6EZN

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 OPMPDBTMMemProtMD

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 2.1 of the entry. See complete history.

Macromolecule Content

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

Macromolecules

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41543
Sequence Annotations Expand
Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P46964
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48439
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99380
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92316
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P39007
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33767
Sequence Annotations Expand
Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02795
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	3D 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	3D 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 O [auth F] SDF format, chain R [auth H] MOL2 format, chain M [auth A] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain R [auth H]	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]	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]	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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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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.

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Help and Resources

6EZN

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

Entity ID: 1

UniProt

Entity Groups

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

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Entity ID: 11

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)