6P25

Structure of S. cerevisiae protein O-mannosyltransferase Pmt1-Pmt2 complex bound to the sugar donor and a peptide acceptor

• PDB DOI: https://doi.org/10.2210/pdb6P25/pdb
• EM Map EMD-20236: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae W303
• Expression System: Saccharomyces cerevisiae W303
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2019-05-21 Released: 2019-07-10 
• Deposition Author(s): Bai, L., Li, H.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 183.57 kDa 
• Atom Count: 11,739 
• Modelled Residue Count: 1,424 
• Deposited Residue Count: 1,580 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dolichyl-phosphate-mannose--protein mannosyltransferase 1	A	817	Saccharomyces cerevisiae W303	Mutation(s): 0  Gene Names: PMT1, YDL095W, D2390 EC: 2.4.1.109 Membrane Entity: Yes
UniProt
Find proteins for P33775 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33775  Go to UniProtKB:  P33775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dolichyl-phosphate-mannose--protein mannosyltransferase 2	B	759	Saccharomyces cerevisiae W303	Mutation(s): 0  Gene Names: PMT2, FUN25, YAL023C EC: 2.4.1.109 Membrane Entity: Yes
UniProt
Find proteins for P31382 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P31382  Go to UniProtKB:  P31382

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
acceptor peptide	C [auth D]	4	Saccharomyces cerevisiae W303	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPL	E [auth A], H [auth B], I [auth B]	1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C42 H80 N O8 P JLPULHDHAOZNQI-ZTIMHPMXSA-N
NNM (Subject of Investigation/LOI)	F [auth A]	(3R)-3,31-dimethyl-7,11,15,19,23,27-hexamethylidenedotriacont-31-en-1-yl dihydrogen phosphate C40 H69 O4 P CTKMEBTWSXRRSJ-RRHRGVEJSA-N
NAG	D [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot
RECONSTRUCTION	Coot
RECONSTRUCTION	UCSF Chimera

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Bai, L., Li, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01-CA231466

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2019-07-24
  Changes: Data collection, Database references
• Version 1.2: 2019-08-21
  Changes: Data collection, Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary