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- EMDB-4315: Subtomogram average of OST-containing ribosome-translocon complex... -

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Basic information

Entry
Database: EMDB / ID: 4315
TitleSubtomogram average of OST-containing ribosome-translocon complexes from canine rough microsomal membranes
Map data
Sample80S ribosome from WT canine rough microsomal membranes bound to the endoplasmic reticulum protein translocon
  • Sec61 protein conducting channel
  • 60S ribosomal subunit
  • Mammalian Oligosaccharyltransferase
  • uL2
  • uL3
  • (Ribosomal protein ...) x 10
  • (60S ribosomal protein ...) x 6
  • uL30
  • eL8
  • uL6
  • eL13
  • uL13
  • uL22
  • (uL14) x 2
  • eL19
  • eL20
  • eL21
  • eL22
  • uL23
  • uL15
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL29
  • eL38
  • eL39
  • eL40
  • eL42
  • eL28
  • 60S acidic ribosomal protein P0
  • (nucleic-acidNucleic acid) x 3
  • (Protein transport protein Sec61 subunit ...Protein targeting) x 3
  • (Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ...) x 2
  • TMEM258
  • Oligosaccharyltransferase complex subunit OSTC
  • OST4
  • DAD1
  • OST48
  • RPN2
  • (ligand) x 6
Function / homologyRibosomal protein L30, central domain, archaeal type / Ribosomal protein L31e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Translocon Sec61/SecY, plug domain / Ribosomal protein L3, conserved site / Ribosomal protein L14P, conserved site ...Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L31e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Translocon Sec61/SecY, plug domain / Ribosomal protein L3, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L23 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L39e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L18e/L15P / Oligosaccharyl transferase complex, subunit OST3/OST6 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L10e, conserved site / Preprotein translocase subunit SecE / Nucleic acid-binding, OB-fold / Ribosomal protein L7, eukaryotic / Ribophorin I / Ribosomal protein L41 / Protein translocase SEC61 complex, gamma subunit / Ribosomal protein L34Ae / Translation protein SH3-like domain superfamily / Translation protein, beta-barrel domain superfamily / TRASH domain / Ribosomal protein L37ae/L37e / Zinc-binding ribosomal protein / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L29, conserved site / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L30, N-terminal / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L25/L23 / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / Protein transport protein SecG/Sec61-beta/Sbh / Ribosomal protein L30, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / KOW / Ribosomal protein L14p/L23e / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L16p/L10e / Ribosomal protein L14 superfamily / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L3 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L30p/L7e / SecY translocase / Ribosomal protein L6 / Ribosomal protein L10 / KOW motif / Ribosomal protein L4/L1 family / SecE/Sec61-gamma subunits of protein translocation complex / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / SecY domain superfamily / 50S ribosomal protein L30e-like / Protein translocase SecE domain superfamily / Ribosomal protein L24e, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L2, archaeal-type / Ribosomal protein L15e core domain superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L4, C-terminal domain / Ribosomal L28e/Mak16 / SecY conserved site / Ribosomal protein L6, alpha-beta domain superfamily / 60S acidic ribosomal protein P0 / Protein transport Sec61-beta/Sbh / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L7, eukaryotic/archaeal
Function and homology information
SourceCanis lupus familiaris (dog) / Oryctolagus cuniculus (rabbit)
Methodsubtomogram averaging / cryo EM / 9.1 Å resolution
AuthorsPfeffer S / Foerster F
CitationJournal: Science / Year: 2018
Title: Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum.
Authors: Katharina Braunger / Stefan Pfeffer / Shiteshu Shrimal / Reid Gilmore / Otto Berninghausen / Elisabet C Mandon / Thomas Becker / Friedrich Förster / Roland Beckmann
Abstract: Protein synthesis, transport, and N-glycosylation are coupled at the mammalian endoplasmic reticulum by complex formation of a ribosome, the Sec61 protein-conducting channel, and ...Protein synthesis, transport, and N-glycosylation are coupled at the mammalian endoplasmic reticulum by complex formation of a ribosome, the Sec61 protein-conducting channel, and oligosaccharyltransferase (OST). Here we used different cryo-electron microscopy approaches to determine structures of native and solubilized ribosome-Sec61-OST complexes. A molecular model for the catalytic OST subunit STT3A (staurosporine and temperature sensitive 3A) revealed how it is integrated into the OST and how STT3-paralog specificity for translocon-associated OST is achieved. The OST subunit DC2 was placed at the interface between Sec61 and STT3A, where it acts as a versatile module for recruitment of STT3A-containing OST to the ribosome-Sec61 complex. This detailed structural view on the molecular architecture of the cotranslational machinery for N-glycosylation provides the basis for a mechanistic understanding of glycoprotein biogenesis at the endoplasmic reticulum.
Validation ReportPDB-ID: 6ftg

SummaryFull reportAbout validation report
DateDeposition: Feb 22, 2018 / Header (metadata) release: Mar 21, 2018 / Map release: Mar 21, 2018 / Last update: Apr 25, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6ftg
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6ftg
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4315.map.gz (map file in CCP4 format, 47410 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
228 pix
2.62 Å/pix.
= 597.36 Å
228 pix
2.62 Å/pix.
= 597.36 Å
228 pix
2.62 Å/pix.
= 597.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.62 Å
Density
Contour Level:2.3 (by emdb), 2 (movie #1):
Minimum - Maximum-20.681034 - 23.787277
Average (Standard dev.)-0.000000001059364 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions228228228
Origin000
Limit227227227
Spacing228228228
CellA=B=C: 597.36 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.622.622.62
M x/y/z228228228
origin x/y/z0.0000.0000.000
length x/y/z597.360597.360597.360
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS228228228
D min/max/mean-20.68123.787-0.000

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Supplemental data

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Sample components

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Entire 80S ribosome from WT canine rough microsomal membranes bound to t...

EntireName: 80S ribosome from WT canine rough microsomal membranes bound to the endoplasmic reticulum protein translocon
Number of components: 68

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Component #1: protein, 80S ribosome from WT canine rough microsomal membranes b...

ProteinName: 80S ribosome from WT canine rough microsomal membranes bound to the endoplasmic reticulum protein translocon
Recombinant expression: No

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Component #2: protein, Sec61 protein conducting channel

ProteinName: Sec61 protein conducting channel / Recombinant expression: No
SourceSpecies: Canis lupus familiaris (dog)

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Component #3: protein, 60S ribosomal subunit

ProteinName: 60S ribosomal subunit / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #4: protein, Mammalian Oligosaccharyltransferase

ProteinName: Mammalian Oligosaccharyltransferase / Recombinant expression: No
SourceSpecies: Canis lupus familiaris (dog)

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Component #5: protein, uL2

ProteinName: uL2 / Recombinant expression: No
MassTheoretical: 26.570105 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #6: protein, uL3

ProteinName: uL3 / Recombinant expression: No
MassTheoretical: 45.119812 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #7: protein, Ribosomal protein L4

ProteinName: Ribosomal protein L460S ribosomal protein L4 / Recombinant expression: No
MassTheoretical: 41.115508 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #8: protein, 60S ribosomal protein L5

ProteinName: 60S ribosomal protein L5 / Recombinant expression: No
MassTheoretical: 34.006312 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #9: protein, 60S ribosomal protein L6

ProteinName: 60S ribosomal protein L6 / Recombinant expression: No
MassTheoretical: 28.529848 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #10: protein, uL30

ProteinName: uL30 / Recombinant expression: No
MassTheoretical: 26.662787 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #11: protein, eL8

ProteinName: eL8 / Recombinant expression: No
MassTheoretical: 27.480555 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #12: protein, uL6

ProteinName: uL6 / Recombinant expression: No
MassTheoretical: 21.627215 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #13: protein, Ribosomal protein L10 (Predicted)

ProteinName: Ribosomal protein L10 (Predicted)Ribosome / Recombinant expression: No
MassTheoretical: 24.511861 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #14: protein, Ribosomal protein L11

ProteinName: Ribosomal protein L11 / Recombinant expression: No
MassTheoretical: 19.270318 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #15: protein, eL13

ProteinName: eL13 / Recombinant expression: No
MassTheoretical: 24.216525 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #16: protein, Ribosomal protein L14

ProteinName: Ribosomal protein L14 / Recombinant expression: No
MassTheoretical: 16.217355 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #17: protein, Ribosomal protein L15

ProteinName: Ribosomal protein L15 / Recombinant expression: No
MassTheoretical: 24.076088 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #18: protein, uL13

