6wlz

The V1 region of human V-ATPase in state 1 (focused refinement)

Method: ELECTRON MICROSCOPY

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

V-type proton ATPase catalytic subunit A

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 17	V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–617； UniProt 1–617 Author chain B； PDBConstruct 1–617； UniProt 1–617 Author chain C； PDBConstruct 1–617； UniProt 1–617

V-type proton ATPase subunit B, brain isoform

OrganismNot specified

UniProt P21281

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 17	V-type proton ATPase catalytic subunit A × 3 （P38606） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATB2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–511； UniProt 1–511 Author chain E； PDBConstruct 1–511； UniProt 1–511 Author chain F； PDBConstruct 1–511； UniProt 1–511

SidK

OrganismNot specified

UniProt Q5ZWW6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 17	V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZWW6_LEGPH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain X； PDBConstruct 1–573； UniProt 1–573 Author chain Y； PDBConstruct 1–573； UniProt 1–573 Author chain Z； PDBConstruct 1–573； UniProt 1–573

V-type proton ATPase subunit E 1

OrganismNot specified

UniProt P36543

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 17	V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATE1_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–226； UniProt 1–226 Author chain I； PDBConstruct 1–226； UniProt 1–226 Author chain J； PDBConstruct 1–226； UniProt 1–226

V-type proton ATPase subunit G 1

OrganismNot specified

UniProt O75348

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 17	V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit D × 1 （Q9Y5K8） V-type proton ATPase subunit F × 1 （Q16864） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATG1_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain K； PDBConstruct 1–118； UniProt 1–118 Author chain L； PDBConstruct 1–118； UniProt 1–118 Author chain M； PDBConstruct 1–118； UniProt 1–118

V-type proton ATPase subunit D

OrganismNot specified

UniProt Q9Y5K8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 17	V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit F × 1 （Q16864） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATD_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–247； UniProt 1–247

V-type proton ATPase subunit F

OrganismNot specified

UniProt Q16864

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 17	V-type proton ATPase catalytic subunit A × 3 （P38606） V-type proton ATPase subunit B, brain isoform × 3 （P21281） SidK × 3 （Q5ZWW6） V-type proton ATPase subunit E 1 × 3 （P36543） V-type proton ATPase subunit G 1 × 3 （O75348） V-type proton ATPase subunit D × 1 （Q9Y5K8） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATF_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain N； PDBConstruct 1–119； UniProt 1–119

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	6wlz
Deposition date deposition_date	2020-04-20
Structure title title	The V1 region of human V-ATPase in state 1 (focused refinement)
Keywords keywords	V-ATPase, proton pump, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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.

6wlz__assembly_1__model_1

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

Download this curve (.dat)

6wlz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wlz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	56.25 Å
Rg (electron density)	55.77 Å
Total Rg	56.03 Å
Atom count	40656
Residues	5139
Excluded volume	726970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wlz__assembly_1__model_1`	heptadecameric （17）	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 proton ATPase catalytic subunit A
Molecular weight formula_weight	68379.9 kDa
EC 编号 ec_number	7.1.2.2
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	40657

MDFSKLPKILDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQVYEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVNVSALSRDIKWDFTPCKNLRVGSHITGGDIYGIVSENSLIKHKIMLPPRNRGTVTYIAPPGNYDTSDVVLELEFEGVKEKFTMVQVWPVRQVRPVTEKLPANHPLLTGQRVLDALFPCVQGGTTAIPGAFGCGKTVISQSLSKYSNSDVIIYVGCGERGNEMSEVLRDFPELTMEVDGKVESIMKRTALVANTSNMPVAAREASIYTGITLSEYFRDMGYHVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGDFSDPVTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYDKHFTEFVPLRTKAKEILQEEEDLAEIVQLVGKASLAETDKITLEVAKLIKDDFLQQNGYTPYDRFCPFYKTVGMLSNMIAFYDMARRAVETTAQSDNKITWSIIREHMGDILYKLSSMKFKDPLKDGEAKIKSDYAQLLEDMQNAFRSLED

Entity 2 Entity 2 polymer

Description description	V-type proton ATPase subunit B, brain isoform
Molecular weight formula_weight	56561.5 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

MALRAMRGIVNGAAPELPVPTGGPAVGAREQALAVSRNYLSQPRLTYKTVSGVNGPLVILDHVKFPRYAEIVHLTLPDGTKRSGQVLEVSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRTPVSEDMLGRVFNGSGKPIDRGPVVLAEDFLDIMGQPINPQCRIYPEEMIQTGISAIDGMNSIARGQKIPIFSAAGLPHNEIAAQICRQAGLVKKSKDVVDYSEENFAIVFAAMGVNMETARFFKSDFEENGSMDNVCLFLNLANDPTIERIITPRLALTTAEFLAYQCEKHVLVILTDMSSYAEALREVSAAREEVPGRRGFPGYMYTDLATIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIYVDRQLHNRQIYPPINVLPSLSRLMKSAIGEGMTRKDHADVSNQLYACYAIGKDVQAMKAVVGEEALTSDDLLYLEFLQKFERNFIAQGPYENRTVFETLDIGWQLLRIFPKEMLKRIPQSTLSEFYPRDSAKH

Entity 3 Entity 3 polymer

Description description	SidK
Molecular weight formula_weight	65505.3 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,Y,Z

MSFIKVGIKMGGLTSEQYHSQVVGKIGYIARCMQTIDPENNLKKIREDYQDVLIWAEKNYRFEEILEASKSGKCPNDLDALSRRSLILQELLRLVSSISPFKMKLDLIESQYEKMKQHVNLWKSDYHVKLNQLNQLTDYLKNAAPTPKNNFLRAMTSVLQMQIAQYGITEDNEGINQLFKLGLHLLAMANEKIDEQYHLFKGYVKDQPEESPFEGILPAEDQKILVKTMIDYAMPKLSSKVLQDKLSALSSSDVLTKTLLDSIDRIVKENEKLNALSKVKLGKFGLDIREIEVIYSQALKISPQDALQYTAQQCDAQLLSMAFPDSQNYIIESISNKKVKTIAELIHSKEFIYQIIKTEVFKQVDPNEKIRLQAATELYQLLGRIMDKQINLFTKMNLEQINEYIQTKTKAILDKIPERVELLTFMGFEIPTFKGIETLMTDISHSQDNETLAIAQEFYTNIKNAKNQLLGDKLIEDITPQDVEKFFNQCSQYGSEAAEKLADNRPVLTKIADILTAIARWAISLIGFNTPPQFLAPTRTCVDQVSDEITKIKLKLEDTLGSLQKVQEESLSL

Entity 4 Entity 4 polymer

Description description	V-type proton ATPase subunit E 1
Molecular weight formula_weight	26183.3 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MALSDADVQKQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKIQMSNLMNQARLKVLRARDDLITDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQDFPLVKAAVQKAIPMYKIATKNDVDVQIDQESYLPEDIAGGVEIYNGDRKIKVSNTLESRLDLIAQQMMPEVRGALFGANANRKFLD

Entity 5 Entity 5 polymer

Description description	V-type proton ATPase subunit G 1
Molecular weight formula_weight	13781.5 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

MASQSQGIQQLLQAEKRAAEKVSEARKRKNRRLKQAKEEAQAEIEQYRLQREKEFKAKEAAALGSRGSCSTEVEKETQEKMTILQTYFRQNRDEVLDNLLAFVCDIRPEIHENYRING

Entity 6 Entity 6 polymer

Description description	V-type proton ATPase subunit D
Molecular weight formula_weight	28311.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MSGKDRIEIFPSRMAQTIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLAEAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYELTGLARGGEQLAKLKRNYAKAVELLVELASLQTSFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKKKILKEKSEKDLEQRRAAGEVLEPANLLAEEKDEDLLFE

Entity 7 Entity 7 polymer

Description description	V-type proton ATPase subunit F
Molecular weight formula_weight	13388.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MAGRGKLIAVIGDEDTVTGFLLGGIGELNKNRHPNFLVVEKDTTINEIEDTFRQFLNRDDIGIILINQYIAEMVRHALDAHQQSIPAVLEIPSKEHPYDAAKDSILRRARGMFTAEDLR

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	1

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (11 domains)

Domain ID domain_id	d6wlzd1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.0 — automated matches

Domain ID domain_id	d6wlzd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d6wlzd3
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.0 — automated matches

Domain ID domain_id	d6wlze1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.0 — automated matches

Domain ID domain_id	d6wlze2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d6wlze3
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.0 — automated matches

Domain ID domain_id	d6wlzf1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	b.49.1.0 — automated matches

Domain ID domain_id	d6wlzf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d6wlzf3
Class class	a — All alpha proteins
Fold Fold fold	a.69 — Left-handed superhelix
Superfamily Superfamily superfamily	a.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family family	a.69.1.0 — automated matches

Domain ID domain_id	d6wlzg_
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.20 — V-type ATPase central rotor subunit D
Family Family family	h.4.20.0 — automated matches

Domain ID domain_id	d6wlzn_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.149 — AtpF-like
Superfamily Superfamily superfamily	c.149.1 — AtpF-like
Family Family family	c.149.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	6wlzG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3240 —

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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	—

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

Resolution resolution	2.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1000000

The V1 region of human V-ATPase in state 1 (focused refinement)

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

V-type proton ATPase catalytic subunit A

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 proton ATPase subunit B, brain isoform

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SidK

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 proton ATPase subunit E 1

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 proton ATPase subunit G 1

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 proton ATPase 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 proton ATPase 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6wlz__assembly_1__model_1

6wlz__assembly_1__model_1 | I(q)

6wlz__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