9UTW | pdb_00009utw

Structure of dimeric FKS1 in complex with tRNA

PDB DOI: https://doi.org/10.2210/pdb9UTW/pdb
EM Map EMD-37613: EMDB EMDataResource
NAKB: 9UTW
EM Map EMD-64502: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2025-05-05 Released: 2025-12-17
Deposition Author(s): Li, J.L., Zhu, A.Q., Liu, J.X., Dai, X.L., Wang, X., Yan, C.Y., Deng, D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.96 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

Structural-guided identification of two modulators of beta-1,3-glucan synthase FKS1.

Li, J.L., Li, J., Zhu, A., Dai, X., Liu, J., Liu, H., Xia, Z., Dong, Y., Qian, W., Dai, L., Guo, L., Yan, C., Deng, D., Luo, Y., Wang, X.

(2025) Nat Commun

PubMed: 41354657 Search on PubMed
DOI: https://doi.org/10.1038/s41467-025-67293-4
Primary Citation of Related Structures:
9UTU, 9UTW

PubMed Abstract:
FKS1 is a β-1,3-glucan synthase critical for fungal cell wall formation and a target for antifungal drugs such as echinocandin and ibrexafungerp. However, the mechanisms regulating FKS1 activity remain largely unknown. Here, we reveal that transfer RNA (tRNA) acts as an endogenous inhibitor, whereas GSR1 functions as a stabilizer of FKS1. The cryo-EM structure of FKS1 adopts a tRNA-mediated homodimer configuration, representing a quiescent state of β-1,3-glucan synthase. Unexpectedly, the copurified endogenous tRNA is identified as a potent inhibitor that suppresses FKS1 activity. Moreover, high-resolution cryo-EM density analysis enable the identification of GSR1 as an additional binding partner of FKS1. Mutagenesis experiments confirm the interaction between FKS1 and GSR1. Evolutionarily conserved GSR1 is found to increase the stability of FKS1 in β-1,3-glucan biosynthesis. Collectively, our findings identify both tRNA and GSR1 as intrinsic modulators of β-1,3-glucan biosynthesis, thereby providing opportunities for the further development of FKS1-targeted antifungal drugs.

Organizational Affiliation

Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China.

Children's Medicine Key Laboratory of Sichuan Province, Chengdu, China.

State Key Laboratory of Synthetic Biology, Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Synthetic Biology and Biomanufacturing, Tianjin University, Tianjin, China.

State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.

The First Clinical Medical College, Lanzhou University, Lanzhou, China.

Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China.

State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics and General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, China.

NHC Key Laboratory of Chronobiology, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China.

Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China. dengd@scu.edu.cn.

NHC Key Laboratory of Chronobiology, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China. dengd@scu.edu.cn.

Children's Medicine Key Laboratory of Sichuan Province, Chengdu, China. xiangwang@scu.edu.cn.

NHC Key Laboratory of Chronobiology, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China. xiangwang@scu.edu.cn.

Department of Andrology/Sichuan Human Sperm Bank, West China Second University Hospital, Sichuan University, Chengdu, Sichuan Province, China. xiangwang@scu.edu.cn.

Macromolecule Content

Total Structure Weight: 508.99 kDa
Atom Count: 25,408
Modeled Residue Count: 2,930
Deposited Residue Count: 4,222
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YMR295C	A [auth C], B [auth G]	197	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q03559 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03559 Go to UniProtKB: Q03559
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03559
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1,3-beta-glucan synthase component FKS1	C [auth H], D [auth B]	1,876	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.4.1.34
UniProt
Find proteins for P38631 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38631 Go to UniProtKB: P38631
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38631
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
tRNA	E [auth A]	76	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	F [auth J]	3		N/A	Interactions Focus chain F [auth J] Interactions & Density Focus chain F [auth J]

