6FTG

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation 3D Report Full Report


This is version 1.5 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
  • Structures With Same Primary Citation

  • PubMed 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 oligosaccharyltransferase (OST). Here we used different cryo-electron m ...

    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.


    Organizational Affiliation

    Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, 81377 Munich, Germany. beckmann@genzentrum.lmu.de pfeffer@biochem.mpg.de f.g.forster@uu.nl.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
uL2
A
244Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
uL3
B
394Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
Find proteins for G1TL06 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TL06

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L4
C
362Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL4
Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
D
292Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL5
Find proteins for G1SYJ6 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6
E
248Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TG04 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
uL30
F
225Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL7
Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
eL8
G
241Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354898
Find proteins for G1STW0 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
uL6
H
190Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354760
Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L10 (Predicted)
I
213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L11
J
169Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
eL13
L
210Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L14
M
138Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
Find proteins for U3KNW6 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15
N
203Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL15
Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
uL13
O
199Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
uL22
P
153Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL17-C18orf32
Find proteins for G1TVT6 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
uL14
Q
187Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
eL19
R
180Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
eL20
S
175Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
eL21
T
159Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
eL22
U
99Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
uL14
V
131Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL23
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L24
W
63Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
uL23
X
119Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100350855
Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L26
Y
134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27
Z
135Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100356974RPL27
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
uL15
a
147Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27ALOC100350771
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
b
75Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100350215
Find proteins for G1TN82 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
eL30
c
94Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
eL31
d
107Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL31
Find proteins for G1SHG0 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
eL32
e
128Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TUN8 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
eL33
f
109Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35A
Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
eL34
g
114Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354714
Find proteins for G1U945 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
eL29
h
122Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35
Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36
i
102Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TTQ5 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37
j
86Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
eL38
k
69Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
eL39
l
50Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL39
Find proteins for G1SYU7 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SYU7

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
eL40
m
52Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60s ribosomal protein l41
n
23Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
eL42
o
104Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353469
Find proteins for G1T040 (Oryctolagus cuniculus)
Go to UniProtKB:  G1T040

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37a
p
91Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100351807LOC100349729RPL37A
Find proteins for G1SY53 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SY53

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
eL28
r
136Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100358162
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
s
198Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L12
t
163Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL12
Find proteins for G1SMR7 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SMR7

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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)
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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)
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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)
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1,RPN1
1
162Canis lupus familiarisMutation(s): 0 
Find proteins for E2RQ08 (Canis lupus familiaris)
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
TMEM258
2
60Canis lupus familiarisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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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)
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
OST4
4
34Canis lupus familiarisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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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)
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
DAD1
6
97Canis lupus familiarisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
OST48
7
25Canis lupus familiarisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
RPN2
8
80Canis lupus familiarisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 45
MoleculeChainsLengthOrganism
28S ribosomal RNAu3662Oryctolagus cuniculus

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Entity ID: 46
MoleculeChainsLengthOrganism
5S ribosomal RNAv120Oryctolagus cuniculus

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Entity ID: 47
MoleculeChainsLengthOrganism
5.8S ribosomal RNAw156Oryctolagus cuniculus
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9UB
Query on 9UB

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 CCD File 
5
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

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5
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

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5
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
ZN
Query on ZN

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g, j, m, o, p
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
B, I, P, V, a, e, g, u, v, w
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Structure Validation

View Full Validation Report



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
    Changes: Author supporting evidence, Data collection, Derived calculations, Refinement description
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.3: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2019-12-11
    Changes: Other