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9h4q

Cryo-EM structure of the SEAC wing - EGOC

Method: ELECTRON MICROSCOPY Dmax: 187.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Maintenance of telomere capping protein 5

OrganismNot specified

UniProt Q03897

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain C； UniProt 1–1148 Not recorded GTP-binding protein GTR1 × 1 （Q00582） GTP-binding protein GTR2 × 1 （P53290） Nitrogen permease regulator 2 × 1 （P39923） Nitrogen permease regulator 3 × 1 （P38742） Vacuolar membrane-associated protein IML1 × 1 （P47170） Protein MEH1 × 1 （Q02205） Protein EGO2 × 1 （Q3E830） Protein SLM4 × 1 （P38247） MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9H4Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8ADL Cryo-EM structure of the SEA complex Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain C 1–1148（1148 aa）
Chain Q 1–1148（1148 aa）
Not recorded ZN ZINC ION × 28 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8AE6 Cryo-EM structure of the SEA complex wing (SEACIT) Deposited 2022-07-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain Q 1–1148（1148 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain C 1–1148（1148 aa）
Chain K 1–1148（1148 aa）
Not recorded ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WDR59_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain C； PDBConstruct 1–1148； UniProt 1–1148

GTP-binding protein GTR1

Saccharomyces cerevisiae

UniProt Q00582

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain a； UniProt 1–310 Not recorded Maintenance of telomere capping protein 5 × 1 （Q03897） GTP-binding protein GTR2 × 1 （P53290） Nitrogen permease regulator 2 × 1 （P39923） Nitrogen permease regulator 3 × 1 （P38742） Vacuolar membrane-associated protein IML1 × 1 （P47170） Protein MEH1 × 1 （Q02205） Protein EGO2 × 1 （Q3E830） Protein SLM4 × 1 （P38247） MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9H4Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3R7W Crystal Structure of Gtr1p-Gtr2p complex Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 8–310（303 aa） Fragment：residues 8-310
Non-standard monomer：Yes (specific site not provided by mmCIF) GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1M HEPES, 10% PEG monomethyl ether 5000, 5%(v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.77 Å R-free 0.283
3R7W Crystal Structure of Gtr1p-Gtr2p complex Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 8–310（303 aa） Fragment：residues 8-310
Non-standard monomer：Yes (specific site not provided by mmCIF) GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1M HEPES, 10% PEG monomethyl ether 5000, 5%(v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.77 Å R-free 0.283
4ARZ The crystal structure of Gtr1p-Gtr2p complexed with GTP-GDP Deposited 2012-04-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–310（310 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 3.10 Å R-free 0.272
6JWP crystal structure of EGOC Deposited 2019-04-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–310（310 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000
Resolution 3.20 Å R-free 0.285
6JWP crystal structure of EGOC Deposited 2019-04-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 1–310（310 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000
Resolution 3.20 Å R-free 0.285
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain a 1–310（310 aa）
Chain b 1–310（310 aa）
Not recorded ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAGAB_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain a； PDBConstruct 1–310； UniProt 1–310

GTP-binding protein GTR2

Saccharomyces cerevisiae

UniProt P53290

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain c； UniProt 1–341 Not recorded Maintenance of telomere capping protein 5 × 1 （Q03897） GTP-binding protein GTR1 × 1 （Q00582） Nitrogen permease regulator 2 × 1 （P39923） Nitrogen permease regulator 3 × 1 （P38742） Vacuolar membrane-associated protein IML1 × 1 （P47170） Protein MEH1 × 1 （Q02205） Protein EGO2 × 1 （Q3E830） Protein SLM4 × 1 （P38247） MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9H4Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3R7W Crystal Structure of Gtr1p-Gtr2p complex Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 11–341（331 aa） Fragment：residues 11-341
Non-standard monomer：Yes (specific site not provided by mmCIF) GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1M HEPES, 10% PEG monomethyl ether 5000, 5%(v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.77 Å R-free 0.283
3R7W Crystal Structure of Gtr1p-Gtr2p complex Deposited 2011-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 11–341（331 aa） Fragment：residues 11-341
Non-standard monomer：Yes (specific site not provided by mmCIF) GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1M HEPES, 10% PEG monomethyl ether 5000, 5%(v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.77 Å R-free 0.283
4ARZ The crystal structure of Gtr1p-Gtr2p complexed with GTP-GDP Deposited 2012-04-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–341（341 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 3.10 Å R-free 0.272
6JWP crystal structure of EGOC Deposited 2019-04-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–341（341 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000
Resolution 3.20 Å R-free 0.285
6JWP crystal structure of EGOC Deposited 2019-04-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain G 1–341（341 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000
Resolution 3.20 Å R-free 0.285
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain c 1–341（341 aa）
Chain d 1–341（341 aa）
Not recorded ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAGCD_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain c； PDBConstruct 1–341； UniProt 1–341

