9NYC | pdb_00009nyc

Cryo-EM structure of the glycosyltransferase GtrB in the substrate-bound state

PDB DOI: https://doi.org/10.2210/pdb9NYC/pdb
EM Map EMD-49930: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-03-27 Released: 2025-12-17
Deposition Author(s): Morgan, R.T., Motta, S., Gil-Iturbe, E., Bhattacharjee, B., di Muccio, G., Romagnoli, A., Anwar, M.T., Mishra, B., Ashraf, K., Bang, I., di Marino, D., Lowary, T.L., Quick, M., Petrou, V.I., Stowell, M.H.B., Nygaard, R., Mancia, F.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.54 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Mechanistic snapshots of lipid-linked sugar transfer

Morgan, R.T., Motta, S., Gil-Iturbe, E., Bhattacharjee, B., Anwar, M.T., Di Muccio, G., Romagnoli, A., Mishra, B., Ashraf, K.U., Bang, I., Di Marino, D., Lowary, T.L., Quick, M., Petrou, V.I., Stowell, M.H.B., Nygaard, R., Mancia, F.

(2025) Nat Commun

DOI: https://doi.org/10.1038/s41467-025-66769-7

Macromolecule Content

Total Structure Weight: 163.03 kDa
Atom Count: 10,516
Modeled Residue Count: 1,264
Deposited Residue Count: 1,364
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase sll0501	A, B [auth D], C [auth B], D [auth C]	341	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Gene Names: sll0501 EC: 2.4
UniProt
Find proteins for Q55487 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55487 Go to UniProtKB: Q55487
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q55487
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5TR (Subject of Investigation/LOI) Query on 5TR Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth D] SDF format, chain L [auth B] SDF format, chain O [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth D] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth D] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C]	F [auth A], I [auth D], L [auth B], O [auth C]	[(2~{E},6~{E},10~{E},14~{E},18~{Z},22~{E},26~{Z},30~{E},34~{E},38~{E})-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenyl] dihydrogen phosphate C₅₅ H₉₁ O₄ P UFPHFKCTOZIAFY-ZUPWODLNSA-N		Interactions Focus chain F [auth A] Focus chain I [auth D] Focus chain L [auth B] Focus chain O [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth D] Focus chain L [auth B] Focus chain O [auth C]
UPG (Subject of Investigation/LOI) Query on UPG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth D] SDF format, chain K [auth B] SDF format, chain N [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C]	E [auth A], H [auth D], K [auth B], N [auth C]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain E [auth A] Focus chain H [auth D] Focus chain K [auth B] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth D] Focus chain K [auth B] Focus chain N [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth D] SDF format, chain M [auth B] SDF format, chain P [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth D] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth D] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C]	G [auth A], J [auth D], M [auth B], P [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth D] Focus chain M [auth B] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth D] Focus chain M [auth B] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.54 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM132120
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS120496
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	K99GM123228
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R00GM123228
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM150831