3j0j

Fitted atomic models of Thermus thermophilus V-ATPase subunits into cryo-EM map

Method: ELECTRON MICROSCOPY

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

V-type ATP synthase alpha chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit C × 1 （P74902） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATA_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–578； UniProt 1–578 Author chain B； PDBConstruct 1–578； UniProt 1–578 Author chain C； PDBConstruct 1–578； UniProt 1–578

V-type ATP synthase beta chain

OrganismNot specified

UniProt Q56404

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit C × 1 （P74902） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATB_THET8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–478； UniProt 1–478 Author chain E； PDBConstruct 1–478； UniProt 1–478 Author chain F； PDBConstruct 1–478； UniProt 1–478

V-type ATP synthase subunit D

OrganismNot specified

UniProt O87880

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit C × 1 （P74902） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATD_THET8
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–223； UniProt 1–223

V-type ATP synthase subunit F

OrganismNot specified

UniProt P74903

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit C × 1 （P74902） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATF_THET8
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–104； UniProt 1–104

V-type ATP synthase, subunit (VAPC-THERM)

OrganismNot specified

UniProt Q5SIT5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit C × 1 （P74902） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SIT5_THET8
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain I； PDBConstruct 2–104； UniProt 18–120 Author chain K； PDBConstruct 2–104； UniProt 18–120

V-type ATP synthase subunit E

OrganismNot specified

UniProt P74901

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit C × 1 （P74902） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATE_THET8
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain J； PDBConstruct 1–188； UniProt 1–188 Author chain L； PDBConstruct 1–188； UniProt 1–188

V-type ATP synthase subunit C

OrganismNot specified

UniProt P74902

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit E × 2 （P74901） ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATC_THET8
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain M； PDBConstruct 1–323； UniProt 1–323

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	3j0j
Deposition date deposition_date	2011-08-24
Structure title title	Fitted atomic models of Thermus thermophilus V-ATPase subunits into cryo-EM map
Keywords keywords	flexible fitting, rigid body fitting, membrane protein complex, HYDROLASE; HYDROLASE
Experimental Method method	ELECTRON 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.

3j0j__assembly_1__model_1

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

Download this curve (.dat)

3j0j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3j0j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.73 Å
Rg (electron density)	57.48 Å
Total Rg	58.10 Å
Atom count	22726
Residues	4154
Excluded volume	375760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3j0j__assembly_1__model_1`	tridecameric （13）	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)

Entity 1 Entity 1 polymer

Description description	V-type ATP synthase alpha chain
Molecular weight formula_weight	63700.0 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	A,B,C
Atom count atom_count	22726

MIQGVIQKIAGPAVIAKGMLGARMYDICKVGEEGLVGEIIRLDGDTAFVQVYEDTSGLKVGEPVVSTGLPLAVELGPGMLNGIYDGIQRPLERIREKTGIYITRGVVVHALDREKKWAWTPMVKPGDEVRGGMVLGTVPEFGFTHKILVPPDVRGRVKEVKPAGEYTVEEPVVVLEDGTELKMYHTWPVRRARPVQRKLDPNTPFLTGMRILDVLFPVAMGGTAAIPGPFGSGKTVTQQSLAKWSNADVVVYVGCGERGNEMTDVLVEFPELTDPKTGGPLMHRTVLIANTSNMPVAAREASIYVGVTIAEYFRDQGFSVALMADSTSRWAEALREISSRLEEMPAEEGYPPYLAARLAAFYERAGKVITLGGEEGAVTIVGAVSPPGGDMSEPVTQSTLRIVGAFWRLDASLAFRRHFPAINWNGSYSLFTSALDPWYRENVAEDYPELRDAISELLQREAGLQEIVQLVGPDALQDAERLVIEVGRIIREDFLQQNAYHEVDAYCSMKKAYGIMKMILAFYKEAEAAIKRGVSIDEILQLPVLERIGRARYVSEEEFPAYFEEAMKEIQGAFKALA

