4z1m

Bovine F1-ATPase inhibited by three copies of the inhibitor protein IF1 crystallised in the presence of thiophosphate.

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP synthase subunit alpha, mitochondrial

OrganismNot specified

UniProt P19483

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ATP synthase subunit beta, mitochondrial × 3 （P00829） ATP synthase subunit gamma, mitochondrial × 1 （P05631） ATPase inhibitor, mitochondrial × 3 （P01096） ADENOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 5 GLYCEROL × 2 CHLORIDE ION × 11 ADENOSINE-5'-DIPHOSPHATE × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPA_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–510； UniProt 44–553 Author chain B； PDBConstruct 1–510； UniProt 44–553 Author chain C； PDBConstruct 1–510； UniProt 44–553

ATP synthase subunit beta, mitochondrial

OrganismNot specified

UniProt P00829

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ATP synthase subunit alpha, mitochondrial × 3 （P19483） ATP synthase subunit gamma, mitochondrial × 1 （P05631） ATPase inhibitor, mitochondrial × 3 （P01096） ADENOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 5 GLYCEROL × 2 CHLORIDE ION × 11 ADENOSINE-5'-DIPHOSPHATE × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPB_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–482； UniProt 47–528 Author chain E； PDBConstruct 1–482； UniProt 47–528 Author chain F； PDBConstruct 1–482； UniProt 47–528

ATP synthase subunit gamma, mitochondrial

OrganismNot specified

UniProt P05631

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ATP synthase subunit alpha, mitochondrial × 3 （P19483） ATP synthase subunit beta, mitochondrial × 3 （P00829） ATPase inhibitor, mitochondrial × 3 （P01096） ADENOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 5 GLYCEROL × 2 CHLORIDE ION × 11 ADENOSINE-5'-DIPHOSPHATE × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATPG_BOVIN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–273； UniProt 26–298

ATPase inhibitor, mitochondrial

Bos taurus

UniProt P01096

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	ATP synthase subunit alpha, mitochondrial × 3 （P19483） ATP synthase subunit beta, mitochondrial × 3 （P00829） ATP synthase subunit gamma, mitochondrial × 1 （P05631） ADENOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 5 GLYCEROL × 2 CHLORIDE ION × 11 ADENOSINE-5'-DIPHOSPHATE × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATIF1_BOVIN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–60； UniProt 26–85 Author chain I； PDBConstruct 1–60； UniProt 26–85 Author chain J； PDBConstruct 1–60； UniProt 26–85

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_id	4z1m
Deposition date deposition_date	2015-03-27
Structure title title	Bovine F1-ATPase inhibited by three copies of the inhibitor protein IF1 crystallised in the presence of thiophosphate.
Keywords keywords	Hydrolase, inhibitor protein; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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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.

4z1m__assembly_1__model_1

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

Download this curve (.dat)

4z1m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4z1m__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	42.80 Å
Rg (electron density)	41.95 Å
Total Rg	42.33 Å
Atom count	24168
Residues	3143
Excluded volume	431720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4z1m__assembly_1__model_1`	decameric （10）	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 (10)

Entity 1 Entity 1 polymer

Description description	ATP synthase subunit alpha, mitochondrial
Molecular weight formula_weight	55302.2 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	24201

EKTGTAEVSSILEERILGADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALLGKIRTDGKISEESDAKLKEIVTNFLAGFEA

Entity 2 Entity 2 polymer

Description description	ATP synthase subunit beta, mitochondrial
Molecular weight formula_weight	51757.8 kDa
EC 编号 ec_number	3.6.3.14
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

AAQASPSPKAGATTGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAIHAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEVFTGHLGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEEHS

Entity 3 Entity 3 polymer

Description description	ATP synthase subunit gamma, mitochondrial
Molecular weight formula_weight	30300.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEKADIKTPEDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTHSDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFSLDTISSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTRQAVITKELIEIISGAAALD

Entity 4 Entity 4 polymer

Description description	ATPase inhibitor, mitochondrial
Molecular weight formula_weight	7404.0 kDa
Mutation mutation	K39A
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I,J

GSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFRARAAEQLAALKKHHENEISHHAKEIHHHHHH

Source Source

Source organism organism	Bos taurus
Common name common_name	Bovine
NCBI taxonomy ID ncbi_taxonomy_id	9913
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Mutation mutation	K39A
Source method src_method	man
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Mutation mutation	K39A
Source method src_method	man
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 9 Entity 9 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	25

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6. Fold Classification (SCOP + CATH) 21 domains

CATH v4.4 (21 domains)

Domain ID domain_id	4z1mA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4z1mA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4z1mA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	150 — Lysin
Homologous superfamily homologous superfamily	20 — ATP synthase alpha/beta chain, C-terminal domain

Domain ID domain_id	4z1mB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4z1mB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4z1mB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	150 — Lysin
Homologous superfamily homologous superfamily	20 — ATP synthase alpha/beta chain, C-terminal domain

Domain ID domain_id	4z1mC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4z1mC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4z1mC03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	150 — Lysin
Homologous superfamily homologous superfamily	20 — ATP synthase alpha/beta chain, C-terminal domain

Domain ID domain_id	4z1mD01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	4z1mD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4z1mD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

Domain ID domain_id	4z1mE01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	4z1mE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4z1mE03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

Domain ID domain_id	4z1mF01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	4z1mF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4z1mF03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

Domain ID domain_id	4z1mG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	80 — ATP synthase, gamma subunit, helix hairpin domain

Domain ID domain_id	4z1mG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — ATP synthase, F1 complex, gamma subunit

Domain ID domain_id	4z1mH00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	500 — Single helix bin

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Unit-cell length a length_a	108.773 Å
Unit-cell length b length_b	155.286 Å
Unit-cell length c length_c	271.018 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	46.310 Å
R factor r_factor	0.2403
R_work r_work	0.2386
R_free r_free	0.2747

Bovine F1-ATPase inhibited by three copies of the inhibitor protein IF1 crystallised in the presence of thiophosphate.

1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP synthase subunit alpha, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP synthase subunit beta, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATP synthase subunit gamma, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ATPase inhibitor, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4z1m__assembly_1__model_1

4z1m__assembly_1__model_1 | I(q)

4z1m__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 21 domains

CATH v4.4 (21 domains)

7. Citations (1)