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	G [auth D]	2		N/A	Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEF (Subject of Investigation/LOI) Query on PEF Download Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain Q [auth H] MOL2 format, chain KA [auth B] MOL2 format, chain Q [auth H] mmCIF format, chain KA [auth B] mmCIF format, chain Q [auth H]	KA [auth B], Q [auth H]	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C₃₇ H₇₄ N O₈ P SLKDGVPOSSLUAI-PGUFJCEWSA-N		Interactions Focus chain KA [auth B] Focus chain Q [auth H] Interactions & Density Focus chain KA [auth B] Focus chain Q [auth H]
XKP (Subject of Investigation/LOI) Query on XKP Download Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain P [auth H] MOL2 format, chain JA [auth B] MOL2 format, chain P [auth H] mmCIF format, chain JA [auth B] mmCIF format, chain P [auth H]	JA [auth B], P [auth H]	(11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate C₂₃ H₄₆ N O₈ P VYUSSAVVRCGYLY-OAQYLSRUSA-N		Interactions Focus chain JA [auth B] Focus chain P [auth H] Interactions & Density Focus chain JA [auth B] Focus chain P [auth H]
DCR (Subject of Investigation/LOI) Query on DCR Download Ideal Coordinates CCD File SDF format, chain PA [auth B] SDF format, chain V [auth H] MOL2 format, chain PA [auth B] MOL2 format, chain V [auth H] mmCIF format, chain PA [auth B] mmCIF format, chain V [auth H]	PA [auth B], V [auth H]	icosanoic acid C₂₀ H₄₀ O₂ VKOBVWXKNCXXDE-UHFFFAOYSA-N		Interactions Focus chain PA [auth B] Focus chain V [auth H] Interactions & Density Focus chain PA [auth B] Focus chain V [auth H]
PLM (Subject of Investigation/LOI) Query on PLM Download Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain QA [auth B] SDF format, chain R [auth H] SDF format, chain RA [auth B] SDF format, chain S [auth H] SDF format, chain SA [auth B] SDF format, chain T [auth H] SDF format, chain TA [auth B] SDF format, chain U [auth H] SDF format, chain UA [auth B] SDF format, chain W [auth H] SDF format, chain X [auth H] SDF format, chain Y [auth H] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth H] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth H] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth H] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth H] MOL2 format, chain UA [auth B] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth H] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth H] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth H] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth H] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth H] mmCIF format, chain UA [auth B] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth H]	LA [auth B] MA [auth B] NA [auth B] OA [auth B] QA [auth B] LA [auth B], MA [auth B], NA [auth B], OA [auth B], QA [auth B], R [auth H], RA [auth B], S [auth H], SA [auth B], T [auth H], TA [auth B], U [auth H], UA [auth B], W [auth H], X [auth H], Y [auth H]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain QA [auth B] Focus chain R [auth H] Focus chain RA [auth B] Focus chain S [auth H] Focus chain SA [auth B] Focus chain T [auth H] Focus chain TA [auth B] Focus chain U [auth H] Focus chain UA [auth B] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth H] Interactions & Density Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain QA [auth B] Focus chain R [auth H] Focus chain RA [auth B] Focus chain S [auth H] Focus chain SA [auth B] Focus chain T [auth H] Focus chain TA [auth B] Focus chain U [auth H] Focus chain UA [auth B] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth H]
D10 (Subject of Investigation/LOI) Query on D10 Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain M [auth H] MOL2 format, chain EA [auth B] MOL2 format, chain M [auth H] mmCIF format, chain EA [auth B] mmCIF format, chain M [auth H]	EA [auth B], M [auth H]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain M [auth H] Interactions & Density Focus chain EA [auth B] Focus chain M [auth H]
DD9 (Subject of Investigation/LOI) Query on DD9 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain L [auth H] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] I [auth H] AA [auth B], BA [auth B], CA [auth B], DA [auth B], I [auth H], J [auth H], K [auth H], L [auth H]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H]
HP6 (Subject of Investigation/LOI) Query on HP6 Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain N [auth H] SDF format, chain O [auth H] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain N [auth H] mmCIF format, chain O [auth H]	FA [auth B] GA [auth B] HA [auth B] IA [auth B] N [auth H] FA [auth B], GA [auth B], HA [auth B], IA [auth B], N [auth H], O [auth H]	HEPTANE C₇ H₁₆ IMNFDUFMRHMDMM-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain N [auth H] Focus chain O [auth H] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain N [auth H] Focus chain O [auth H]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain H SDF format, chain Z [auth B] MOL2 format, chain H MOL2 format, chain Z [auth B] mmCIF format, chain H mmCIF format, chain Z [auth B]	H, Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H Focus chain Z [auth B] Interactions & Density Focus chain H Focus chain Z [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900024 Query on PRD_900024	G [auth D]	beta-laminaribiose	Oligosaccharide / Antimicrobial		Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]