23GF | pdb_000023gf

The atomic coordinate of GPI-MT-I complex with Gpi14 D38A mutation

PDB DOI: https://doi.org/10.2210/pdb23GF/pdb
EM Map EMD-68941: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Saccharomyces cerevisiae
Mutation(s): Yes

Deposited: 2026-02-05 Released: 2026-09-09
Deposition Author(s): Liu, J., Yang, Y.Z., Zhang, M., Yu, H.J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

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

wwPDB Validation

Currently 23GF does not have a validation slider image.

This is version 1.0 of the entry. See complete history.

Literature

Structure of a membrane-bound glycosyltransferase

Liu, J., Yang, Y.Z., Zhang, M., Yu, H.J.

To be published.

Macromolecule Content

Total Structure Weight: 95.44 kDa
Atom Count: 6,687
Modeled Residue Count: 795
Deposited Residue Count: 795
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein PBN1	A	405	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: PBN1, YCL052C, YCL52C
UniProt
Find proteins for P25580 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25580 Go to UniProtKB: P25580
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25580
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A	Go to GlyGen: P25580-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GPI mannosyltransferase 1	B	390	Saccharomyces cerevisiae S288C	Mutation(s): 1 Gene Names: GPI14, PMH1, YJR013W, J1444, YJR83.11 EC: 2.4.1
UniProt
Find proteins for P47088 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47088 Go to UniProtKB: P47088
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P47088
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E	2	N/A	N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Interactions & Density Focus chain C Focus chain D Focus chain E

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MJC( Subject of Investigation/LOI) Query on MJC Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	dolichyl phosphate mannose C₆₁ H₁₀₃ O₉ P FVCCNKBLEFCPJO-ALFQADJPSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
A1E5V Query on A1E5V Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	[(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-decanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] dodecanoate C₄₂ H₇₉ O₁₄ P TZRQRTUJJJVTAX-RFVQHFLWSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

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	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2026-09-09
Type: Initial release

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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.