Nitrogen permease regulator 2

OrganismNot specified

UniProt P39923

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain T； UniProt 1–615 Not recorded Maintenance of telomere capping protein 5 × 1 （Q03897） GTP-binding protein GTR1 × 1 （Q00582） GTP-binding protein GTR2 × 1 （P53290） Nitrogen permease regulator 3 × 1 （P38742） Vacuolar membrane-associated protein IML1 × 1 （P47170） Protein MEH1 × 1 （Q02205） Protein EGO2 × 1 （Q3E830） Protein SLM4 × 1 （P38247） MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9H4Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8ADL Cryo-EM structure of the SEA complex Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain S 1–615（615 aa）
Chain T 1–615（615 aa）
Not recorded ZN ZINC ION × 28 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8AE6 Cryo-EM structure of the SEA complex wing (SEACIT) Deposited 2022-07-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain S 1–615（615 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain T 1–615（615 aa）
Chain g 1–615（615 aa）
Not recorded ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NPR2_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain T； PDBConstruct 1–615； UniProt 1–615

Nitrogen permease regulator 3

OrganismNot specified

UniProt P38742

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain h； UniProt 1–1146 Not recorded Maintenance of telomere capping protein 5 × 1 （Q03897） GTP-binding protein GTR1 × 1 （Q00582） GTP-binding protein GTR2 × 1 （P53290） Nitrogen permease regulator 2 × 1 （P39923） Vacuolar membrane-associated protein IML1 × 1 （P47170） Protein MEH1 × 1 （Q02205） Protein EGO2 × 1 （Q3E830） Protein SLM4 × 1 （P38247） MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9H4Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8ADL Cryo-EM structure of the SEA complex Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain U 1–1146（1146 aa）
Chain V 1–1146（1146 aa）
Not recorded ZN ZINC ION × 28 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8AE6 Cryo-EM structure of the SEA complex wing (SEACIT) Deposited 2022-07-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain U 1–1146（1146 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain h 1–1146（1146 aa）
Chain i 1–1146（1146 aa）
Not recorded ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NPR3_YEAST
Isoform —
PDB entities 5
Chains and sequence ranges Author chain h； PDBConstruct 1–1146； UniProt 1–1146

Vacuolar membrane-associated protein IML1

OrganismNot specified

UniProt P47170

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain X； UniProt 1–1584 Not recorded Maintenance of telomere capping protein 5 × 1 （Q03897） GTP-binding protein GTR1 × 1 （Q00582） GTP-binding protein GTR2 × 1 （P53290） Nitrogen permease regulator 2 × 1 （P39923） Nitrogen permease regulator 3 × 1 （P38742） Protein MEH1 × 1 （Q02205） Protein EGO2 × 1 （Q3E830） Protein SLM4 × 1 （P38247） MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9H4Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8ADL Cryo-EM structure of the SEA complex Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain W 1–1584（1584 aa）
Chain X 1–1584（1584 aa）
Not recorded ZN ZINC ION × 28 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8AE6 Cryo-EM structure of the SEA complex wing (SEACIT) Deposited 2022-07-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain W 1–1584（1584 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain X 1–1584（1584 aa）
Chain j 1–1584（1584 aa）
Not recorded ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IML1_YEAST
Isoform —
PDB entities 6
Chains and sequence ranges Author chain X； PDBConstruct 1–1584； UniProt 1–1584

Protein MEH1

Saccharomyces cerevisiae

UniProt Q02205

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain R； UniProt 1–184 Not recorded Maintenance of telomere capping protein 5 × 1 （Q03897） GTP-binding protein GTR1 × 1 （Q00582） GTP-binding protein GTR2 × 1 （P53290） Nitrogen permease regulator 2 × 1 （P39923） Nitrogen permease regulator 3 × 1 （P38742） Vacuolar membrane-associated protein IML1 × 1 （P47170） Protein EGO2 × 1 （Q3E830） Protein SLM4 × 1 （P38247） MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9H4Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4XPM Crystal structure of EGO-TC Deposited 2015-01-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 146–184（39 aa） Fragment：UNP RESIDUES 146-184
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.2M NaCl, 0.1M Bis-Tris (pH 5.5), 25% PEG 3350
Resolution 2.40 Å R-free 0.217
6JWP crystal structure of EGOC Deposited 2019-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 33–184（152 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000
Resolution 3.20 Å R-free 0.285
6JWP crystal structure of EGOC Deposited 2019-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 33–184（152 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000
Resolution 3.20 Å R-free 0.285
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain R 1–184（184 aa）
Chain S 1–184（184 aa）
Not recorded ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MEH1_YEAST
Isoform —
PDB entities 7
Chains and sequence ranges Author chain R； PDBConstruct 1–184； UniProt 1–184

Protein EGO2

Saccharomyces cerevisiae

UniProt Q3E830

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain U； UniProt 1–75 Not recorded Maintenance of telomere capping protein 5 × 1 （Q03897） GTP-binding protein GTR1 × 1 （Q00582） GTP-binding protein GTR2 × 1 （P53290） Nitrogen permease regulator 2 × 1 （P39923） Nitrogen permease regulator 3 × 1 （P38742） Vacuolar membrane-associated protein IML1 × 1 （P47170） Protein MEH1 × 1 （Q02205） Protein SLM4 × 1 （P38247） MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9H4Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4XPM Crystal structure of EGO-TC Deposited 2015-01-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–75（75 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.2M NaCl, 0.1M Bis-Tris (pH 5.5), 25% PEG 3350
Resolution 2.40 Å R-free 0.217
6JWP crystal structure of EGOC Deposited 2019-04-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–75（75 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000
Resolution 3.20 Å R-free 0.285
6JWP crystal structure of EGOC Deposited 2019-04-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 1–75（75 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000
Resolution 3.20 Å R-free 0.285
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain U 1–75（75 aa）
Chain W 1–75（75 aa）
Not recorded ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EGO2_YEAST
Isoform —
PDB entities 8
Chains and sequence ranges Author chain U； PDBConstruct 1–75； UniProt 1–75

Protein SLM4

Saccharomyces cerevisiae

UniProt P38247

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain Y； UniProt 1–162 Not recorded Maintenance of telomere capping protein 5 × 1 （Q03897） GTP-binding protein GTR1 × 1 （Q00582） GTP-binding protein GTR2 × 1 （P53290） Nitrogen permease regulator 2 × 1 （P39923） Nitrogen permease regulator 3 × 1 （P38742） Vacuolar membrane-associated protein IML1 × 1 （P47170） Protein MEH1 × 1 （Q02205） Protein EGO2 × 1 （Q3E830） MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.10 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9H4Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3LGO Structure of Gse1p, member of the GSE/EGO complex Deposited 2010-01-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–162（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；293 K；100 mM sodium citrate buffer, pH 2.0, 500-800 mM ammonium sulfate, 200 mM lithium sulfate, 200-350 mM L-arginine-HCl, pH 5.75, 5% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.85 Å R-free 0.351
3LGO Structure of Gse1p, member of the GSE/EGO complex Deposited 2010-01-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–162（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；293 K；100 mM sodium citrate buffer, pH 2.0, 500-800 mM ammonium sulfate, 200 mM lithium sulfate, 200-350 mM L-arginine-HCl, pH 5.75, 5% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.85 Å R-free 0.351
4FTX Crystal structure of Ego3 homodimer Deposited 2012-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–162（162 aa）
Chain B 1–162（162 aa）
Not recorded SIN SUCCINIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；35% tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.10 Å R-free 0.221
4FUW Crystal structure of Ego3 mutant Deposited 2012-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–162（162 aa）
Chain B 1–162（162 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6M ammonium sulfate, 0.1M MES monohydrate, 10% 1,4-dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.60 Å R-free 0.253
4XPM Crystal structure of EGO-TC Deposited 2015-01-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–162（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.2M NaCl, 0.1M Bis-Tris (pH 5.5), 25% PEG 3350
Resolution 2.40 Å R-free 0.217
6JWP crystal structure of EGOC Deposited 2019-04-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–162（162 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000
Resolution 3.20 Å R-free 0.285
6JWP crystal structure of EGOC Deposited 2019-04-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain J 1–162（162 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000
Resolution 3.20 Å R-free 0.285
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric
Chain Y 1–162（162 aa）
Chain Z 1–162（162 aa）
Not recorded ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SLM4_YEAST
Isoform —
PDB entities 9
Chains and sequence ranges Author chain Y； PDBConstruct 1–162； UniProt 1–162

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9h4q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9h4q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9h4q
Deposition date deposition_date2024-10-21
Structure title titleCryo-EM structure of the SEAC wing - EGOC
Keywords keywordsGTPase activating protein, GTPase, nutrient-sensing, amino acid signaling, cell growth, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier54.67 Å
Radius of gyration Rg (electron density) rg_electron54.32 Å
Forward intensity I(0) i02049710000.00
Molecular weight molecular_weight390190.0 kDa
Excluded volume excluded_volume492700 ų
Envelope volume envelope_volume731560 ų
Hydration-shell volume shell_volume111160 ų
Envelope diameter envelope_diameter200.9 Å
Shell Rg shell_rg58.50 Å
Envelope Rg envelope_rg53.87 Å
Shape Rg shape_rg54.32 Å
Total Rg total_rg54.45 Å
Total atoms total_atoms27485
Residues n_residues3362
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax187.4 Å
Rg (real space) rg_real54.69 Å
Rg uncertainty (real space) rg_real_error1.30 Å
I(0) (real space) i0_real2.0500e+09
I(0) uncertainty (real space) i0_real_error3.4730e+07
Rg (reciprocal space) rg_reciprocal54.64 Å
I(0) (reciprocal space) i0_reciprocal2050000000.0000
Solution quality estimate total_estimate0.6370
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary64.6 Å
Skewness Skewness skewness0.393
Kurtosis Kurtosis kurtosis-0.167
Angular range angular_range— – 0.1450 Å−1
Current regularization parameter α current_alpha0.0003
Highest regularization parameter α highest_alpha155900000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 0.017; Positv: 1.000; Valcen: 0.994; Smooth: 0.812
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (12)

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8. Citations (1)

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9. Files and Curves (10)