SAXSdb — 8igu

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

V-type sodium ATPase catalytic subunit A

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 6	V-type sodium ATPase subunit B × 3 （Q08637） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NTPA_ENTHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–596； UniProt 1–593 Author chain B； PDBConstruct 4–596； UniProt 1–593 Author chain C； PDBConstruct 4–596； UniProt 1–593

V-type sodium ATPase subunit B

Enterococcus hirae ATCC 9790

UniProt Q08637

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	V-type sodium ATPase catalytic subunit A × 3 （Q08636） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NTPB_ENTHA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–458； UniProt 1–458 Author chain E； PDBConstruct 1–458； UniProt 1–458 Author chain F； PDBConstruct 1–458； UniProt 1–458

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	8igu
Deposition date deposition_date	2023-02-21
Structure title title	Hexameric Ring Complex of Engineered V1-ATPase: A3(De)3_empty
Keywords keywords	Computational Design, Rotary Molecular Motor, Complex, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

8igu__assembly_1__model_1

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

Download this curve (.dat)

8igu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8igu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.77 Å
Rg (electron density)	44.94 Å
Total Rg	45.32 Å
Atom count	24028
Residues	3082
Excluded volume	428270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8igu__assembly_1__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	V-type sodium ATPase catalytic subunit A
Molecular weight formula_weight	66059.5 kDa
EC 编号 ec_number	7.2.2.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	24292

SSGMQIGKIIKVSGPLVMAENMSEASIQDMCLVGDLGVIGEIIEMRQDVASIQVYEETSGIGPGEPVRSTGEALSVELGPGIISQMFDGIQRPLDTFMEVTQSNFLGRGVQLPALDHEKQWWFEATIEEGTEVSAGDIIGYVDETKIIQHKIMVPNGIKGTVQKIESGSFTIDDPICVIETEQGLKELTMMQKWPVRRGRPIKQKLNPDVPMITGQRVIDTFFPVTKGGAAAVPGPFGAGKTVVQHQIAKWSDVDLVVYVGCGERGNEMTDVVNEFPELIDPNTGESLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVAIMADSTSRWAEALREMSGRLEEMPGDEGYPAYLGSRLAEYYERSGRVIALGSDQREGSITAISAVSPSGGDISEPVTQNTLRVVKVFWGLDSSLAQKRHFPSINWIQSYSLYSTEVGRYMDQILQQDWSDMVTEGMRILQEEEQLNEIVRLVGIDSLSDNDRLTLEVAKSIREDYLQQNAFDDVDTFTSREKQFNMLKVILTFGKEARKALSLGAYFNEIMEGTVAVRERISRSKYIPEEELAKISSINEEIKETIQLIVSEGGMTDD

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 B
Molecular weight formula_weight	51017.2 kDa
Mutation mutation	S151G, G152P, S153P, L155A, P156G, G157K, K158S, E159A, T248E, Q339S
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MIKEYRTIKEVVGPLMAVEKVSGVKYEELIEVRMQNGEIRRGQVLEVQEDKAMVQIFEGTSGINLKNSSVRFLGHPLQLGVSEDMIGRVFDGLGRPKDNGPEILPEKYLDINGEVINPIARDYPDEFIQTGISAIDHLNTLVRGQKLPVFGPPGAGKSALAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERIATPRMALTAAEYLAYEKGMHVLVIMEDMTNYAEALREISAARREVPGRRGYPGYLYTNLATLFERAGRIRGLKGSVTQIPILTMPEDDKTHPIPDLTGYITEGQIILTRELYKSGISPPIDVLPSLSRLKDKGTGAGKTREDHAATMNQLFAAYAQGKQAKELAVVLGESALSDIDKIYAKFAERFENEYVNQGFYTNRTITETLDLGWELLAMLPRTELKRIKDDLLDKYLPEGK

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	253

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Unit-cell length a length_a	122.449 Å
Unit-cell length b length_b	122.653 Å
Unit-cell length c length_c	128.704 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.74 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.770 Å
Low-resolution limit resolution_low	44.640 Å
R factor r_factor	0.2187
R_work r_work	0.2165
R_free r_free	0.2624

Hexameric Ring Complex of Engineered V1-ATPase: A3(De)3_empty

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

V-type sodium ATPase catalytic subunit A

State in the Current Structure

Other States of the Same Protein in the Database

V-type sodium ATPase subunit B

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

8igu__assembly_1__model_1

8igu__assembly_1__model_1 | I(q)

8igu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)

Hexameric Ring Complex of Engineered V1-ATPase: A3(De)3_empty

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

V-type sodium 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 sodium ATPase subunit B

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

8igu__assembly_1__model_1

8igu__assembly_1__model_1 | I(q)

8igu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)