7bgy

Cryo-EM Structure of KdpFABC in E2Pi state with MgF4

Method: ELECTRON MICROSCOPY

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

Potassium-transporting ATPase potassium-binding subunit

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Potassium-transporting ATPase ATP-binding subunit × 1 （P03960） Potassium-transporting ATPase KdpC subunit × 1 （P03961） Potassium-transporting ATPase KdpF subunit × 1 （P36937） (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 1 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 1 MAGNESIUM ION × 1 TETRAFLUOROMAGNESATE(2-) × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDPA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–557； UniProt 1–557

Potassium-transporting ATPase ATP-binding subunit

Escherichia coli K-12

UniProt P03960

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Potassium-transporting ATPase potassium-binding subunit × 1 （P03959） Potassium-transporting ATPase KdpC subunit × 1 （P03961） Potassium-transporting ATPase KdpF subunit × 1 （P36937） (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 1 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 1 MAGNESIUM ION × 1 TETRAFLUOROMAGNESATE(2-) × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDPB_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–682； UniProt 1–682

Potassium-transporting ATPase KdpC subunit

Escherichia coli K-12

UniProt P03961

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Potassium-transporting ATPase potassium-binding subunit × 1 （P03959） Potassium-transporting ATPase ATP-binding subunit × 1 （P03960） Potassium-transporting ATPase KdpF subunit × 1 （P36937） (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 1 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 1 MAGNESIUM ION × 1 TETRAFLUOROMAGNESATE(2-) × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDPC_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–190； UniProt 1–190

Potassium-transporting ATPase KdpF subunit

Escherichia coli K-12

UniProt P36937

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Potassium-transporting ATPase potassium-binding subunit × 1 （P03959） Potassium-transporting ATPase ATP-binding subunit × 1 （P03960） Potassium-transporting ATPase KdpC subunit × 1 （P03961） (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 1 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 1 MAGNESIUM ION × 1 TETRAFLUOROMAGNESATE(2-) × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDPF_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–29； UniProt 1–29

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	7bgy
Deposition date deposition_date	2021-01-09
Structure title title	Cryo-EM Structure of KdpFABC in E2Pi state with MgF4
Keywords keywords	P-type ATPase, ATP-dependent potassium 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.

7bgy__assembly_1__model_1

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

Download this curve (.dat)

7bgy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7bgy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.12 Å
Rg (electron density)	42.69 Å
Total Rg	42.52 Å
Atom count	22232
Residues	1450
Excluded volume	198230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7bgy__assembly_1__model_1`	tetrameric （4）	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	Potassium-transporting ATPase potassium-binding subunit
Molecular weight formula_weight	59247.7 kDa
Mutation mutation	Q116R
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	22271

MAAQGFLLIATFLLVLMVLARPLGSGLARLINDIPLPGTTGVERVLFRALGVSDREMNWKQYLCAILGLNMLGLAVLFFMLLGQHYLPLNPQQLPGLSWDLALNTAVSFVTNTNWRSYSGETTLSYFSQMAGLTVQNFLSAASGIAVIFALIRAFTRQSMSTLGNAWVDLLRITLWVLVPVALLIALFFIQQGALQNFLPYQAVNTVEGAQQLLPMGPVASQEAIKMLGTNGGGFFNANSSHPFENPTALTNFVQMLAIFLIPTALCFAFGEVMGDRRQGRMLLWAMSVIFVICVGVVMWAEVQGNPHLLALGTDSSINMEGKESRFGVLVSSLFAVVTTAASCGAVIAMHDSFTALGGMVPMWLMQIGEVVFGGVGSGLYGMMLFVLLAVFIAGLMIGRTPEYLGKKIDVREMKLTALAILVTPTLVLMGAALAMMTDAGRSAMLNPGPHGFSEVLYAVSSAANNNGSAFAGLSANSPFWNCLLAFCMFVGRFGVIIPVMAIAGSLVSKKSQAASSGTLPTHGPLFVGLLIGTVLLVGALTFIPALALGPVAEYLS

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Potassium-transporting ATPase ATP-binding subunit
Molecular weight formula_weight	72251.9 kDa
EC 编号 ec_number	7.2.2.6
Mutation mutation	S162A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSRKQLALFEPTLVVQALKEAVKKLNPQAQWRNPVMFIVWIGSLLTTCISIAMASGAMPGNALFSAAISGWLWITVLFANFAEALAEGRSKAQANSLKGVKKTAFARKLREPKYGAAADKVPADQLRKGDIVLVEAGDIIPCDGEVIEGGASVDESAITGEAAPVIRESGGDFASVTGGTRILSDWLVIECSVNPGETFLDRMIAMVEGAQRRKTPNEIALTILLIALTIVFLLATATLWPFSAWGGNAVSVTVLVALLVCLIPTTIGGLLSAIGVAGMSRMLGANVIATSGRAVEAAGDVDVLLLDKTGTITLGNRQASEFIPAQGVDEKTLADAAQLASLADETPEGRSIVILAKQRFNLRERDVQSLHATFVPFTAQSRMSGINIDNRMIRKGSVDAIRRHVEANGGHFPTDVDQKVDQVARQGATPLVVVEGSRVLGVIALKDIVKGGIKERFAQLRKMGIKTVMITGDNRLTAAAIAAEAGVDDFLAEATPEAKLALIRQYQAEGRLVAMTGDGTNDAPALAQADVAVAMNSGTQAAKEAGNMVDLDSNPTKLIEVVHIGKQMLMTRGSLTTFSIANDVAKYFAIIPAAFAATYPQLNALNIMCLHSPDSAILSAVIFNALIIVFLIPLALKGVSYKPLTASAMLRRNLWIYGLGGLLVPFIGIKVIDLLLTVCGLV

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Potassium-transporting ATPase KdpC subunit
Molecular weight formula_weight	22299.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSGLRPALSTFIFLLLITGGVYPLLTTVLGQWWFPWQANGSLIREGDTVRGSALIGQNFTGNGYFHGRPSATAEMPYNPQASGGSNLAVSNPELDKLIAARVAALRAANPDASASVPVELVTASASGLDNNITPQAAAWQIPRVAKARNLSVEQLTQLIAKYSQQPLVKYIGQPVVNIVELNLALDKLDEGTGLVPRGSSHHHHHHHH

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Potassium-transporting ATPase KdpF subunit
Molecular weight formula_weight	3071.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSAGVITGVLLVFLLLGYLVYALINAEAF

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
Molecular weight formula_weight	720.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	(2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
Molecular weight formula_weight	718.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 non-polymer

Description description	TETRAFLUOROMAGNESATE(2-)
Molecular weight formula_weight	100.3 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7bgyB01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	150 — Calcium-transporting ATPase, cytoplasmic transduction domain A
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic transduction domain A

Domain ID domain_id	7bgyB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1110 — Calcium-transporting ATPase, cytoplasmic domain N
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic domain N

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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	212120

Cryo-EM Structure of KdpFABC in E2Pi state with MgF4

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

Potassium-transporting ATPase potassium-binding subunit

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 ATP-binding subunit

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 KdpC subunit

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 KdpF subunit

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

7bgy__assembly_1__model_1

7bgy__assembly_1__model_1 | I(q)

7bgy__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)