6FTG

Subtomogram average of OST-containing ribosome-translocon complexes from canine rough microsomal membranes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum.

Braunger, K.Pfeffer, S.Shrimal, S.Gilmore, R.Berninghausen, O.Mandon, E.C.Becker, T.Forster, F.Beckmann, R.

(2018) Science 360: 215-219

  • DOI: 10.1126/science.aar7899
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein synthesis, transport and N-glycosylation are coupled at the mammalian endoplasmic reticulum (ER) by complex formation between the ribosome, the Sec61 protein-conducting channel and the oligosaccharyltransferase (OST). Here, we used different ...

    Protein synthesis, transport and N-glycosylation are coupled at the mammalian endoplasmic reticulum (ER) by complex formation between the ribosome, the Sec61 protein-conducting channel and the 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 revealed how STT3A 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 co-translational machinery for N-glycosylation provides the basis for a mechanistic understanding of glycoprotein biogenesis at the ER.


    Organizational Affiliation

    Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, 81377 Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
uL2
A
244Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL8
Find proteins for G1TT27 (Oryctolagus cuniculus)
Go to Gene View: RPL8
Go to UniProtKB:  G1TT27
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
uL3
B
394Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
Find proteins for G1TL06 (Oryctolagus cuniculus)
Go to Gene View: RPL3
Go to UniProtKB:  G1TL06
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L4
C
362Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL4
Find proteins for G1SVW5 (Oryctolagus cuniculus)
Go to Gene View: RPL4
Go to UniProtKB:  G1SVW5
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
D
292Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL5
Find proteins for G1SYJ6 (Oryctolagus cuniculus)
Go to Gene View: RPL5
Go to UniProtKB:  G1SYJ6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6
E
248Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TG04 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TG04
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
uL30
F
225Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL7
Find proteins for G1SV32 (Oryctolagus cuniculus)
Go to Gene View: RPL7
Go to UniProtKB:  G1SV32
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
eL8
G
241Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1STW0 (Oryctolagus cuniculus)
Go to UniProtKB:  G1STW0
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
uL6
H
190Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TX33 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TX33
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L10 (Predicted)
I
213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
Go to Gene View: RPL10
Go to UniProtKB:  B7NZQ2
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L11
J
169Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL11
Find proteins for G1TUB8 (Oryctolagus cuniculus)
Go to Gene View: RPL11
Go to UniProtKB:  G1TUB8
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
eL13
L
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L14
M
138Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
Find proteins for U3KNW6 (Oryctolagus cuniculus)
Go to Gene View: RPL14
Go to UniProtKB:  U3KNW6
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15
N
203Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL15 (LOC100358370)
Find proteins for G1T0C1 (Oryctolagus cuniculus)
Go to Gene View: RPL15
Go to UniProtKB:  G1T0C1
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
uL13
O
199N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
uL22
P
153Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC108175352
Find proteins for G1TVT6 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TVT6
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
uL14
Q
187N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
eL19
R
180N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
eL20
S
175N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
eL21
T
159Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC108175794 (LOC108178019)
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SHQ2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
eL22
U
99N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
uL14
V
131Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100351949
Find proteins for G1T6D1 (Oryctolagus cuniculus)
Go to UniProtKB:  G1T6D1
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L24
W
63Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
Find proteins for G1SE28 (Oryctolagus cuniculus)
Go to Gene View: RPL24
Go to UniProtKB:  G1SE28
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
uL23
X
119Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC108177974
Find proteins for G1SE76 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SE76
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L26
Y
134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
Find proteins for G1SQH0 (Oryctolagus cuniculus)
Go to Gene View: RPL26
Go to UniProtKB:  G1SQH0
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27
Z
135Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100356974 (RPL27)
Find proteins for G1TXF6 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TXF6
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
uL15
a
147Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27A
Find proteins for G1SNY0 (Oryctolagus cuniculus)
Go to Gene View: RPL27A
Go to UniProtKB:  G1SNY0
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
b
75Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100350215
Find proteins for G1TN82 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TN82
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
eL30
c
94N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
eL31
d
107Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL31
Find proteins for G1SHG0 (Oryctolagus cuniculus)
Go to Gene View: RPL31
Go to UniProtKB:  G1SHG0
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
eL32
e
128Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TUN8 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TUN8
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
eL33
f
109Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35A
Find proteins for G1SF08 (Oryctolagus cuniculus)
Go to Gene View: RPL35A
Go to UniProtKB:  G1SF08
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
eL34
g
114Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354714
Find proteins for G1U945 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U945
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
eL29
h
122Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35
Find proteins for G1SIT5 (Oryctolagus cuniculus)
Go to Gene View: RPL35
Go to UniProtKB:  G1SIT5
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36
i
102Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348796
Find proteins for G1TTQ5 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TTQ5
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37
j
86Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
Find proteins for U3KPD5 (Oryctolagus cuniculus)
Go to Gene View: RPL37
Go to UniProtKB:  U3KPD5
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
eL38
k
69N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
eL39
l
50Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC108178831
Find proteins for G1SYU7 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SYU7
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
eL40
m
52N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60s ribosomal protein l41
n
23Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
Go to UniProtKB:  A0A087WNH4
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
eL42
o
104Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353469
Find proteins for G1T040 (Oryctolagus cuniculus)
Go to UniProtKB:  G1T040
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37a
p
91Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100351807
Find proteins for G1SY53 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SY53
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
eL28
r
136Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100358162
Find proteins for G1U7L1 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U7L1
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
s
198Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U6N2 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U6N2
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L12
t
163Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL12
Find proteins for G1SMR7 (Oryctolagus cuniculus)
Go to Gene View: RPL12
Go to UniProtKB:  G1SMR7
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein Sec61 subunit alpha isoform 1
x
461Canis lupus familiarisMutation(s): 0 
Gene Names: SEC61A1
Find proteins for P38377 (Canis lupus familiaris)
Go to Gene View: SEC61A1
Go to UniProtKB:  P38377
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein Sec61 subunit gamma
y
62Canis lupus familiarisMutation(s): 0 
Gene Names: SEC61G
Find proteins for P60058 (Canis lupus familiaris)
Go to Gene View: SEC61G
Go to UniProtKB:  P60058
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein Sec61 subunit beta
z
29Canis lupus familiarisMutation(s): 0 
Gene Names: SEC61B
Find proteins for P60467 (Canis lupus familiaris)
Go to Gene View: SEC61B
Go to UniProtKB:  P60467
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1,RPN1
1
162Canis lupus familiarisMutation(s): 0 
Gene Names: RPN1
Find proteins for E2RQ08 (Canis lupus familiaris)
Go to Gene View: RPN1
Go to UniProtKB:  E2RQ08
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
TMEM258
2
60N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Oligosaccharyltransferase complex subunit OSTC
3
120Canis lupus familiarisMutation(s): 0 
Gene Names: OSTC
Find proteins for P86218 (Canis lupus familiaris)
Go to Gene View: OSTC
Go to UniProtKB:  P86218
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
OST4
4
34N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
5
705Canis lupus familiarisMutation(s): 0 
Gene Names: STT3A
EC: 2.4.99.18
Find proteins for F1PJP5 (Canis lupus familiaris)
Go to Gene View: STT3A
Go to UniProtKB:  F1PJP5
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
DAD1
6
97N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
OST48
7
25N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
RPN2
8
80N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 45
MoleculeChainsLengthOrganism
28S ribosomal RNAu3662Oryctolagus cuniculus
Entity ID: 46
MoleculeChainsLengthOrganism
5S ribosomal RNAv120Oryctolagus cuniculus
Entity ID: 47
MoleculeChainsLengthOrganism
5.8S ribosomal RNAw156Oryctolagus cuniculus
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
g, j, m, o, p
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
5
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
5
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
a, B, e, g, I, P, u, V, v, w
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
9UB
Query on 9UB

Download SDF File 
Download CCD File 
5
[(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
C29 H51 N O11 P2
ZBWKCDFMHFZRQG-MJTKDKBSSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
5
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
1, 2, 6, 7, 8
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGRK1721
European Research CouncilGermany724425
German Research FoundationGermanyFO 716/4-1

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-04
    Type: Author supporting evidence, Data collection, Derived calculations, Refinement description
  • Version 1.2: 2018-04-25
    Type: Data collection, Database references
  • Version 1.3: 2018-10-24
    Type: Advisory, Data collection, Derived calculations
  • Version 1.4: 2018-11-21
    Type: Advisory, Data collection, Derived calculations