9uuu

Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH

Method: ELECTRON MICROSCOPY

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

Na(+)-translocating NADH-quinone reductase subunit A

Vibrio cholerae O395

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Na(+)-translocating NADH-quinone reductase subunit B × 1 （A5F5X0） Na(+)-translocating NADH-quinone reductase subunit C × 1 （A5F5Y7） Na(+)-translocating NADH-quinone reductase subunit D × 1 （A5F5Y6） Na(+)-translocating NADH-quinone reductase subunit E × 1 （A5F5Y5） Na(+)-translocating NADH-quinone reductase subunit F × 1 （A5F5Y4） FLAVIN MONONUCLEOTIDE × 2 RIBOFLAVIN × 1 CALCIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2 FLAVIN-ADENINE DINUCLEOTIDE × 1 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQRA_VIBC3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–446； UniProt 1–446

Na(+)-translocating NADH-quinone reductase subunit B

Vibrio cholerae O395

UniProt A5F5X0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Na(+)-translocating NADH-quinone reductase subunit A × 1 （A5F5X1） Na(+)-translocating NADH-quinone reductase subunit C × 1 （A5F5Y7） Na(+)-translocating NADH-quinone reductase subunit D × 1 （A5F5Y6） Na(+)-translocating NADH-quinone reductase subunit E × 1 （A5F5Y5） Na(+)-translocating NADH-quinone reductase subunit F × 1 （A5F5Y4） FLAVIN MONONUCLEOTIDE × 2 RIBOFLAVIN × 1 CALCIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2 FLAVIN-ADENINE DINUCLEOTIDE × 1 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQRB_VIBC3
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–415； UniProt 1–415

Na(+)-translocating NADH-quinone reductase subunit C

Vibrio cholerae O395

UniProt A5F5Y7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Na(+)-translocating NADH-quinone reductase subunit A × 1 （A5F5X1） Na(+)-translocating NADH-quinone reductase subunit B × 1 （A5F5X0） Na(+)-translocating NADH-quinone reductase subunit D × 1 （A5F5Y6） Na(+)-translocating NADH-quinone reductase subunit E × 1 （A5F5Y5） Na(+)-translocating NADH-quinone reductase subunit F × 1 （A5F5Y4） FLAVIN MONONUCLEOTIDE × 2 RIBOFLAVIN × 1 CALCIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2 FLAVIN-ADENINE DINUCLEOTIDE × 1 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQRC_VIBC3
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–257； UniProt 1–257

Na(+)-translocating NADH-quinone reductase subunit D

Vibrio cholerae O395

UniProt A5F5Y6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Na(+)-translocating NADH-quinone reductase subunit A × 1 （A5F5X1） Na(+)-translocating NADH-quinone reductase subunit B × 1 （A5F5X0） Na(+)-translocating NADH-quinone reductase subunit C × 1 （A5F5Y7） Na(+)-translocating NADH-quinone reductase subunit E × 1 （A5F5Y5） Na(+)-translocating NADH-quinone reductase subunit F × 1 （A5F5Y4） FLAVIN MONONUCLEOTIDE × 2 RIBOFLAVIN × 1 CALCIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2 FLAVIN-ADENINE DINUCLEOTIDE × 1 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQRD_VIBC3
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–210； UniProt 1–210

Na(+)-translocating NADH-quinone reductase subunit E

Vibrio cholerae O395

UniProt A5F5Y5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Na(+)-translocating NADH-quinone reductase subunit A × 1 （A5F5X1） Na(+)-translocating NADH-quinone reductase subunit B × 1 （A5F5X0） Na(+)-translocating NADH-quinone reductase subunit C × 1 （A5F5Y7） Na(+)-translocating NADH-quinone reductase subunit D × 1 （A5F5Y6） Na(+)-translocating NADH-quinone reductase subunit F × 1 （A5F5Y4） FLAVIN MONONUCLEOTIDE × 2 RIBOFLAVIN × 1 CALCIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2 FLAVIN-ADENINE DINUCLEOTIDE × 1 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQRE_VIBC3
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–198； UniProt 1–198