Entity 2 Entity 2 polymer

Description description	V-type ATP synthase beta chain
Molecular weight formula_weight	53219.5 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MDLLKKEYTGITYISGPLLFVENAKDLAYGAIVDIKDGTGRVRGGQVIEVSEEYAVIQVFEETTGLDLATTSVSLVEDVARLGVSKEMLGRRFNGIGKPIDGLPPITPEKRLPITGLPLNPVARRKPEQFIQTGISTIDVMNTLVRGQKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSRSVLFLNKADDPTIERILTPRMALTVAEYLAFEHDYHVLVILTDMTNYCEALREIGAAREEIPGRRGYPGYMYTDLATIYERAGVVEGKKGSVTQIPILSMPDDDRTHPIPDLTGYITEGQIQLSRELHRKGIYPPIDPLPSLSRLMNNGVGKGKTREDHKQVSDQLYSAYANGVDIRKLVAIIGEDALTENDRRYLQFADAFERFFINQGQQNRSIEESLQIAWALLSMLPQGELKRISKDHIGKYYGQKLEEIWGAPQALD

Entity 3 Entity 3 polymer

Description description	V-type ATP synthase subunit D
Molecular weight formula_weight	24715.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MSQVSPTRMNLLQRRGQLRLAQKGVDLLKKKRDALVAEFFGLVREAMEARKALDQAAKEAYAALLLAQAFDGPEVVAGAALGVPPLEGVEAEVENVWGSKVPRLKATFPDGALLSPVGTPAYTLEASRAFRRYAEALIRVANTETRLKKIGEEIKKTTRRVNALEQVVIPGIRAQIRFIQQVLEQREREDTFRLKRIKGKIEAREAEEEGGRPNPQVEIGAGL

Entity 4 Entity 4 polymer

Description description	V-type ATP synthase subunit F
Molecular weight formula_weight	11294.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MAVIADPETAQGFRLAGLEGYGASSAEEAQSLLETLVERGGYALVAVDEALLPDPERAVERLMRGRDLPVLLPIAGLKEAFQGHDVEGYMRELVRKTIGFDIKL

Entity 5 Entity 5 polymer

Description description	V-type ATP synthase, subunit (VAPC-THERM)
Molecular weight formula_weight	11621.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,K

GGGLGLIKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAMARLDEAVALVLKEVLP

Entity 6 Entity 6 polymer

Description description	V-type ATP synthase subunit E
Molecular weight formula_weight	20699.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MSKLEAILSQEVEAEIQALLQEAEAKAEAVKREAEEKAKALLQARERALEAQYRAALRRAESAGELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPEVVRKLALEALEALPGAKALVANPEDLPHLEAMARERGVELQAEPALRLGVRAVGAEGKTQVENSLLARMDRAWDAMSSKVAQALWG

Entity 7 Entity 7 polymer

Description description	V-type ATP synthase subunit C
Molecular weight formula_weight	35968.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MADDFAYLNARVRVRRGTLLKESFFQEALDLSFADFLRLLSETVYGGELAGQGLPDVDRAVLRTQAKLVGDLPRLVTGEAREAVRLLLLRNDLHNLQALLRAKATGRPFEEVLLLPGTLREEVWRQAYEAQDPAGMAQVLAVPGHPLARALRAVLRETQDLARVEALLAKRFFEDVAKAAKGLDQPALRDYLALEVDAENLRTAFKLQGSGLAPDAFFLKGGRFVDRVRFARLMEGDYAVLDELSGTPFSGLSGVRDLKALERGLRCVLLKEAKKGVQDPLGVGLVLAYVKEREWEAVRLRLLARRAYFGLPRAQVEEEVVCP

Entity 8 Entity 8 non-polymer

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

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	9.70 Å
Resolution测定Method resolution_method	Fourier sinc interpolation (Build_fspace)
颗粒数 num_particles	46105

Fitted atomic models of Thermus thermophilus V-ATPase subunits into cryo-EM map

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

V-type ATP synthase alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type ATP synthase beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type ATP synthase subunit D

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type ATP synthase subunit F

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type ATP synthase, subunit (VAPC-THERM)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type ATP synthase subunit E

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

V-type ATP synthase subunit C

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

3j0j__assembly_1__model_1

3j0j__assembly_1__model_1 | I(q)

3j0j__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer