6EZN | pdb_00006ezn

Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex

PDB DOI: https://doi.org/10.2210/pdb6EZN/pdb
EM Map EMD-4161: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae S288C
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2017-11-16 Released: 2018-01-17
Deposition Author(s): Wild, R., Kowal, J., Eyring, J., Ngwa, E.M., Aebi, M., Locher, K.P.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.3 of the entry. See complete history.

Literature

Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation.

Wild, R., Kowal, J., Eyring, J., Ngwa, E.M., Aebi, M., Locher, K.P.

(2018) Science 359: 545-550

PubMed: 29301962 Search on PubMed
DOI: https://doi.org/10.1126/science.aar5140
Primary Citation Related Structures:
6EZN

PubMed Abstract:
Oligosaccharyltransferase (OST) is an essential membrane protein complex in the endoplasmic reticulum, where it transfers an oligosaccharide from a dolichol-pyrophosphate-activated donor to glycosylation sites of secretory proteins. Here we describe the atomic structure of yeast OST determined by cryo-electron microscopy, revealing a conserved subunit arrangement. The active site of the catalytic STT3 subunit points away from the center of the complex, allowing unhindered access to substrates. The dolichol-pyrophosphate moiety binds to a lipid-exposed groove of STT3, whereas two noncatalytic subunits and an ordered N-glycan form a membrane-proximal pocket for the oligosaccharide. The acceptor polypeptide site faces an oxidoreductase domain in stand-alone OST complexes or is immediately adjacent to the translocon, suggesting how eukaryotic OSTs efficiently glycosylate a large number of polypeptides before their folding.

Organizational Affiliation

Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland.

Macromolecule Content

Total Structure Weight: 291.41 kDa
Atom Count: 17,008
Modeled Residue Count: 2,090
Deposited Residue Count: 2,512
Unique protein chains: 8

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1	A	476	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.4.99.18 Membrane Entity: Yes
UniProt
Find proteins for P41543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41543 Go to UniProtKB: P41543
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41543
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: P41543-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2	B	130	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.4.99.18 Membrane Entity: Yes
UniProt
Find proteins for P46964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P46964 Go to UniProtKB: P46964
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46964
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3	C	350	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.4.99.18 Membrane Entity: Yes
UniProt
Find proteins for P48439 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P48439 Go to UniProtKB: P48439
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48439
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4	D	36	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.4.99.18 Membrane Entity: Yes
UniProt
Find proteins for Q99380 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q99380 Go to UniProtKB: Q99380
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99380
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5	E	86	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.4.99.18 Membrane Entity: Yes
UniProt
Find proteins for Q92316 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q92316 Go to UniProtKB: Q92316
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92316
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3	F	718	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.4.99.18 Membrane Entity: Yes
UniProt
Find proteins for P39007 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39007 Go to UniProtKB: P39007
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39007
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain F	Go to GlyGen: P39007-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1	G	430	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.4.99.18 Membrane Entity: Yes
UniProt
Find proteins for P33767 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33767 Go to UniProtKB: P33767
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33767
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain G	Go to GlyGen: P33767-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1	H	286	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.4.99.18 Membrane Entity: Yes
UniProt
Find proteins for Q02795 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02795 Go to UniProtKB: Q02795
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02795
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	3		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, L	2		N-Glycosylation	Interactions Focus chain J Focus chain L Interactions & Density Focus chain J Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G83582BK GlyCosmos: G83582BK GlyGen: G83582BK

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CPL Query on CPL Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth E] SDF format, chain R [auth H] SDF format, chain O [auth F] MOL2 format, chain M [auth A] MOL2 format, chain N [auth E] MOL2 format, chain R [auth H] MOL2 format, chain O [auth F] mmCIF format, chain M [auth A] mmCIF format, chain N [auth E] mmCIF format, chain R [auth H] mmCIF format, chain O [auth F]	M [auth A], N [auth E], O [auth F], R [auth H]	1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₂ H₈₀ N O₈ P JLPULHDHAOZNQI-ZTIMHPMXSA-N		Interactions Focus chain M [auth A] Focus chain N [auth E] Focus chain O [auth F] Focus chain R [auth H] Interactions & Density Focus chain M [auth A] Focus chain N [auth E] Focus chain O [auth F] Focus chain R [auth H]
PTY Query on PTY Download:Ideal Coordinates CCD File SDF format, chain P [auth F] MOL2 format, chain P [auth F] mmCIF format, chain P [auth F]	P [auth F]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain P [auth F] Interactions & Density Focus chain P [auth F]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Q [auth G] MOL2 format, chain Q [auth G] mmCIF format, chain Q [auth G]	Q [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain Q [auth G] Interactions & Density Focus chain Q [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.0
MODEL REFINEMENT	PHENIX	1.11

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-01-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	SNF Synergia Transglyco: CRSII3_147632
Swiss National Science Foundation	Switzerland	SNF Sinergia GlycoSTART: CRSII5_173709/1

Revision History (Full details and data files)

Version 1.0: 2018-01-17
Type: Initial release
Version 1.1: 2018-02-21
Changes: Database references
Version 1.2: 2019-12-11
Changes: Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2022-12-07
Changes: Database references, Derived calculations, Structure summary
Version 2.2: 2024-11-06
Changes: Data collection, Structure summary
Version 2.3: 2024-12-11
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

6EZN | pdb_00006ezn

Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex

Literature

Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Oligosaccharides

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Entity ID: 11

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)