Na(+)-translocating NADH-quinone reductase subunit F

Vibrio cholerae O395

UniProt A5F5Y4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Na(+)-translocating NADH-quinone reductase subunit A × 1 （A5F5X1） Na(+)-translocating NADH-quinone reductase subunit B × 1 （A5F5X0） Na(+)-translocating NADH-quinone reductase subunit C × 1 （A5F5Y7） Na(+)-translocating NADH-quinone reductase subunit D × 1 （A5F5Y6） Na(+)-translocating NADH-quinone reductase subunit E × 1 （A5F5Y5） FLAVIN MONONUCLEOTIDE × 2 RIBOFLAVIN × 1 CALCIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 2 FLAVIN-ADENINE DINUCLEOTIDE × 1 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NQRF_VIBC3
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–408； UniProt 1–408

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	9uuu
Deposition date deposition_date	2025-05-08
Last revision last_revision	2025-06-25
Structure title title	Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH
Keywords keywords	Na+-NQR, Na+ pump, oxidoreductase, 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.

9uuu__assembly_1__model_1

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

Download this curve (.dat)

9uuu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9uuu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.72 Å
Rg (electron density)	43.03 Å
Total Rg	43.15 Å
Atom count	14694
Residues	1892
Excluded volume	264960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9uuu__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 (12)

Entity 1 Entity 1 polymer

Description description	Na(+)-translocating NADH-quinone reductase subunit A
Molecular weight formula_weight	48680.7 kDa
EC 编号 ec_number	7.2.1.1
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	14694

MITIKKGLDLPIAGTPSQVISDGKAIKKVALLGEEYVGMRPTMHVRVGDEVKKAQILFEDKKNPGVKFTSPVSGKVVEINRGAKRVLQSVVIEVAGDDQVTFDKFEANQLASLNRDAIKTQLVESGLWTAFRTRPFSKVPAIDSTSEAIFVTAMDTNPLAAEPTVVINEQSEAFVAGLDVLSALTTGKVYVCKKGTSLPRSQQPNVEEHVFDGPHPAGLAGTHMHFLYPVSADHVAWSINYQDVIAVGQLFLTGELYTQRVVSLAGPVVNKPRLVRTVMGASLEQLVDSEIMPGEVRIISGSVLSGTKATGPHAYLGRYHLQVSVLREGRDKELFGWAMPGKNKFSVTRSFLGHLFKGQVYNMTTTTNGSDRSMVPIGNYEKVMPLDMEPTLLLRDLCAGDSDSAVRLGALELDEEDLALCTFVCPGKYEYGQLLRECLDKIEKEG

Source Source

Source organism organism	Vibrio cholerae O395
NCBI taxonomy ID ncbi_taxonomy_id	345073
Host organism host_organism	Vibrio cholerae

Entity 2 Entity 2 polymer

Description description	Na(+)-translocating NADH-quinone reductase subunit B
Molecular weight formula_weight	45390.9 kDa
EC 编号 ec_number	7.2.1.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGLKKFLEDIEHHFEPGGKHEKWFALYEAAATLFYTPGLVTKRSSHVRDSVDLKRIMIMVWLAVFPAMFWGMYNAGGQAIAALNHLYSGDQLAAIVAGNWHYWLTEMLGGTMSSDAGWGSKMLLGATYFLPIYATVFIVGGFWEVLFCMVRKHEVNEGFFVTSILFALIVPPTLPLWQAALGITFGVVVAKEVFGGTGRNFLNPALAGRAFLFFAYPAQISGDLVWTAADGYSGATALSQWAQGGAGALINNATGQTITWMDAFIGNIPGSIGEVSTLALMIGAAFIVYMGIASWRIIGGVMIGMILLSTLFNVIGSDTNAMFNMPWHWHLVLGGFAFGMFFMATDPVSASFTNSGKWAYGILIGVMCVLIRVVNPAYPEGMMLAILFANLFAPLFDHVVVERNIKRRLARYGKQ

Source Source

Source organism organism	Vibrio cholerae O395
NCBI taxonomy ID ncbi_taxonomy_id	345073
Host organism host_organism	Vibrio cholerae

Entity 3 Entity 3 polymer

Description description	Na(+)-translocating NADH-quinone reductase subunit C
Molecular weight formula_weight	27652.3 kDa
EC 编号 ec_number	7.2.1.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MASNNDSIKKTLFVVIALSLVCSIIVSAAAVGLRDKQKENAALDKQSKILQVAGIEAKGSKQIVELFNKSIEPRLVDFNTGDFVEGDAANYDQRKAAKEASESIKLTAEQDKAKIQRRANVGVVYLVKDGDKTSKVILPVHGNGLWSMMYAFVAVETDGNTVSGLTYYEQGETPGLGGEVENPAWRAQWVGKKLFDENHKPAIKIVKGGAPQGSEHGVDGLSGATLTSNGVQNTFDFWLGDMGFGPFLTKVRDGGLN

