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9uuu

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

Method: ELECTRON MICROSCOPY D_max: 145.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uuu
deposition_date	2025-05-08
last_revision	2025-06-25
title	Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH
keywords	Na+-NQR, Na+ pump, oxidoreductase, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	43.72 Å
rg_electron	43.03 Å
i0	595752000.00
molecular_weight	209080.0 kDa
excluded_volume	264960 Å³
envelope_volume	365340 Å³
shell_volume	70368 Å³
envelope_diameter	144.1 Å
shell_rg	48.60 Å
envelope_rg	42.21 Å
shape_rg	43.08 Å
total_rg	43.15 Å
total_atoms	14694
n_residues	1892
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	145.2 Å
rg_real	43.67 Å
rg_real_error	1.20 Å
i0_real	5.9580e+08
i0_real_error	1.2260e+07
rg_reciprocal	43.72 Å
i0_reciprocal	595800000.0000
total_estimate	0.8938
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	52.4 Å
skewness	0.256
kurtosis	-0.509
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0001
highest_alpha	96680000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.904

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4. Crystallography & Experiment

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5. Entities & Polymer Info (12)

Entity 1 polymer

description	Na(+)-translocating NADH-quinone reductase subunit A
formula_weight	48680.7 kDa
ec_number	7.2.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	14694

MITIKKGLDLPIAGTPSQVISDGKAIKKVALLGEEYVGMRPTMHVRVGDEVKKAQILFEDKKNPGVKFTSPVSGKVVEINRGAKRVLQSVVIEVAGDDQVTFDKFEANQLASLNRDAIKTQLVESGLWTAFRTRPFSKVPAIDSTSEAIFVTAMDTNPLAAEPTVVINEQSEAFVAGLDVLSALTTGKVYVCKKGTSLPRSQQPNVEEHVFDGPHPAGLAGTHMHFLYPVSADHVAWSINYQDVIAVGQLFLTGELYTQRVVSLAGPVVNKPRLVRTVMGASLEQLVDSEIMPGEVRIISGSVLSGTKATGPHAYLGRYHLQVSVLREGRDKELFGWAMPGKNKFSVTRSFLGHLFKGQVYNMTTTTNGSDRSMVPIGNYEKVMPLDMEPTLLLRDLCAGDSDSAVRLGALELDEEDLALCTFVCPGKYEYGQLLRECLDKIEKEG

Source

organism	Vibrio cholerae O395
ncbi_taxonomy_id	345073
host_organism	Vibrio cholerae

Entity 2 polymer

description	Na(+)-translocating NADH-quinone reductase subunit B
formula_weight	45390.9 kDa
ec_number	7.2.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MGLKKFLEDIEHHFEPGGKHEKWFALYEAAATLFYTPGLVTKRSSHVRDSVDLKRIMIMVWLAVFPAMFWGMYNAGGQAIAALNHLYSGDQLAAIVAGNWHYWLTEMLGGTMSSDAGWGSKMLLGATYFLPIYATVFIVGGFWEVLFCMVRKHEVNEGFFVTSILFALIVPPTLPLWQAALGITFGVVVAKEVFGGTGRNFLNPALAGRAFLFFAYPAQISGDLVWTAADGYSGATALSQWAQGGAGALINNATGQTITWMDAFIGNIPGSIGEVSTLALMIGAAFIVYMGIASWRIIGGVMIGMILLSTLFNVIGSDTNAMFNMPWHWHLVLGGFAFGMFFMATDPVSASFTNSGKWAYGILIGVMCVLIRVVNPAYPEGMMLAILFANLFAPLFDHVVVERNIKRRLARYGKQ

Source

organism	Vibrio cholerae O395
ncbi_taxonomy_id	345073
host_organism	Vibrio cholerae

Entity 3 polymer

description	Na(+)-translocating NADH-quinone reductase subunit C
formula_weight	27652.3 kDa
ec_number	7.2.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MASNNDSIKKTLFVVIALSLVCSIIVSAAAVGLRDKQKENAALDKQSKILQVAGIEAKGSKQIVELFNKSIEPRLVDFNTGDFVEGDAANYDQRKAAKEASESIKLTAEQDKAKIQRRANVGVVYLVKDGDKTSKVILPVHGNGLWSMMYAFVAVETDGNTVSGLTYYEQGETPGLGGEVENPAWRAQWVGKKLFDENHKPAIKIVKGGAPQGSEHGVDGLSGATLTSNGVQNTFDFWLGDMGFGPFLTKVRDGGLN

Source

organism	Vibrio cholerae O395
ncbi_taxonomy_id	345073
host_organism	Vibrio cholerae

Entity 4 polymer

description	Na(+)-translocating NADH-quinone reductase subunit D
formula_weight	22853.2 kDa
ec_number	7.2.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MSSAKELKKSVLAPVLDNNPIALQVLGVCSALAVTTKLETAFVMTLAVMFVTALSNFFVSLIRNHIPNSVRIIVQMAIIASLVIVVDQILKAYLYDISKQLSVFVGLIITNCIVMGRAEAFAMKSEPIPSFIDGIGNGLGYGFVLMTVGFFRELLGSGKLFGLEVLPLISNGGWYQPNGLMLLAPSAFFLIGFMIWAIRTFKPEQVEAKE

Source

organism	Vibrio cholerae O395
ncbi_taxonomy_id	345073
host_organism	Vibrio cholerae

Entity 5 polymer

description	Na(+)-translocating NADH-quinone reductase subunit E
formula_weight	21481.7 kDa
ec_number	7.2.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MEHYISLLVKSIFIENMALSFFLGMCTFLAVSKKVKTSFGLGIAVIVVLTISVPVNNLVYNLVLKPDALVEGVDLSFLNFITFIGVIAALVQILEMILDRFFPPLYNALGIFLPLITVNCAIFGGVSFMVQRDYSFAESVVYGFGSGVGWMLAIVALAGIREKMKYSDVPPGLRGLGITFITAGLMALGFMSFSGVQL

Source

organism	Vibrio cholerae O395
ncbi_taxonomy_id	345073
host_organism	Vibrio cholerae

Entity 6 polymer

description	Na(+)-translocating NADH-quinone reductase subunit F
formula_weight	45942.4 kDa
ec_number	7.2.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MSTIIFGVVMFTLIILALVLVILFAKSKLVPTGDITISINGDPEKAIVTQPGGKLLTALAGAGVFVSSACGGGGSCGQCRVKIKSGGGDILPTELDHISKGEAREGERLACQVAVKADMDLELPEEIFGVKKWECTVISNDNKATFIKELKLAIPDGESVPFRAGGYIQIEAPAHHVKYADFDVPEKYRGDWDKFNLFRYESKVDEPIIRAYSMANYPEEFGIIMLNVRIATPPPNNPNVPPGQMSSYIWSLKAGDKCTISGPFGEFFAKDTDAEMVFIGGGAGMAPMRSHIFDQLKRLKSKRKMSYWYGARSKREMFYVEDFDGLAAENDNFVWHCALSDPQPEDNWTGYTGFIHNVLYENYLKDHEAPEDCEYYMCGPPMMNAAVINMLKNLGVEEENILLDDFGGHHHHHH

Source

organism	Vibrio cholerae O395
ncbi_taxonomy_id	345073
host_organism	Vibrio cholerae

Entity 7 non-polymer

description	FLAVIN MONONUCLEOTIDE
formula_weight	456.3 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	RIBOFLAVIN
formula_weight	376.4 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 10 non-polymer

description	FE2/S2 (INORGANIC) CLUSTER
formula_weight	175.8 kDa
src_method	syn
entity_count	2

Entity 11 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	1

Entity 12 non-polymer

description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
formula_weight	665.4 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.17 Å
resolution_method	—
num_particles	245271

fit	/app/data/saxs_computation/uu/9uuu/9uuu.fit
pddf	/app/data/pr_computation/uu/9uuu/9uuu.pr.out
profile	/app/data/saxs_computation/uu/9uuu/9uuu.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (12)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)