9vvo

cryo-EM structure of gastric proton pump bound to YK01

Method: ELECTRON MICROSCOPY

▼

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

Sodium/potassium-transporting ATPase subunit alpha

Sus scrofa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Potassium-transporting ATPase subunit beta × 1 （P18434） 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 MAGNESIUM ION × 1 YK01-b × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CHOLESTEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8D1T4M7_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–983； UniProt 51–1033

Potassium-transporting ATPase subunit beta

Sus scrofa

UniProt P18434

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Sodium/potassium-transporting ATPase subunit alpha × 1 （A0A8D1T4M7） 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 MAGNESIUM ION × 1 YK01-b × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CHOLESTEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATP4B_PIG
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–268； UniProt 23–290

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9vvo
Deposition date deposition_date	2025-07-16
Structure title title	cryo-EM structure of gastric proton pump bound to YK01
Keywords keywords	P-type ATPase, transporters, gastric, P-CABs, proton pump, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

9vvo__assembly_1__model_1

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

Download this curve (.dat)

9vvo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vvo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.76 Å
Rg (electron density)	47.01 Å
Total Rg	46.73 Å
Atom count	10118
Residues	1250
Excluded volume	182570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vvo__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Sodium/potassium-transporting ATPase subunit alpha
Molecular weight formula_weight	108832.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10491

NDHQLSVAELEQKYQTSATKGLSASLAAELLLRDGPNALRPPRGTPEYVKFARQLAGGLQCLMWVAAAICLIAFAIQASEGDLTTDDNLYLALALIAVVVVTGCFGYYQEFKSTNIIASFKNLVPQQATVIRDGDKFQINADQLVVGDLVEMKGGDRVPADIRILQAQGCKVDNSSLTGESEPQTRSPECTHESPLETRNIAFFSTMCLEGTAQGLVVNTGDRTIIGRIASLASGVENEKTPIAIEIEHFVDIIAGLAILFGATFFIVAMCIGYTFLRAMVFFMAIVVAYVPEGLLATVTVCLSLTAKRLASKNCVVKNLEAVETLGSTSVICSDKTGTLTQNRMTVSHLWFDNHIHSADTTEDQSGQTFDQSSETWRALCRVLTLCNRAAFKSGQDAVPVPKRIVIGDASETALLKFSELTLGNAMGYRERFPKVCEIPFNSTNKFQLSIHTLEDPRDPRHVLVMKGAPERVLERCSSILIKGQELPLDEQWREAFQTAYLSLGGLGERVLGFCQLYLSEKDYPPGYAFDVEAMNFPTSGLCFAGLVSMIDPPRATVPDAVLKCRTAGIRVIMVTGDHPITAKAIAASVGIISEGSETVEDIAARLRVPVDQVNRKDARACVINGMQLKDMDPSELVEALRTHPEMVFARTSPQQKLVIVESCQRLGAIVAVTGDGVNDSPALKKADIGVAMGIAGSDAAKNAADMILLDDNFASIVTGVEQGRLIFDNLKKSIAYTLTKNIPELTPYLIYITVSVPLPLGCITILFIELCTDIFPSVSLAYEKAESDIMHLRPRNPKRDRLVNEPLAAYSYFQIGAIQSFAGFTDYFTAMAQEGWFPLLCVGLRPQWENHHLQDLQDSYGQEWTFGQRLYQQYTCYTVFFISIEMCQIADVLIRKTRRLSAFQQGFFRNRILVIAIVFQVCIGCFLCYCPGMPNIFNFMPIRFQWWLVPMPFSLLIFVYDEIRKLGVRCCPGSWWDQELYY

Source Source

Source organism organism	Sus scrofa
Common name common_name	pig
NCBI taxonomy ID ncbi_taxonomy_id	9823
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Potassium-transporting ATPase subunit beta
Molecular weight formula_weight	30374.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

NPDTGQMLGRTLSRWVWISLYYVAFYVVMSGIFALCIYVLMRTIDPYTPDYQDQLKSPGVTLRPDVYGEKGLDISYNVSDSTTWAGLAHTLHRFLAGYSPAAQEGSINCTSEKYFFQESFLAPNHTKFSCKFTADMLQNCSGRPDPTFGFAEGKPCFIIKMNRIVKFLPGNSTAPRVDCAFLDQPRDGPPLQVEYFPANGTYSLHYFPYYGKKAQPHYSNPLVAAKLLNVPRNRDVVIVCKILAEHVSFDNPHDPYEGKVEFKLKIQK

Source Source

Source organism organism	Sus scrofa
Common name common_name	pig
NCBI taxonomy ID ncbi_taxonomy_id	9823
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 non-polymer

Description description	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	787.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	YK01-b
Molecular weight formula_weight	347.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	373

▶

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	2.66 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	177544

cryo-EM structure of gastric proton pump bound to YK01

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

Sodium/potassium-transporting ATPase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Potassium-transporting ATPase subunit beta

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

9vvo__assembly_1__model_1

9vvo__assembly_1__model_1 | I(q)

9vvo__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

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

cryo-EM structure of gastric proton pump bound to YK01

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

Sodium/potassium-transporting ATPase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Potassium-transporting ATPase subunit beta

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

9vvo__assembly_1__model_1

9vvo__assembly_1__model_1 | I(q)

9vvo__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

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)