Source Source

Source organism organism	Vibrio cholerae O395
NCBI taxonomy ID ncbi_taxonomy_id	345073
Host organism host_organism	Vibrio cholerae

Entity 4 Entity 4 polymer

Description description	Na(+)-translocating NADH-quinone reductase subunit D
Molecular weight formula_weight	22853.2 kDa
EC 编号 ec_number	7.2.1.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSSAKELKKSVLAPVLDNNPIALQVLGVCSALAVTTKLETAFVMTLAVMFVTALSNFFVSLIRNHIPNSVRIIVQMAIIASLVIVVDQILKAYLYDISKQLSVFVGLIITNCIVMGRAEAFAMKSEPIPSFIDGIGNGLGYGFVLMTVGFFRELLGSGKLFGLEVLPLISNGGWYQPNGLMLLAPSAFFLIGFMIWAIRTFKPEQVEAKE

Source Source

Source organism organism	Vibrio cholerae O395
NCBI taxonomy ID ncbi_taxonomy_id	345073
Host organism host_organism	Vibrio cholerae

Entity 5 Entity 5 polymer

Description description	Na(+)-translocating NADH-quinone reductase subunit E
Molecular weight formula_weight	21481.7 kDa
EC 编号 ec_number	7.2.1.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MEHYISLLVKSIFIENMALSFFLGMCTFLAVSKKVKTSFGLGIAVIVVLTISVPVNNLVYNLVLKPDALVEGVDLSFLNFITFIGVIAALVQILEMILDRFFPPLYNALGIFLPLITVNCAIFGGVSFMVQRDYSFAESVVYGFGSGVGWMLAIVALAGIREKMKYSDVPPGLRGLGITFITAGLMALGFMSFSGVQL

Source Source

Source organism organism	Vibrio cholerae O395
NCBI taxonomy ID ncbi_taxonomy_id	345073
Host organism host_organism	Vibrio cholerae

Entity 6 Entity 6 polymer

Description description	Na(+)-translocating NADH-quinone reductase subunit F
Molecular weight formula_weight	45942.4 kDa
EC 编号 ec_number	7.2.1.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSTIIFGVVMFTLIILALVLVILFAKSKLVPTGDITISINGDPEKAIVTQPGGKLLTALAGAGVFVSSACGGGGSCGQCRVKIKSGGGDILPTELDHISKGEAREGERLACQVAVKADMDLELPEEIFGVKKWECTVISNDNKATFIKELKLAIPDGESVPFRAGGYIQIEAPAHHVKYADFDVPEKYRGDWDKFNLFRYESKVDEPIIRAYSMANYPEEFGIIMLNVRIATPPPNNPNVPPGQMSSYIWSLKAGDKCTISGPFGEFFAKDTDAEMVFIGGGAGMAPMRSHIFDQLKRLKSKRKMSYWYGARSKREMFYVEDFDGLAAENDNFVWHCALSDPQPEDNWTGYTGFIHNVLYENYLKDHEAPEDCEYYMCGPPMMNAAVINMLKNLGVEEENILLDDFGGHHHHHH

Source Source

Source organism organism	Vibrio cholerae O395
NCBI taxonomy ID ncbi_taxonomy_id	345073
Host organism host_organism	Vibrio cholerae

Entity 7 Entity 7 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	RIBOFLAVIN
Molecular weight formula_weight	376.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Molecular weight formula_weight	665.4 kDa
Source method src_method	syn
Copy count entity_count	1

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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	3.17 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	245271

Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH

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

Na(+)-translocating NADH-quinone reductase 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

Na(+)-translocating NADH-quinone reductase 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

Na(+)-translocating NADH-quinone reductase 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

Na(+)-translocating NADH-quinone reductase subunit D

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Na(+)-translocating NADH-quinone reductase subunit E

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Na(+)-translocating NADH-quinone reductase subunit F

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

9uuu__assembly_1__model_1

9uuu__assembly_1__model_1 | I(q)

9uuu__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 (12)

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 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer