8xli

Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus

Method: ELECTRON MICROSCOPY

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

V-type proton ATPase 116 kDa subunit a 1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 16 其他Polymer 4	ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit S1 × 1 （O54715） V-type proton ATPase subunit × 1 V-type proton ATPase subunit e 2 × 1 （Q5EB76） Ribonuclease K × 1 V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor cytoplasmic fragment × 1 （Q6AXS4） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPP1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain a； PDBConstruct 1–828； UniProt 4–831

ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a

OrganismNot specified

UniProt B0K022

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 16 其他Polymer 4	V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） V-type proton ATPase subunit S1 × 1 （O54715） V-type proton ATPase subunit × 1 V-type proton ATPase subunit e 2 × 1 （Q5EB76） Ribonuclease K × 1 V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor cytoplasmic fragment × 1 （Q6AXS4） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B0K022_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain b； PDBConstruct 1–203； UniProt 2–204

V-type proton ATPase subunit S1

OrganismNot specified

UniProt O54715

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 16 其他Polymer 4	V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit × 1 V-type proton ATPase subunit e 2 × 1 （Q5EB76） Ribonuclease K × 1 V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor cytoplasmic fragment × 1 （Q6AXS4） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VAS1_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain c； PDBConstruct 1–204； UniProt 248–451

V-type proton ATPase subunit e 2

OrganismNot specified

UniProt Q5EB76

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 16 其他Polymer 4	V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit S1 × 1 （O54715） V-type proton ATPase subunit × 1 Ribonuclease K × 1 V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） Renin receptor cytoplasmic fragment × 1 （Q6AXS4） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VA0E2_RAT
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain e； PDBConstruct 1–77； UniProt 3–79

V-type proton ATPase 16 kDa proteolipid subunit c

OrganismNot specified

UniProt P63081

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 16 其他Polymer 4	V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit S1 × 1 （O54715） V-type proton ATPase subunit × 1 V-type proton ATPase subunit e 2 × 1 （Q5EB76） Ribonuclease K × 1 Renin receptor cytoplasmic fragment × 1 （Q6AXS4） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VATL_RAT
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain g； PDBConstruct 1–150； UniProt 6–155 Author chain h； PDBConstruct 1–150； UniProt 6–155 Author chain i； PDBConstruct 1–150； UniProt 6–155 Author chain j； PDBConstruct 1–150； UniProt 6–155 Author chain k； PDBConstruct 1–150； UniProt 6–155 Author chain l； PDBConstruct 1–150； UniProt 6–155 Author chain m； PDBConstruct 1–150； UniProt 6–155 Author chain n； PDBConstruct 1–150； UniProt 6–155 Author chain o； PDBConstruct 1–150； UniProt 6–155

Renin receptor cytoplasmic fragment

OrganismNot specified

UniProt Q6AXS4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 16 其他Polymer 4	V-type proton ATPase 116 kDa subunit a 1 × 1 （P25286） ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a × 1 （B0K022） V-type proton ATPase subunit S1 × 1 （O54715） V-type proton ATPase subunit × 1 V-type proton ATPase subunit e 2 × 1 （Q5EB76） Ribonuclease K × 1 V-type proton ATPase 16 kDa proteolipid subunit c × 9 （P63081） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RENR_RAT
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain p； PDBConstruct 1–49； UniProt 292–340

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	8xli
Deposition date deposition_date	2023-12-26
Structure title title	Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus
Keywords keywords	Vo sector of V-ATPase, 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.

8xli__assembly_1__model_1

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

Download this curve (.dat)

8xli__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8xli__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.47 Å
Rg (electron density)	44.52 Å
Total Rg	44.83 Å
Atom count	23024
Residues	3075
Excluded volume	418920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8xli__assembly_1__model_1`	hexadecameric （16）	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 (9)

Entity 1 Entity 1 polymer

Description description	V-type proton ATPase 116 kDa subunit a 1
Molecular weight formula_weight	95248.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a
Atom count atom_count	23024

LFRSEEMTLAQLFLQSEAAYCCVSELEELGKVQFRDLNPDVNVFQRKFVNEVRRCEEMDRKLRFVEKEIRKANIPIMDTGENPEVPFPRDMIDLEANFEKIENELKEINTNQEALKRNFLELTELKFILRKTQQFFDEMADPDLLEESSSLLEPNEMGRGAPLRLGFVAGVINRERIPTFERMLWRVCRGNVFLRQAEIENPLEDPVTGDYVHKSVFIIFFQGDQLKNRVKKICEGFRASLYPCPETPQERKEMASGVNTRIDDLQMVLNQTEDHRQRVLQAAAKNIRVWFIKVRKMKAIYHTLNLCNIDVTQKCLIAEVWCPVTDLDSIQFALRRGTEHSGSTVPSILNRMQTNQTPPTYNKTNKFTHGFQNIVDAYGIGTYREINPAPYTVITFPFLFAVMFGDFGHGILMTLFAVWMVLRESRILSQKNENEMFSMVFSGRYIILLMGLFSIYTGLIYNDCFSKSLNIFGSSWSVRPMFTIGNWTEETLLGSSVLQLNPAIPGVFGGPYPFGIDPIWNIATNKLTFLNSFKMKMSVILGIIHMLFGVSLSLFNHIYFKKPLNIYFGFIPEIIFMSSLFGYLVILIFYKWTAYDAHSSRNAPSLLIHFINMFLFSYPESGNAMLYSGQKGIQCFLIVVAMLCVPWMLLFKPLILRHQYLRKKHLGTLNFGGIRVGNGPTEEDAEIIQHDQLSTHSEDAEEPTEDEVFDFGDTMVHQAIHTIEYCLGCISNTASYLRLWALSLAHAQLSEVLWTMVIHIGLHVRSLAGGLGLFFIFAAFATLTVAILLIMEGLSAFLHALRLHWVEFQNKFYTGTGFKFLPFSFEHI