ProteinName: uL13 / Recombinant expression: No
MassTheoretical: 23.248924 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #19: protein, uL22

ProteinName: uL22 / Recombinant expression: No
MassTheoretical: 17.757627 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #20: protein, uL14

ProteinName: uL14 / Recombinant expression: No
MassTheoretical: 21.457391 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #21: protein, eL19

ProteinName: eL19 / Recombinant expression: No
MassTheoretical: 21.613033 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #22: protein, eL20

ProteinName: eL20 / Recombinant expression: No
MassTheoretical: 20.696363 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #23: protein, eL21

ProteinName: eL21 / Recombinant expression: No
MassTheoretical: 18.478791 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #24: protein, eL22

ProteinName: eL22 / Recombinant expression: No
MassTheoretical: 11.481249 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #25: protein, uL14

ProteinName: uL14 / Recombinant expression: No
MassTheoretical: 13.972425 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #26: protein, Ribosomal protein L24

ProteinName: Ribosomal protein L24 / Recombinant expression: No
MassTheoretical: 7.512774 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #27: protein, uL23

ProteinName: uL23 / Recombinant expression: No
MassTheoretical: 13.85636 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #28: protein, Ribosomal protein L26

ProteinName: Ribosomal protein L26 / Recombinant expression: No
MassTheoretical: 15.891787 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #29: protein, 60S ribosomal protein L27

ProteinName: 60S ribosomal protein L27 / Recombinant expression: No
MassTheoretical: 15.704635 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #30: protein, uL15

ProteinName: uL15 / Recombinant expression: No
MassTheoretical: 16.489363 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #31: protein, 60S ribosomal protein L29

ProteinName: 60S ribosomal protein L29 / Recombinant expression: No
MassTheoretical: 8.706283 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #32: protein, eL30

ProteinName: eL30 / Recombinant expression: No
MassTheoretical: 10.496355 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #33: protein, eL31

ProteinName: eL31 / Recombinant expression: No
MassTheoretical: 12.635694 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #34: protein, eL32

ProteinName: eL32CD59 / Recombinant expression: No
MassTheoretical: 15.022021 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #35: protein, eL33

ProteinName: eL33 / Recombinant expression: No
MassTheoretical: 12.449612 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #36: protein, eL34

ProteinName: eL34 / Recombinant expression: No
MassTheoretical: 12.994621 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #37: protein, eL29

ProteinName: eL29 / Recombinant expression: No
MassTheoretical: 14.435403 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #38: protein, 60S ribosomal protein L36

ProteinName: 60S ribosomal protein L36 / Recombinant expression: No
MassTheoretical: 11.888371 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #39: protein, Ribosomal protein L37

ProteinName: Ribosomal protein L37 / Recombinant expression: No
MassTheoretical: 10.090891 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #40: protein, eL38

ProteinName: eL38 / Recombinant expression: No
MassTheoretical: 8.107752 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #41: protein, eL39

ProteinName: eL39 / Recombinant expression: No
MassTheoretical: 6.295562 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #42: protein, eL40

ProteinName: eL40 / Recombinant expression: No
MassTheoretical: 6.199574 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #43: protein, 60s ribosomal protein l41

ProteinName: 60s ribosomal protein l41 / Recombinant expression: No
MassTheoretical: 3.213075 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #44: protein, eL42

ProteinName: eL42 / Recombinant expression: No
MassTheoretical: 12.198603 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #45: protein, Ribosomal protein L37a

ProteinName: Ribosomal protein L37aRibosome / Recombinant expression: No
MassTheoretical: 10.168153 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #46: protein, eL28

ProteinName: eL28 / Recombinant expression: No
MassTheoretical: 15.652419 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #47: protein, 60S acidic ribosomal protein P0

ProteinName: 60S acidic ribosomal protein P0 / Recombinant expression: No
MassTheoretical: 21.747293 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #48: protein, Ribosomal protein L12

ProteinName: Ribosomal protein L12 / Recombinant expression: No
MassTheoretical: 17.689461 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #49: nucleic-acid, 28S ribosomal RNA

Nucleic-acidName: 28S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGACCUCA GAUCAGACGU GGCGACCCGC UGAAUUUAAG CAUAUUAGUC AGCGGAGGAG AAGAAACUAA CCAGGAUUCC CUCAGUAACG GCGAGUGAAC AGGGAAGAGC CCAGCGCCGA AUCCCCGCCC CGCGGCGGGG CGCGGGACAU GUGGCGUACG GAAGACCCGC UCCCCGGCGC CGCUCGUGGG GGGCCCAAGU CCUUCUGAUC GAGGCCCAGC CCGUGGACGG UGUGAGGCCG GUAGCGGCCC CCGGCGCGCC GGGCCCGGGU CUUCCCGGAG UCGGGUUGCU UGGGAAUGCA GCCCAAAGCG GGUGGUAAAC UCCAUCUAAG GCUAAAUACC GGCACGAGAC CGAUAGUCAA CAAGUACCGU AAGGGAAAGU UGAAAAGAAC UUUGAAGAGA GAGUUCAAGA GGGCGUGAAA CCGUUAAGAG GUAAACGGGU GGGGUCCGCG CAGUCCGCCC GGAGGAUUCA ACCCGGCGGC GGGUCCGGCC GUGUCGGCGG CCCGGCGGAU CUUUCCCGCG CGGGGGACCG UCCCCCGACC GGCGACCGGC CGCCGCCGGG CGCAUUUCCA CCGCGGCGGU GCGCCGCGAC CGGCUCCGGG ACGGCUGGGA AGGCCCGGCG GGGAAGGUGG CUCGGCCGAG UGUUACAGCC CCCCCGGCAG CAGCACUCGC CGAAUCCCGG GGCCGAGGGA GCGAGACCCG UCGCCGCGCU CUCCCCCCUC CCGGCGCCGC CGGGGGGGGC CGGGCCACCC CUCCCACGGC GCGACCGCUC GGGGCGGACU GUCCCCAGUG CGCCCCGGGC GGGUCGCGCC GUCGGGCCCG GGGGAGGGGC CACGCGCGCG UCCCCCGAAG AGGGGGACGG CGGAGCGAGC GCACGGGGUC GGCGGCGACG UCGGCUACCC ACCCGACCCG UCUUGAAACA CGGACCAAGG AGUCUAACAC GUGCGCGAGU CGGGGGCUCG CACGAAAGCC GCCGUGGCGC AAUGAAGGUG AAGGCCGGCG CGCUCGCCGG CCGAGGUGGG AUCCCGAGGC CUCUCCAGUC CGCCGAGGGC GCACCACCGG CCCGUCUCGC CCGCCGCGCC GGGGAGGUGG AGCACGAGCG CACGUGUUAG GACCCGAAAG AUGGUGAACU AUGCCUGGGC AGGGCGAAGC CAGAGGAAAC UCUGGUGGAG GUCCGUAGCG GUCCUGACGU GCAAAUCGGU CGUCCGACCU GGGUAUAGGG GCGAAAGACU AAUCGAACCA UCUAGUAGCU GGUUCCCUCC GAAGUUUCCC UCAGGAUAGC UGGCGCUCUC GCACACGCAG UUUUAUCCGG UAAAGCGAAU GAUUAGAGGU CUUGGGGCCG AAACGAUCUC AACCUAUUCU CAAACUUUAA AUGGGUAAGA AGCCCGGCUC GCUGGCGUGA GCCGGGCGUG GAAUGGAGUG CCUAGUGGGC CACUUUUGGU AAGCAGAACU GGCGCUGCGG GAUGAACCGA ACGCCGGGUU AAGGCGCCCG AUGCCGACGC UCAUCAGACC CCAGAAAAGG UGUUGGUUGA UAUAGACAGC AGGACGGUGG CCAUGGAAGU CGGAAUCCGC UAAGGAGUGU GUAACAACUC ACCUGCCGAA UCAACUAGCC CUGAAAAUGG AUGGCGCUGG AGCGUCGGGC CCAUACCCGG CCGUCGCCGG CAGUCGAGAG UGGACGGGAG CGGCGGGGGC GGCGCGCGCG CGCGCCCGCC CCCGGAGCCC CGCGGACGCU ACGCCGCGAC GAGUAGGAGG GCCGCUGCGG UGAGCCUUGA AGCCUAGGGC GCGGGCCCGG GUGGAGCCGC CGCAGGUGCA GAUCUUGGUG GUAGUAGCAA AUAUUCAAAC GAGAACUUUG AAGGCCGAAG UGGAGAAGGG UUCCAUGUGA ACAGCAGUUG AACAUGGGUC AGUCGGUCCU GAGAGAUGGG CGAGCGCCGU UCCGAAGGGA CGGGCGAUGG CCUCCGUUGC CCUCGGCCGA UCGAAAGGGA GUCGGGUUCA GAUCCCCGAA UCCGGAGUGG CGGAGAUGGG CGCCGCGAGG CGUCCAGUGC GGUAACGCGA CCGAUCCCGG AGAAGCCGGC GGGAGCCCCG GGGAGAGUUC UCUUUUCUUU GUGAAGGGCA GGGCGCCCUG GAAUGGGUUC GCCCCGAGAG AGGGGCCCGU GCCUUGGAAA GCGUCGCGGU UCCGGCGGCG UCCGGUGAGC UCUCGCUGGC CCUUGAAAAU CCGGGGGAGA GGGUGUAAAU CUCGCGCCGG GCCGUACCCA UAUCCGCAGC AGGUCUCCAA GGUGAACAGC CUCUGGCAUG UUGGAACAAU GUAGGUAAGG GAAGUCGGCA AGCCGGAUCC GUAACUUCGG GAUAAGGAUU GGCUCUAAGG GCUGGGUCGG UCGUCGGCCG GCGCCUAGCA GCCGACUUAG AACUGGUGCG GACCAGGGGA AUCCGACUGU UUAAUUAAAA CAAAGCAUCG CGAAGGCCCG CGGCGGGUGU UGACGCGAUG UGAUUUCUGC CCAGUGCUCU GAAUGUCAAA GUGAAGAAAU UCAAUGAAGC GCGGGUAAAC GGCGGGAGUA ACUAUGACUC UCUUAAGGUA GCCAAAUGCC UCGUCAUCUA AUUAGUGACG CGCAUGAAUG GAUGAACGAG AUUCCCACUG UCCCUACCUA CUAUCCAGCG AAACCACAGC CAAGGGAACG GGCUUGGCGG AAUCAGCGGG GAAAGAAGAC CCUGUUGAGC UUGACUCUAG UCUGGCACGG UGAAGAGACA UGUUUUUUCA CUGACCCGGU GAGGCGGGGG GGCGAGCCCC GAGGGGCUCU CGCUUCUGGC GCCAAGCGCC CGGCCGCGCG CCGGCCGGGC GCGACCCGCU CCGGGGACAG UGCCAGGUGG GGAGUUUGAC UGGGGCGGUA CACCUGUCAA ACGGUAACGC AGGUGUCCUA AGGCGAGCUC AGGGAGGACA GAAACCUCCC GUGGAGCAGA AGGGCAAAAG CUCGCUUGAU CUUGAUUUUC AGUACGAAUA CAGACCGUGA AAGCGGGGCC UCACGAUCCU UCUGACCUUU UGGGUUUUAA GCAGGAGGUG UCAGAAAAGU UACCACAGGG AUAACUGGCU UGUGGCGGCC AAGCGUUCAU AGCGACGUCG CUUUUUGAUC CUUCGAUGUC GGCUCUUCCU AUCAUUGUGA AGCAGAAUUC ACCAAGCGUU GGAUUGUUCA CCCACUAAUA GGGAACGUGA GCUGGGUUUA GACCGUCGUG AGACAGGUUA GUUUUACCCU ACUGAUGAUG UGUUGUUGCC AUGGUAAUCC UGCUCAGUAC GAGAGGAACC GCAGGUUCAG ACAUUUGGUG UAUGUGCUUG GCUGAGGAGC CAAUGGGGCG AAGCUACCAU CUGUGGGAUU AUGACUGAAC GCCUCUAAGU CAGAAUCCCG CCCAGGCGGA ACGAUACGGC AGCGCCGCGG AGCCUCGGUU GGCCUCGGAU AGCCGGUCCC CCGCGGGGUC CGGUGCGGAG UGCCCUUCGU CCUGGGAAAC GGGGCGCGGC CGGAGAGGCG GCCGCCCCCU CGCCCGUCAC GCACGCCGUU CGUGGGGAAC CUGGCGCUAA ACCAUUCGUA GACGACCUGC UUCUGGGUCG GGGUUUCGUA CGUAGCAGAG CAGCUCCCUC GCUGCGAUCU AUUGAAAGUC AGCCCUCGAC ACAAGGGUUU GU
MassTheoretical: 1.1865795 MDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #50: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUCUACGGCC AUACCACCCU GAACGCGCCC GAUCUCGUCU GAUCUCGGAA GCUAAGCAGG GUCGGGCCUG GUUAGUACUU GGAUGGGAGA CCGCCUGGGA AUACCGGGUG CUGUAGGCUU
MassTheoretical: 38.691914 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #51: nucleic-acid, 5.8S ribosomal RNA

Nucleic-acidName: 5.8S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGACUCUUAG CGGUGGAUCA CUCGGCUCGU GCGUCGAUGA AGAACGCAGC UAGCUGCGAG AAUUAAUGUG AAUUGCAGGA CACAUUGAUC AUCGACACUU CGAACGCACU UGCGGCCCCG GGUUCCUCCC GGGGCUACGC CUGUCUGAGC GUCGCU
MassTheoretical: 50.143648 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #52: protein, Protein transport protein Sec61 subunit alpha isoform 1

ProteinName: Protein transport protein Sec61 subunit alpha isoform 1Protein targeting
Recombinant expression: No
MassTheoretical: 50.758504 kDa
SourceSpecies: Canis lupus familiaris (dog)

+
Component #53: protein, Protein transport protein Sec61 subunit gamma

ProteinName: Protein transport protein Sec61 subunit gammaProtein targeting
Recombinant expression: No
MassTheoretical: 7.019456 kDa
SourceSpecies: Canis lupus familiaris (dog)

+
Component #54: protein, Protein transport protein Sec61 subunit beta

ProteinName: Protein transport protein Sec61 subunit betaProtein targeting
Recombinant expression: No
MassTheoretical: 3.265008 kDa
SourceSpecies: Canis lupus familiaris (dog)

+
Component #55: protein, Dolichyl-diphosphooligosaccharide--protein glycosyltrans...

ProteinName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1,RPN1
Recombinant expression: No
MassTheoretical: 14.515871 kDa
SourceSpecies: Canis lupus familiaris (dog)

+
Component #56: protein, TMEM258

ProteinName: TMEM258 / Recombinant expression: No
MassTheoretical: 5.124308 kDa
SourceSpecies: Canis lupus familiaris (dog)

+
Component #57: protein, Oligosaccharyltransferase complex subunit OSTC

ProteinName: Oligosaccharyltransferase complex subunit OSTC / Recombinant expression: No
MassTheoretical: 13.375942 kDa
SourceSpecies: Canis lupus familiaris (dog)

+
Component #58: protein, OST4

ProteinName: OST4 / Recombinant expression: No
MassTheoretical: 3.809582 kDa
SourceSpecies: Canis lupus familiaris (dog)

+
Component #59: protein, Dolichyl-diphosphooligosaccharide--protein glycosyltrans...

ProteinName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
Recombinant expression: No
MassTheoretical: 80.657375 kDa
SourceSpecies: Canis lupus familiaris (dog)

+
Component #60: protein, DAD1

ProteinName: DAD1 / Recombinant expression: No
MassTheoretical: 8.273189 kDa
SourceSpecies: Canis lupus familiaris (dog)

+
Component #61: protein, OST48

ProteinName: OST48 / Recombinant expression: No
MassTheoretical: 2.145636 kDa
SourceSpecies: Canis lupus familiaris (dog)

+
Component #62: protein, RPN2

ProteinName: RPN2 / Recombinant expression: No
MassTheoretical: 6.826406 kDa
SourceSpecies: Canis lupus familiaris (dog)

+
Component #63: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 159 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #64: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #65: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

+
Component #66: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

+
Component #67: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

+
Component #68: ligand, [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxyme...

LigandName: [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.651663 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/ml / pH: 7.6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE MIXTURE / Humidity: 7 % / Details: Blot 3 seconds before plunging.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 3000.0 - 4000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -60 - 60 deg.
CameraDetector: GATAN K2 (4k x 4k)

-
Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: BACK PROJECTION / CTF correction: On each individual tilt image / Resolution: 9.1 Å / Resolution method: FSC 0.5 CUT-OFF

-
Atomic model buiding

Output model

+
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Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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