5tsj

Thermus thermophilus V/A-ATPase bound to VH dAbs

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 28	V-type ATP synthase beta chain × 3 （Q72J73） V-type ATP synthase subunit E × 2 （P74901） V-type ATPase subunit G × 2 （H9ZQR3） V-type ATP synthase subunit D × 1 （Q72J74） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase subunit C × 1 （P74902） Archaeal/vacuolar-type H+-ATPase subunit I × 1 （H9ZQR4） Vacuolar type ATP synthase subunit × 12 （P74900） Human heavy chain domain antibody × 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 1–577； UniProt 1–577 Author chain B； PDBConstruct 1–577； UniProt 1–577 Author chain C； PDBConstruct 1–577； UniProt 1–577

V-type ATP synthase beta chain

OrganismNot specified

UniProt Q72J73

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 28	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase subunit E × 2 （P74901） V-type ATPase subunit G × 2 （H9ZQR3） V-type ATP synthase subunit D × 1 （Q72J74） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase subunit C × 1 （P74902） Archaeal/vacuolar-type H+-ATPase subunit I × 1 （H9ZQR4） Vacuolar type ATP synthase subunit × 12 （P74900） Human heavy chain domain antibody × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATB_THET2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–457； UniProt 7–463 Author chain E； PDBConstruct 1–457； UniProt 7–463 Author chain F； PDBConstruct 1–457； UniProt 7–463

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 28	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q72J73） V-type ATPase subunit G × 2 （H9ZQR3） V-type ATP synthase subunit D × 1 （Q72J74） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase subunit C × 1 （P74902） Archaeal/vacuolar-type H+-ATPase subunit I × 1 （H9ZQR4） Vacuolar type ATP synthase subunit × 12 （P74900） Human heavy chain domain antibody × 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	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–186； UniProt 3–188 Author chain H； PDBConstruct 1–186； UniProt 3–188

V-type ATPase subunit G

OrganismNot specified

UniProt H9ZQR3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 28	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q72J73） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit D × 1 （Q72J74） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase subunit C × 1 （P74902） Archaeal/vacuolar-type H+-ATPase subunit I × 1 （H9ZQR4） Vacuolar type ATP synthase subunit × 12 （P74900） Human heavy chain domain antibody × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H9ZQR3_THETH
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain I； PDBConstruct 2–105； UniProt 1–104 Author chain J； PDBConstruct 2–105； UniProt 1–104

V-type ATP synthase subunit D

OrganismNot specified

UniProt Q72J74

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 28	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q72J73） V-type ATP synthase subunit E × 2 （P74901） V-type ATPase subunit G × 2 （H9ZQR3） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase subunit C × 1 （P74902） Archaeal/vacuolar-type H+-ATPase subunit I × 1 （H9ZQR4） Vacuolar type ATP synthase subunit × 12 （P74900） Human heavy chain domain antibody × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATD_THET2
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain K； PDBConstruct 1–210； UniProt 2–211

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 28	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q72J73） V-type ATP synthase subunit E × 2 （P74901） V-type ATPase subunit G × 2 （H9ZQR3） V-type ATP synthase subunit D × 1 （Q72J74） V-type ATP synthase subunit C × 1 （P74902） Archaeal/vacuolar-type H+-ATPase subunit I × 1 （H9ZQR4） Vacuolar type ATP synthase subunit × 12 （P74900） Human heavy chain domain antibody × 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	6
Chains and sequence ranges	Author chain L； PDBConstruct 1–100； UniProt 1–100

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 28	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q72J73） V-type ATP synthase subunit E × 2 （P74901） V-type ATPase subunit G × 2 （H9ZQR3） V-type ATP synthase subunit D × 1 （Q72J74） V-type ATP synthase subunit F × 1 （P74903） Archaeal/vacuolar-type H+-ATPase subunit I × 1 （H9ZQR4） Vacuolar type ATP synthase subunit × 12 （P74900） Human heavy chain domain antibody × 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

Archaeal/vacuolar-type H+-ATPase subunit I

OrganismNot specified

UniProt H9ZQR4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 28	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q72J73） V-type ATP synthase subunit E × 2 （P74901） V-type ATPase subunit G × 2 （H9ZQR3） V-type ATP synthase subunit D × 1 （Q72J74） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase subunit C × 1 （P74902） Vacuolar type ATP synthase subunit × 12 （P74900） Human heavy chain domain antibody × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H9ZQR4_THETH
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain N； PDBConstruct 1–652； UniProt 1–652

Vacuolar type ATP synthase subunit

OrganismNot specified

UniProt P74900

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 28	V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q72J73） V-type ATP synthase subunit E × 2 （P74901） V-type ATPase subunit G × 2 （H9ZQR3） V-type ATP synthase subunit D × 1 （Q72J74） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase subunit C × 1 （P74902） Archaeal/vacuolar-type H+-ATPase subunit I × 1 （H9ZQR4） Human heavy chain domain antibody × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P74900_THETH
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain O； PDBConstruct 1–99； UniProt 1–99 Author chain P； PDBConstruct 1–99； UniProt 1–99 Author chain Q； PDBConstruct 1–99； UniProt 1–99 Author chain R； PDBConstruct 1–99； UniProt 1–99 Author chain S； PDBConstruct 1–99； UniProt 1–99 Author chain T； PDBConstruct 1–99； UniProt 1–99 Author chain U； PDBConstruct 1–99； UniProt 1–99 Author chain V； PDBConstruct 1–99； UniProt 1–99 Author chain W； PDBConstruct 1–99； UniProt 1–99 Author chain X； PDBConstruct 1–99； UniProt 1–99 Author chain Y； PDBConstruct 1–99； UniProt 1–99 Author chain Z； PDBConstruct 1–99； UniProt 1–99

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	5tsj
Deposition date deposition_date	2016-10-29
Structure title title	Thermus thermophilus V/A-ATPase bound to VH dAbs
Keywords keywords	V/A-ATPase, membrane protein, complex, antibody, HYDROLASE; membrane protein, 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.

5tsj__assembly_1__model_1

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

Download this curve (.dat)

5tsj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5tsj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	75.46 Å
Rg (electron density)	76.87 Å
Total Rg	76.84 Å
Atom count	24625
Residues	6112
Excluded volume	343020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5tsj__assembly_1__model_1`	28-meric （28）	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	V-type ATP synthase alpha chain
Molecular weight formula_weight	63628.9 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	24625

MIQGVIQKIAGPAVIAKGMLGARMYDICKVGEEGLVGEIIRLDGDTAFVQVYEDTSGLKVGEPVVSTGLPLAVELGPGMLNGIYDGIQRPLERIREKTGIYITRGVVVHALDREKKWAWTPMVKPGDEVRGGMVLGTVPEFGFTHKILVPPDVRGRVKEVKPAGEYTVEEPVVVLEDGTELKMYHTWPVRRARPVQRKLDPNTPFLTGMRILDVLFPVAMGGTAAIPGPFGSGKTVTQQSLAKWSNADVVVYVGCGERGNEMTDVLVEFPELTDPKTGGPLMHRTVLIANTSNMPVAAREASIYVGVTIAEYFRDQGFSVALMADSTSRWAEALREISSRLEEMPAEEGYPPYLAARLAAFYERAGKVITLGGEEGAVTIVGAVSPPGGDMSEPVTQSTLRIVGAFWRLDASLAFRRHFPAINWNGSYSLFTSALDPWYRENVAEDYPELRDAISELLQREAGLQEIVQLVGPDALQDAERLVIEVGRIIREDFLQQNAYHEVDAYCSMKKAYGIMKMILAFYKEAEAAIKRGVSIDEILQLPVLERIGRARYVSEEEFPAYFEEAMKEIQGAFKAL

Entity 2 Entity 2 polymer

Description description	V-type ATP synthase beta chain
Molecular weight formula_weight	50850.7 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

EYTGITYISGPLLFVENAKDLAYGAIVDIKDGTGRVRGGQVIEVSEEYAVIQVFEETTGLDLATTSVSLVEDVARLGVSKEMLGRRFNGIGKPIDGLPPITPEKRLPITGLPLNPVARRKPEQFIQTGISTIDVMNTLVRGQKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSRSVLFLNKADDPTIERILTPRMALTVAEYLAFEHDYHVLVILTDMTNYCEALREIGAAREEIPGRRGYPGYMYTDLATIYERAGVVEGKKGSVTQIPILSMPDDDRTHPIPDLTGYITEGQIQLSRELHRKGIYPPIDPLPSLSRLMNNGVGKGKTREDHKQVSDQLYSAYANGVDIRKLVAIIGEDALTENDRRYLQFADAFERFFINQGQQNRSIEESLQIAWALLSMLPQGELKRISKDHIGKYY

