Frauenfeld / James Gumbart / Eli O van der Sluis / Soledad Funes / Marco Gartmann / Birgitta Beatrix / Thorsten Mielke / Otto Berninghausen / Thomas Becker / Klaus Schulten / Roland Beckmann /
Abstract: The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent- ...The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent-solubilized Sec complexes have been reported. Here we present a single-particle cryo-EM structure of the SecYEG complex in a membrane environment, bound to a translating ribosome, at subnanometer resolution. Using the SecYEG complex reconstituted in a so-called Nanodisc, we could trace the nascent polypeptide chain from the peptidyltransferase center into the membrane. The reconstruction allowed for the identification of ribosome-lipid interactions. The rRNA helix 59 (H59) directly contacts the lipid surface and appears to modulate the membrane in immediate vicinity to the proposed lateral gate of the protein-conducting channel (PCC). On the basis of our map and molecular dynamics simulations, we present a model of a signal anchor-gated PCC in the membrane.
History
DepositionFeb 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references / Structure summary
SupersessionDec 10, 2014ID: 3J00, 3J01
Revision 1.2Dec 10, 2014Group: Other
Revision 1.3Apr 1, 2015Group: Other
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.5Dec 18, 2019Group: Database references / Other / Category: atom_sites / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_ref_seq_dif.details
Revision 1.6Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
AA: 16S RIBOSOMAL RNA
AX: mRNA
AV: FtsQ nascent chain
AZ: Cell division protein FtsQ
A0: Apolipoprotein A-I
A1: Apolipoprotein A-I
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein S21
B7: 5S RIBOSOMAL RNA
B8: 23S RIBOSOMAL RNA
BA: Preprotein translocase secY subunit
BB: Preprotein translocase secE subunit
B5: 50S ribosomal protein L1
B6: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L9
BI: 50S ribosomal protein L11
BJ: 50S ribosomal protein L13
BK: 50S ribosomal protein L14
BL: 50S ribosomal protein L15
BM: 50S ribosomal protein L16
BN: 50S ribosomal protein L17
BO: 50S ribosomal protein L18
BP: 50S ribosomal protein L19
BQ: 50S ribosomal protein L20
BR: 50S ribosomal protein L21
BS: 50S ribosomal protein L22
BT: 50S ribosomal protein L23
BU: 50S ribosomal protein L24
BV: 50S ribosomal protein L25
BW: 50S ribosomal protein L27
BX: 50S ribosomal protein L28
BY: 50S ribosomal protein L29
BZ: 50S ribosomal protein L30
B0: 50S ribosomal protein L32
B1: 50S ribosomal protein L33
B2: 50S ribosomal protein L34
B3: 50S ribosomal protein L35
B4: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,410,929193
Polymers2,314,24060
Non-polymers96,689133
Water00
1


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

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Components

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RNA chain , 5 types, 5 molecules AAAXAVB7B8

#1: RNA chain 16S RIBOSOMAL RNA


Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: J01695
#2: RNA chain mRNA


Mass: 3442.106 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: RNA chain FtsQ nascent chain


Mass: 24876.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli DH1 (bacteria) / References: GenBank: AP012030
#26: RNA chain 5S RIBOSOMAL RNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli DH1 (bacteria) / References: GenBank: AP012030
#27: RNA chain 23S RIBOSOMAL RNA


Mass: 941612.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli DH1 (bacteria) / References: GenBank: AP012030

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Protein , 2 types, 3 molecules AZA0A1

#4: Protein Cell division protein FtsQ / Cell division protein / ingrowth of wall at septum


Mass: 11085.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli O157:H7 (bacteria) / References: UniProt: Q8X9Y5
#5: Protein Apolipoprotein A-I / Apo-AI / ApoA-I / Apolipoprotein A1 / Apolipoprotein A-I(1-242)


Mass: 23309.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: nanodiscs derived from human Apo-A1 / Source: (synth.) Homo sapiens (human) / References: UniProt: P02647

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30S ribosomal protein ... , 20 types, 20 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU

#6: Protein 30S ribosomal protein S2


Mass: 26650.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7V0
#7: Protein 30S ribosomal protein S3


Mass: 25900.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7V3
#8: Protein 30S ribosomal protein S4


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7V8
#9: Protein 30S ribosomal protein S5


Mass: 17498.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7W1
#10: Protein 30S ribosomal protein S6 / 30S ribosomal protein S6 / fully modified isoform / 30S ribosomal protein S6 / non-modified isoform