Entity 2 Entity 2 polymer

Description description	ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
Molecular weight formula_weight	21372.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b

TGLELLYLGIFVAFWACMIVVGICYTIFDLGFRFDVAWFLTETSPFMWSNLGIGLAISLSVVGAAWGIYITGSSIIGGGVKAPRIKTKNLVSIIFCEAVAIYGIIMAIVISNMAEPFSATDPKAIGHRNYHAGYSMFGAGLTVGLSNLFCGVCVGIVGSGAALADAQNPSLFVKILIVEIFGSAIGLFGVIVAILQTSRVKMG

Entity 3 Entity 3 polymer

Description description	V-type proton ATPase subunit S1
Molecular weight formula_weight	23360.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	c

IHPPVSYNDTAPRILFWAQNFSVAYKDEWKDLTSLTFGVENLNLTGSFWNDSFAMLSLTYEPLFGATVTFKFILASRFYPVSARYWFTMERLEIHSNGSVAHFNVSQVTGPSIYSFHCEYVSSLSKKGSLLVTNVPSLWQMTLHNFQIQAFNVTGEQFSYASDCAGFFSPGIWMGLLTTLFMLFIFTYGLHMILSLKTMDRFDD

Entity 4 Entity 4 polymer

Description description	V-type proton ATPase subunit
Molecular weight formula_weight	39285.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d

SFFPELYFNVDNGYLEGLVRGLKAGVLSQADYLNLVQCETLEDLKLHLQSTDYGNFLANEASPLTVSVIDDKLKEKMVVEFRHMRNHAYEPLASFLDFITYSYMIDNVILLITGTLHQKCHPLGSFEQMEAVNIAQTPAELYNAILVDTPLAAFFQDCISEQDLDAMNIEIIRNTLYKAYLESFYKFCTLLGGTTADAMCPILEFEADRRAFIITINSFGTELSKEDRAKLFPHCGRLYPEGLAQLARADDYEQVKNVADYYPEYKLLFEGAGSNPGDKTLEDRFFEHEVKLNKLAFLNQFHFGVFYAFVKLKEQECRNIVWIAECIAQRHRAKIDNYIPIF

Entity 5 Entity 5 polymer

Description description	V-type proton ATPase subunit e 2
Molecular weight formula_weight	8655.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	e

AHSFALPVIIFTTFWGLIGIAGPWFVPKGPNRGVIITMLVATAVCCYLFWLIAILAQLNPLFGPQLKNETIWYVRFL

Entity 6 Entity 6 polymer

Description description	Ribonuclease K
Molecular weight formula_weight	9933.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	f

CCGPKLAACGIVLSAWGVIMLIMLGIFFNVHSAVLIEDVPFTEKDFENGPQNIYNLYEQVSYNCFIAAGLYLLLGGFSFCQVRLNKRKE

Entity 7 Entity 7 polymer

Description description	V-type proton ATPase 16 kDa proteolipid subunit c
Molecular weight formula_weight	15256.1 kDa
Source method src_method	nat
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	g,h,i,j,k,l,m,n,o

NNPEYSSFFGVMGASSAMVFSAMGAAYGTAKSGTGIAAMSVMRPELIMKSIIPVVMAGIIAIYGLVVAVLIANSLTDGITLYRSFLQLGAGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAEVLGLYGLIVALILSTK

Entity 8 Entity 8 polymer

Description description	Renin receptor cytoplasmic fragment
Molecular weight formula_weight	5740.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	p

PYNLAYKYNLEYSVVFNLVLWIMTGLALAVIITSYNIWNMDPGYDSIIY

Entity 9 Entity 9 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	syn
Copy count entity_count	4

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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	3.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	34147

Structure of the Vo sector of V-ATPase in the adult cortex and hippocampus

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

V-type proton ATPase 116 kDa subunit a 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

ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_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 S1

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 2

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 16 kDa proteolipid 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

Renin receptor cytoplasmic fragment

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

8xli__assembly_1__model_1

8xli__assembly_1__model_1 | I(q)

8xli__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 (9)

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

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 branched

7. Citations (1)