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7md3

The F1 region of apoptolidin-bound Saccharomyces cerevisiae ATP synthase

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP synthase subunit alpha

OrganismNot specified

UniProt A0A6A5Q4L9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 ATP synthase subunit beta × 3 （A0A6A5PX46） ATP synthase subunit gamma × 1 （A0A6A5Q493） ATP synthase subunit epsilon, mitochondrial × 1 （P21306） ADENOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 3 PHOSPHATE ION × 1 ;(3~{E},5~{E},7~{E},9~{R},10~{R},11~{E},13~{E},17~{S},18~{S},20~{S})-18-methoxy-20-[(~{R})-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[(2~{R})-3-methoxy-2-[(2~{R},4~{S},5~{S},6~{S})-5-[(2~{S},4~{R},5~{R},6~{R})-4-methoxy-6-methyl-5-oxidanyl-oxan-2-yl]oxy-4,6-dimethyl-4-oxidanyl-oxan-2-yl]oxy-propyl]-3,5-dimethyl-2,4-bis(oxidanyl)oxan-2-yl]-oxidanyl-methyl]-10-[(2~{R},3~{S},4~{S},5~{R},6~{S})-5-methoxy-6-methyl-3,4-bis(oxidanyl)oxan-2-yl]oxy-3,5,7,9,13-pentamethyl-17-oxidanyl-1-oxacycloicosa-3,5,7,11,13-pentaen-2-one ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
7md2 7md3 7tjs 8f2k 8fkj 8fl8

6 assemblies

View Construct and Data Evidence
UniProt name A0A6A5Q4L9_YEASX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–510； UniProt 36–545 Author chain B； PDBConstruct 1–510； UniProt 36–545 Author chain C； PDBConstruct 1–510； UniProt 36–545

ATP synthase subunit beta

OrganismNot specified

UniProt A0A6A5PX46

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 ATP synthase subunit alpha × 3 （A0A6A5Q4L9） ATP synthase subunit gamma × 1 （A0A6A5Q493） ATP synthase subunit epsilon, mitochondrial × 1 （P21306） ADENOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 3 PHOSPHATE ION × 1 ;(3~{E},5~{E},7~{E},9~{R},10~{R},11~{E},13~{E},17~{S},18~{S},20~{S})-18-methoxy-20-[(~{R})-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[(2~{R})-3-methoxy-2-[(2~{R},4~{S},5~{S},6~{S})-5-[(2~{S},4~{R},5~{R},6~{R})-4-methoxy-6-methyl-5-oxidanyl-oxan-2-yl]oxy-4,6-dimethyl-4-oxidanyl-oxan-2-yl]oxy-propyl]-3,5-dimethyl-2,4-bis(oxidanyl)oxan-2-yl]-oxidanyl-methyl]-10-[(2~{R},3~{S},4~{S},5~{R},6~{S})-5-methoxy-6-methyl-3,4-bis(oxidanyl)oxan-2-yl]oxy-3,5,7,9,13-pentamethyl-17-oxidanyl-1-oxacycloicosa-3,5,7,11,13-pentaen-2-one ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
7md2 7md3 7tjs 8f2k 8fkj 8fl8

6 assemblies

View Construct and Data Evidence
UniProt name A0A6A5PX46_YEASX
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 1–478； UniProt 34–511 Author chain E； PDBConstruct 1–478； UniProt 34–511 Author chain F； PDBConstruct 1–478； UniProt 34–511

ATP synthase subunit gamma

OrganismNot specified

UniProt A0A6A5Q493

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 ATP synthase subunit alpha × 3 （A0A6A5Q4L9） ATP synthase subunit beta × 3 （A0A6A5PX46） ATP synthase subunit epsilon, mitochondrial × 1 （P21306） ADENOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 3 PHOSPHATE ION × 1 ;(3~{E},5~{E},7~{E},9~{R},10~{R},11~{E},13~{E},17~{S},18~{S},20~{S})-18-methoxy-20-[(~{R})-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[(2~{R})-3-methoxy-2-[(2~{R},4~{S},5~{S},6~{S})-5-[(2~{S},4~{R},5~{R},6~{R})-4-methoxy-6-methyl-5-oxidanyl-oxan-2-yl]oxy-4,6-dimethyl-4-oxidanyl-oxan-2-yl]oxy-propyl]-3,5-dimethyl-2,4-bis(oxidanyl)oxan-2-yl]-oxidanyl-methyl]-10-[(2~{R},3~{S},4~{S},5~{R},6~{S})-5-methoxy-6-methyl-3,4-bis(oxidanyl)oxan-2-yl]oxy-3,5,7,9,13-pentamethyl-17-oxidanyl-1-oxacycloicosa-3,5,7,11,13-pentaen-2-one ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
7md2 7md3 7tjs 8f2k 8fkj

5 assemblies

View Construct and Data Evidence
UniProt name A0A6A5Q493_YEASX
Isoform —
PDB entities 3
Chains and sequence ranges Author chain G； PDBConstruct 1–278； UniProt 34–311

ATP synthase subunit epsilon, mitochondrial

OrganismNot specified

UniProt P21306

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 ATP synthase subunit alpha × 3 （A0A6A5Q4L9） ATP synthase subunit beta × 3 （A0A6A5PX46） ATP synthase subunit gamma × 1 （A0A6A5Q493） ADENOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 3 PHOSPHATE ION × 1 ;(3~{E},5~{E},7~{E},9~{R},10~{R},11~{E},13~{E},17~{S},18~{S},20~{S})-18-methoxy-20-[(~{R})-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[(2~{R})-3-methoxy-2-[(2~{R},4~{S},5~{S},6~{S})-5-[(2~{S},4~{R},5~{R},6~{R})-4-methoxy-6-methyl-5-oxidanyl-oxan-2-yl]oxy-4,6-dimethyl-4-oxidanyl-oxan-2-yl]oxy-propyl]-3,5-dimethyl-2,4-bis(oxidanyl)oxan-2-yl]-oxidanyl-methyl]-10-[(2~{R},3~{S},4~{S},5~{R},6~{S})-5-methoxy-6-methyl-3,4-bis(oxidanyl)oxan-2-yl]oxy-3,5,7,9,13-pentamethyl-17-oxidanyl-1-oxacycloicosa-3,5,7,11,13-pentaen-2-one ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2hld 2hld 2hld 2wpd 3fks 3fks 3fks 3oe7 3oe7 3oe7 3oee 3oee

60 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ATP5E_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain H； PDBConstruct 1–61； UniProt 2–62

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id7md3
Deposition date deposition_date2021-04-03
Structure title titleThe F1 region of apoptolidin-bound Saccharomyces cerevisiae ATP synthase
Keywords keywordsF1-ATPase, inhibitor, anti-cancer, HYDROLASE, TRANSLOCASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method methodELECTRON MICROSCOPY
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7md3__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7md3__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

7md3__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）42.49 Å
Rg (electron density)41.60 Å
Total Rg41.98 Å
Atom count46124
Residues3133
Excluded volume412920 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7md3__assembly_1__model_1 octameric （8） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

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7. Citations (1)