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P02358
#11: Protein 30S ribosomal protein S7


Mass: 19923.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P02359
#12: Protein 30S ribosomal protein S8


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7W7
#13: Protein 30S ribosomal protein S9


Mass: 14755.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7X3
#14: Protein 30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7R5
#15: Protein 30S ribosomal protein S11


Mass: 13739.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7R9
#16: Protein 30S ribosomal protein S12


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7S3
#17: Protein 30S ribosomal protein S13


Mass: 12997.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0ADZ4
#18: Protein 30S ribosomal protein S14


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG59
#19: Protein 30S ribosomal protein S15


Mass: 10188.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7S3
#20: Protein 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7T3
#21: Protein 30S ribosomal protein S17


Mass: 9593.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG63
#22: Protein 30S ribosomal protein S18


Mass: 8874.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7T7
#23: Protein 30S ribosomal protein S19


Mass: 10324.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7U3
#24: Protein 30S ribosomal protein S20


Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7U7
#25: Protein 30S ribosomal protein S21


Mass: 8392.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P68679

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Preprotein translocase ... , 2 types, 2 molecules BABB

#28: Protein Preprotein translocase secY subunit


Mass: 47669.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli 536 (bacteria) / Strain: UTI89 / UPEC / References: UniProt: Q0TCG1, UniProt: A0A454A8B1*PLUS
#29: Protein Preprotein translocase secE subunit / Inner membrane preprotein translocase


Mass: 12623.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli 536 (bacteria) / Strain: UTI89 / UPEC / References: UniProt: Q0TA84, UniProt: A0A454AA55*PLUS

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50S ribosomal protein ... , 30 types, 30 molecules B5B6BDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZB0B1B2B3B4

#30: Protein 50S ribosomal protein L1


Mass: 24765.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7L0
#31: Protein 50S ribosomal protein L2


Mass: 29792.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P60422
#32: Protein 50S ribosomal protein L3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P60438
#33: Protein 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P60723
#34: Protein 50S ribosomal protein L5


Mass: 20202.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P62399
#35: Protein 50S ribosomal protein L6


Mass: 18801.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG55
#36: Protein 50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7R1
#37: Protein 50S ribosomal protein L11


Mass: 14763.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7J7
#38: Protein 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AA10
#39: Protein 50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0ADY3
#40: Protein 50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P02413
#41: Protein 50S ribosomal protein L16


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0ADY7
#42: Protein 50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG44
#43: Protein 50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0C018
#44: Protein 50S ribosomal protein L19


Mass: 13028.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7K6
#45: Protein 50S ribosomal protein L20


Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7L3
#46: Protein 50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG48
#47: Protein 50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P61175
#48: Protein 50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0ADZ0
#49: Protein 50S ribosomal protein L24


Mass: 11208.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P60624
#50: Protein 50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P68919
#51: Protein 50S ribosomal protein L27


Mass: 9015.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7L8
#52: Protein 50S ribosomal protein L28


Mass: 8896.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7M2
#53: Protein 50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7M6
#54: Protein 50S ribosomal protein L30


Mass: 6423.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG51
#55: Protein 50S ribosomal protein L32


Mass: 6332.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7N4
#56: Protein 50S ribosomal protein L33


Mass: 6257.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7N9
#57: Protein/peptide 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7P5
#58: Protein 50S ribosomal protein L35 / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7Q1
#59: Protein/peptide 50S ribosomal protein L36 / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7Q6

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Non-polymers , 2 types, 133 molecules

#60: Chemical...
ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 720.012 Da / Num. of mol.: 101 / Source method: obtained synthetically / Formula: C39H78NO8P / Comment: POPE, phospholipid*YM
#61: Chemical...
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM

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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: An active E. coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E. coli ribosome
Type: RIBOSOME
Details: The heterotrimeric SecYEG complex was embedded in a lipid bilayer (nascent HDL, Nanodisc)
Buffer solutionName: 20 mM Hepes (pH 7.2), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol
pH: 7.2
Details: 20 mM Hepes (pH 7.2), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Details: liquid ethane was used as a cryogen

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 38000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Cs: 2.26 mm
Image recordingElectron dose: 22 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1MDFFmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: DEFOCUS GROUP VOLUMES
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.1 Å / Num. of particles: 85664 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: REFINEMENT PROTOCOL--flexible fitting
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms24247 34960 6581 0 65788

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