SAXSdb — 8wci

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

V-type sodium ATPase subunit K

Enterococcus hirae ATCC 9790

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	V-type sodium ATPase subunit I × 1 （P43439） CARDIOLIPIN × 5 SODIUM ION × 9 N,N-dimethyl-4-(5-methyl-1H-benzimidazol-2-yl)aniline × 1 water × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NTPK_ENTHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–156； UniProt 1–156 Author chain B； PDBConstruct 1–156； UniProt 1–156 Author chain C； PDBConstruct 1–156； UniProt 1–156 Author chain D； PDBConstruct 1–156； UniProt 1–156 Author chain E； PDBConstruct 1–156； UniProt 1–156 Author chain F； PDBConstruct 1–156； UniProt 1–156 Author chain G； PDBConstruct 1–156； UniProt 1–156 Author chain H； PDBConstruct 1–156； UniProt 1–156 Author chain I； PDBConstruct 1–156； UniProt 1–156 Author chain J； PDBConstruct 1–156； UniProt 1–156

V-type sodium ATPase subunit I

Enterococcus hirae ATCC 9790

UniProt P43439

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	V-type sodium ATPase subunit K × 10 （P43457） CARDIOLIPIN × 5 SODIUM ION × 9 N,N-dimethyl-4-(5-methyl-1H-benzimidazol-2-yl)aniline × 1 water × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NTPI_ENTHA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–664； UniProt 1–664

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	8wci
Deposition date deposition_date	2023-09-12
Structure title title	Cryo-EM structure of the inhibitor-bound Vo complex from Enterococcus hirae
Keywords keywords	V-ATPase, Na+-transporting, membrane protein, ATP hydrolyses, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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.

8wci__assembly_1__model_1

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

Download this curve (.dat)

8wci__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8wci__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.05 Å
Rg (electron density)	40.10 Å
Total Rg	40.40 Å
Atom count	14393
Residues	1903
Excluded volume	266030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8wci__assembly_1__model_1`	undecameric （11）	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 (6)

Entity 1 Entity 1 polymer

Description description	V-type sodium ATPase subunit K
Molecular weight formula_weight	16043.9 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	14876

MMDYLITQNGGMVFAVLAMATATIFSGIGSAKGVGMTGEAAAALTTSQPEKFGQALILQLLPGTQGLYGFVIAFLIFINLGSDMSVVQGLNFLGASLPIAFTGLFSGIAQGKVAAAGIQILAKKPEHATKGIIFAAMVETYAILGFVISFLLVLNA

Source Source

Source organism organism	Enterococcus hirae ATCC 9790
NCBI taxonomy ID ncbi_taxonomy_id	768486
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	V-type sodium ATPase subunit I
Molecular weight formula_weight	76515.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MAVTKMEKVTLISDKKNREILLQAVQGLHAVEIRDLFQESENNQWVETFFPEPEMIDKDKELAKLSYKLTDIRTAIQFIEHHGEKSQKKQHLKRRELSLDTLEKNYSEEAFSKKLEEVLLLKEQWEQLVDERQQLEDQENWLLNWQNLDLAPKAFDSQMTKLVIGTVNAKNAESFKAEVAEINEAYLEEINSSPTTTYFAYIVLRADESRMEEIASRYGFVKEDYLYEGTPQQQLVAAKQSLQEIKDQQKKLSSAIGACSGYIKDFEWTEEIFLARSEREAIKDRIIHTPYLILIQGWVDHEEKQELIHMLQNILASEEVYLTFDEPTDNEIAEEVPTKLKNHPIVAPFEMLTEMYSLPKYEEVDPTPWMMPFYLVFFGMMVADIGYGLLMFLGAFLLQKLVVLPRGMQRFAKFFEILAIPSIIWGFIYSSFFGAALPKEIFGIHLPFPILSTTDDVNTILILSVIFGLIQILVGLFIAAKEHIKRKAYVDAVNDGFAWQGILLGIILILLGTMILKNNAFVYLGGALAVLSAVCILIIPVFQSSSKAKGIAKGAYNLYGLTGYIGDLVSYTRLMALGISGGSIAAAFNMLVAFMPPAARFSVGILLIIVLQALNMFLTLLSAYVHGARLQYVEFFGKFYTGGGRSFKPLKTVEKYVNINHKKKEHLYFQGG

Source Source

Source organism organism	Enterococcus hirae ATCC 9790
NCBI taxonomy ID ncbi_taxonomy_id	768486
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CARDIOLIPIN
Molecular weight formula_weight	1464.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 non-polymer

Description description	N,N-dimethyl-4-(5-methyl-1H-benzimidazol-2-yl)aniline
Molecular weight formula_weight	251.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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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	triclinic

Resolution resolution	2.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	225359

Cryo-EM structure of the inhibitor-bound Vo complex from Enterococcus hirae

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

V-type sodium ATPase subunit K

State in the Current Structure

Other States of the Same Protein in the Database

V-type sodium ATPase subunit I

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8wci__assembly_1__model_1

8wci__assembly_1__model_1 | I(q)

8wci__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Cryo-EM structure of the inhibitor-bound Vo complex from Enterococcus hirae

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

V-type sodium ATPase subunit K

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 sodium 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8wci__assembly_1__model_1

8wci__assembly_1__model_1 | I(q)

8wci__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)