Entity 3 Entity 3 polymer

Description description	V-type ATP synthase subunit E
Molecular weight formula_weight	20481.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H

KLEAILSQEVEAEIQALLQEAEAKAEAVKREAEEKAKALLQARERALEAQYRAALRRAESAGELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPEVVRKLALEALEALPGAKALVANPEDLPHLEAMARERGVELQAEPALRLGVRAVGAEGKTQVENSLLARMDRAWDAMSSKVAQALWG

Entity 4 Entity 4 polymer

Description description	V-type ATPase subunit G
Molecular weight formula_weight	11752.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

GMGGLGLIKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAMARLDEAVALVLKEVLP

Entity 5 Entity 5 polymer

Description description	V-type ATP synthase subunit D
Molecular weight formula_weight	23351.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

SQVSPTRMNLLQRRGQLRLAQKGVDLLKKKRDALVAEFFGLVREAMEARKALDQAAKEAYAALLLAQAFDGPEVVAGAALGVPPLEGVEAEVENVWGSKVPRLKATFPDGALLSPVGTPAYTLEASRAFRRYAEALIRVANTETRLKKIGEEIKKTTRRVNALEQVVIPGIRAQIRFIQQVLEQREREDTFRLKRIKGKIEAREAEEEGG

Entity 6 Entity 6 polymer

Description description	V-type ATP synthase subunit F
Molecular weight formula_weight	10824.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MAVIADPETAQGFRLAGLEGYGASSAEEAQSLLETLVERGGYALVAVDEALLPDPERAVERLMRGRDLPVLLPIAGLKEAFQGHDVEGYMRELVRKTIGF

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 polymer

Description description	Archaeal/vacuolar-type H+-ATPase subunit I
Molecular weight formula_weight	72272.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MIAPMEKLVLAGPKGRAKELLQSLQQAGVVHLETLRPEALSAYQLSPEERAELRRWEAVSAGAEHTLSLLGLEAEPARPFPEGLEAAEKALSPIQAHAEGLTRQKQELEEELALAQAYLEPLERLAALAHGLDKSPFLRVIPFLLTEKELPLVEEALRKALEDRYLLAHEAYAGGVPALVVVHRKEVDQAKAALSRAGVAELRLPGALGELPLSEAARRLKERAEAAPRELSEVRQHLAKLARESASTLQSLWTRAQDEVARLKALEELASGRFGFALLGYVPVKAKPKVEEALARHKENVVYAFEPVDEHHEADRIPVVLDNPPWVKPFELLVSFLNTPKYGTFDPTPVVPIFFPFWFGMIVGDIGYALLFYLVGRWLSGYVKRNEPLVIDLFALKLKPPVLAKLVYILNWMVFWTVVWGLIYGEFFGTFLEHLGVFGTPEHPGLIPILIHRIDTAKTANLLILLSVAFGVVMVFAGLILRAYLGLKHRHMAHFWEGVGYLGGLLGILALAASYLGNLQAGWLSALMYLGFGVFLLSVVMSSIWLMIPEIFTQAGHILSHIRIYAVGAAGGILAGLLTDVGFAMAERLGLIGVLLGIVVAGVLHLLILLLTTLGHMLQPIRLIWVEFFTKFGFYEENGRPYRPFKSVRETQ

Entity 9 Entity 9 polymer

Description description	Vacuolar type ATP synthase subunit
Molecular weight formula_weight	9841.7 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,P,Q,R,S,T,U,V,W,X,Y,Z

MKKLLVTVLLAVFGALAFAAEEAAASGGLDRGLIAVGMGLAVGLAALGTGVAQARIGAAGVGAIAEDRSNFGTALIFLLLPETLVIFGLLIAFILNGRL

Entity 10 Entity 10 polymer

Description description	Human heavy chain domain antibody
Molecular weight formula_weight	16345.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2

STEVQLLESGGGLVQPGGSLRLSCAASGFTFSTYMMSWVRQAPGKGLEWVSSIEGSGSKTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKRDSSFGFDYWGQGTLVTVSSAAALEIKRASQPELAPEDPEDVEHHHHHH

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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Resolution resolution	8.70 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	61045

Thermus thermophilus V/A-ATPase bound to VH dAbs

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 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 ATPase subunit G

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 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

Archaeal/vacuolar-type H+-ATPase subunit I

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vacuolar type ATP synthase subunit

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

5tsj__assembly_1__model_1

5tsj__assembly_1__model_1 | I(q)

5tsj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment