6FTJ

Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Non-programmed 80S Ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



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
uL2A244Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
uL3B394Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L4C362Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL4
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5D292Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL5
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6E248Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ul30F225Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL7
Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
uL8G241Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354898
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
uL6H190Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354760
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L10 (Predicted)I213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L11J169Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
eL13L210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15N203Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL15
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
uL13O199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
uL22P153Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL17-C18orf32
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
uL14Q187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
eL19R180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
eL20S175Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L22U99Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL22
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
uL14V131Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL23
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L24W63Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
uL23X119Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100350855
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L26Y134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
uL15a147Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27ALOC100350771
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29b75Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100350215
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
eL30c94Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
eL31d107Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL31
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
eL32e128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
eL34g114Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354714
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
uL29h122Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37j86Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
eL38k69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
eL40m52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60s ribosomal protein l41n23Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
eL42o104Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353469
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37ap91Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100351807LOC100349729RPL37A
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0s198Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L12t163Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL12
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein Sec61 subunit alpha isoform 1x426Canis lupus familiarisMutation(s): 0 
Gene Names: SEC61A1
Find proteins for P38377 (Canis lupus familiaris)
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein Sec61 subunit betaz29Canis lupus familiarisMutation(s): 0 
Gene Names: SEC61B
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1,RPN11162Canis lupus familiarisMutation(s): 0 
Gene Names: RPN1
Find proteins for E2RQ08 (Canis lupus familiaris)
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
TMEM258260Canis lupus familiarisMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Oligosaccharyltransferase complex subunit OSTC3120Canis lupus familiarisMutation(s): 0 
Gene Names: OSTC
Find proteins for P86218 (Canis lupus familiaris)
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
OST4434Canis lupus familiarisMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A5696Canis lupus familiarisMutation(s): 0 
Gene Names: STT3A
EC: 2.4.99.18
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
DAD1697Canis lupus familiarisMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
OST48725Canis lupus familiarisMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
RPN2880Canis lupus familiarisMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L14M138Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
eL21T159Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27Z135Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100356974RPL27
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
eL33f109Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35A
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36i102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
eL39l50Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL39
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
eL28r136Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100358162
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein Sec61 subunit gammay62Canis lupus familiarisMutation(s): 0 
Gene Names: SEC61G
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Entity ID: 45
MoleculeChainsLengthOrganism
28S rRNAu3662Oryctolagus 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
Oligosaccharides
Entity ID: 59
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K
8 N-Glycosylation
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9UB
Query on 9UB

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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
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

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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: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGRK1721
European Research CouncilGermanyCRYOTRANSLATION
German Research FoundationGermanySFB646
Center for Integrated Protein Science MunichGermany--
Boehringer-Ingelheim-FondsGermanyPhD Fellowship

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 2.0: 2018-04-04
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations
  • Version 2.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 2.2: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.3: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.4: 2019-12-11
    Changes: Other
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary