9H5K | pdb_00009h5k

Cryo-EM structure of the SEAC-EGOC supercomplex

PDB DOI: https://doi.org/10.2210/pdb9H5K/pdb
EM Map EMD-51887: EMDB EMDataResource

Classification: SIGNALING PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-22 Released: 2025-11-05
Deposition Author(s): Tafur, L., Loewith, R.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

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

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structure and function of the yeast amino acid-sensing SEAC-EGOC supercomplex

Tafur, L., Bonadei, L., Zheng, Y., Loewith, R.

To be published.

Macromolecule Content

Total Structure Weight: 2,344.49 kDa
Atom Count: 114,318
Modeled Residue Count: 14,138
Deposited Residue Count: 20,652
Unique protein chains: 13

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maintenance of telomere capping protein 5	A [auth C], I [auth K]	1,148	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q03897 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03897 Go to UniProtKB: Q03897
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03897
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein transport protein SEC13	B [auth H], J [auth P]	297	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q04491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04491 Go to UniProtKB: Q04491
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04491
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Restriction of telomere capping protein 1	C [auth A], K [auth I]	1,341	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q08281 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08281 Go to UniProtKB: Q08281
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08281
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoporin SEH1	D [auth F] E H [auth D] L [auth N] M D [auth F], E, H [auth D], L [auth N], M, P [auth L]	349	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P53011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53011 Go to UniProtKB: P53011
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53011
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
SEH-associated protein 4	F [auth G], G [auth B], N [auth O], O [auth J]	1,038	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38164 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38164 Go to UniProtKB: P38164
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38164
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein GTR1	Q [auth a], Y [auth b]	310	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: GTR1, YML121W, YM7056.05 EC: 3.6.5
UniProt
Find proteins for Q00582 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q00582 Go to UniProtKB: Q00582
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q00582
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein GTR2	R [auth c], Z [auth d]	341	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: GTR2, YGR163W EC: 3.6.5
UniProt
Find proteins for P53290 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53290 Go to UniProtKB: P53290
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53290
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogen permease regulator 2	AA [auth g], S [auth T]	615	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P39923 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39923 Go to UniProtKB: P39923
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P39923
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogen permease regulator 3	BA [auth i], T [auth h]	1,146	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38742 Go to UniProtKB: P38742
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38742
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar membrane-associated protein IML1	CA [auth j], U [auth X]	1,584	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P47170 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47170 Go to UniProtKB: P47170
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P47170
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein MEH1	DA [auth S], V [auth R]	184	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: MEH1, EGO1, GSE2, YKR007W, YK106
UniProt
Find proteins for Q02205 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02205 Go to UniProtKB: Q02205
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02205
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein EGO2	EA [auth W], W [auth U]	75	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: EGO2, YCR075W-A
UniProt
Find proteins for Q3E830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E830 Go to UniProtKB: Q3E830
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3E830
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SLM4	FA [auth Z], X [auth Y]	162	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SLM4, EGO3, GSE1, YBR077C, YBR0723
UniProt
Find proteins for P38247 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38247 Go to UniProtKB: P38247
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38247
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain LB [auth c] SDF format, chain OB [auth b] SDF format, chain PB [auth d] SDF format, chain KB [auth a] MOL2 format, chain LB [auth c] MOL2 format, chain OB [auth b] MOL2 format, chain PB [auth d] MOL2 format, chain KB [auth a] mmCIF format, chain LB [auth c] mmCIF format, chain OB [auth b] mmCIF format, chain PB [auth d] mmCIF format, chain KB [auth a]	KB [auth a], LB [auth c], OB [auth b], PB [auth d]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain KB [auth a] Focus chain LB [auth c] Focus chain OB [auth b] Focus chain PB [auth d] Interactions & Density Focus chain KB [auth a] Focus chain LB [auth c] Focus chain OB [auth b] Focus chain PB [auth d]
AF3 (Subject of Investigation/LOI) Query on AF3 Download Ideal Coordinates CCD File SDF format, chain JB [auth a] SDF format, chain NB [auth b] MOL2 format, chain JB [auth a] MOL2 format, chain NB [auth b] mmCIF format, chain JB [auth a] mmCIF format, chain NB [auth b]	JB [auth a], NB [auth b]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain JB [auth a] Focus chain NB [auth b] Interactions & Density Focus chain JB [auth a] Focus chain NB [auth b]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain EB [auth J] SDF format, chain HB [auth J] SDF format, chain IA [auth C] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain OA [auth G] SDF format, chain PA [auth G] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain UA [auth K] SDF format, chain VA [auth K] SDF format, chain WA [auth K] SDF format, chain XA [auth I] SDF format, chain YA [auth I] SDF format, chain ZA [auth I] SDF format, chain NA [auth G] SDF format, chain MA [auth G] SDF format, chain JA [auth A] SDF format, chain HA [auth C] SDF format, chain GB [auth J] SDF format, chain GA [auth C] SDF format, chain FB [auth J] SDF format, chain DB [auth O] SDF format, chain CB [auth O] SDF format, chain BB [auth O] SDF format, chain AB [auth O] MOL2 format, chain EB [auth J] MOL2 format, chain HB [auth J] MOL2 format, chain IA [auth C] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain PA [auth G] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth K] MOL2 format, chain VA [auth K] MOL2 format, chain WA [auth K] MOL2 format, chain XA [auth I] MOL2 format, chain YA [auth I] MOL2 format, chain ZA [auth I] MOL2 format, chain NA [auth G] MOL2 format, chain MA [auth G] MOL2 format, chain JA [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain GB [auth J] MOL2 format, chain GA [auth C] MOL2 format, chain FB [auth J] MOL2 format, chain DB [auth O] MOL2 format, chain CB [auth O] MOL2 format, chain BB [auth O] MOL2 format, chain AB [auth O] mmCIF format, chain EB [auth J] mmCIF format, chain HB [auth J] mmCIF format, chain IA [auth C] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain OA [auth G] mmCIF format, chain PA [auth G] mmCIF format, chain QA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth K] mmCIF format, chain VA [auth K] mmCIF format, chain WA [auth K] mmCIF format, chain XA [auth I] mmCIF format, chain YA [auth I] mmCIF format, chain ZA [auth I] mmCIF format, chain NA [auth G] mmCIF format, chain MA [auth G] mmCIF format, chain JA [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain GB [auth J] mmCIF format, chain GA [auth C] mmCIF format, chain FB [auth J] mmCIF format, chain DB [auth O] mmCIF format, chain CB [auth O] mmCIF format, chain BB [auth O] mmCIF format, chain AB [auth O]	AB [auth O] BB [auth O] CB [auth O] DB [auth O] EB [auth J] AB [auth O], BB [auth O], CB [auth O], DB [auth O], EB [auth J], FB [auth J], GA [auth C], GB [auth J], HA [auth C], HB [auth J], IA [auth C], JA [auth A], KA [auth A], LA [auth A], MA [auth G], NA [auth G], OA [auth G], PA [auth G], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth K], VA [auth K], WA [auth K], XA [auth I], YA [auth I], ZA [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth O] Focus chain BB [auth O] Focus chain CB [auth O] Focus chain DB [auth O] Focus chain EB [auth J] Focus chain FB [auth J] Focus chain GA [auth C] Focus chain GB [auth J] Focus chain HA [auth C] Focus chain HB [auth J] Focus chain IA [auth C] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth K] Focus chain VA [auth K] Focus chain WA [auth K] Focus chain XA [auth I] Focus chain YA [auth I] Focus chain ZA [auth I] Interactions & Density Focus chain AB [auth O] Focus chain BB [auth O] Focus chain CB [auth O] Focus chain DB [auth O] Focus chain EB [auth J] Focus chain FB [auth J] Focus chain GA [auth C] Focus chain GB [auth J] Focus chain HA [auth C] Focus chain HB [auth J] Focus chain IA [auth C] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth K] Focus chain VA [auth K] Focus chain WA [auth K] Focus chain XA [auth I] Focus chain YA [auth I] Focus chain ZA [auth I]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain IB [auth a] SDF format, chain MB [auth b] MOL2 format, chain IB [auth a] MOL2 format, chain MB [auth b] mmCIF format, chain IB [auth a] mmCIF format, chain MB [auth b]	IB [auth a], MB [auth b]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain IB [auth a] Focus chain MB [auth b] Interactions & Density Focus chain IB [auth a] Focus chain MB [auth b]