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

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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-IApolipoprotein
  • Cell division protein FtsQ
  • FtsQ nascent chain
  • mRNAMessenger RNA
KeywordsRIBOSOME/RIBOSOMAL PROTEIN / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / TRANSLATION / ZINC-FINGER / 70S RIBOSOME / RIBOSOME / TRANSLOCON / SECYEG / NANODISC / RIBOSOME-RIBOSOMAL PROTEIN complex
Function / homologyRibosomal protein L35, conserved site / Ribosomal protein L25, short-form / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L9, N-terminal ...Ribosomal protein L35, conserved site / Ribosomal protein L25, short-form / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L9, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L16, conserved site / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S10, conserved site / Ribosomal protein S14, bacterial/plastid / Cell division protein FtsQ / Ribosomal protein L28/L24 / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S6, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Ribosomal protein L18e/L15P / Ribosomal protein L34, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L1/ribosomal biogenesis protein / KOW / Ribosomal protein L9/RNase H1, N-terminal / K homology domain superfamily, prokaryotic type / Translation protein, beta-barrel domain superfamily / Translation protein SH3-like domain superfamily / Ribosomal protein L11, bacterial-type / Ribosomal protein S12/S23 / Ribosomal protein L30, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L1, bacterial-type / Ribosomal protein L24/L26, conserved site / Ribosomal protein L13, bacterial-type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L13 / Ribosomal protein L20 / Ribosomal protein L15, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S3, bacterial / S15/NS1, RNA-binding / Zinc-binding ribosomal protein / Ribosomal protein L27, conserved site / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L22/L17, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein L30, conserved site / Ribosomal protein L10e/L16 / Ribosomal protein L30, ferredoxin-like fold domain / Nucleic acid-binding, OB-fold / K homology domain-like, alpha/beta / Ribosomal protein L2, domain 3 / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5, N-terminal
Function and homology information
Specimen sourceEscherichia 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 / 7.1 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 8, 2011 / Release: Jul 9, 2014
RevisionDateData content typeGroupProviderType
1.0Jul 9, 2014Structure modelrepositoryInitial release
1.1Aug 20, 2014Structure modelDatabase references / Structure summary
1.2Dec 10, 2014Structure modelOther
1.3Apr 1, 2015Structure modelOther

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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
Polyers2,314,24060
Non-polymers96,689133
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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RNA chain , 5 types, 5 molecules AAAXAVB7B8

#1: RNA chain 16S RIBOSOMAL RNA /


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


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


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


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


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

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Protein/peptide , 2 types, 3 molecules AZA0A1

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


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


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

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

#6: Protein/peptide 30S ribosomal protein S2 /


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


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


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


Mass: 17498.203 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7W1
#10: Protein/peptide 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: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P02358
#11: Protein/peptide 30S ribosomal protein S7 /


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 8392.844 Da / Num. of mol.: 1 / 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/peptide Preprotein translocase secY subunit


Mass: 47669.277 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli 536 (bacteria) / Strain: UTI89 / UPEC / References: UniProt: Q0TCG1
#29: Protein/peptide Preprotein translocase secE subunit / Inner membrane preprotein translocase


Mass: 12623.296 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli 536 (bacteria) / Strain: UTI89 / UPEC / References: UniProt: Q0TA84

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

#30: Protein/peptide 50S ribosomal protein L1 /


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 6257.436 Da / Num. of mol.: 1 / 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: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7P5
#58: Protein/peptide 50S ribosomal protein L35 / / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 1 / 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: (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 / Formula: C39H78NO8P / Phosphatidylethanolamine / 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 / Formula: C40H77O10P / Phosphatidylglycerol / Comment: phospholipid *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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
Details: 20 mM Hepes (pH 7.2), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol
pH: 7.2
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
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 / Calibrated magnification: 38000 / 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
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m 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
3D reconstructionResolution: 7.1 Å / Number of particles: 85664 / Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--flexible fitting / Ref protocol: FLEXIBLE FIT / Ref space: REAL
Number of atoms included #LASTProtein: 24247 / Nucleic acid: 34960 / Ligand: 6581 / Solvent: 0 / Total: 65788

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