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9udg

;Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, with bound aurachin D-42 ;

Method: ELECTRON MICROSCOPY D_max: 145.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9udg
deposition_date	2025-04-06
last_revision	2025-06-25
title	;Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, with bound aurachin D-42 ;
keywords	Na+-NQR, Na+ pump, oxidoreductase, inhibitor, 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	43.53 Å
rg_electron	43.06 Å
i0	1257500000.00
molecular_weight	199010.0 kDa
excluded_volume	194900 Å³
envelope_volume	373790 Å³
shell_volume	71585 Å³
envelope_diameter	145.9 Å
shell_rg	48.94 Å
envelope_rg	42.30 Å
shape_rg	43.06 Å
total_rg	43.26 Å
total_atoms	15071
n_residues	1919
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	145.6 Å
rg_real	43.47 Å
rg_real_error	1.16 Å
i0_real	1.2570e+09
i0_real_error	2.0840e+07
rg_reciprocal	43.53 Å
i0_reciprocal	1258000000.0000
total_estimate	0.8927
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	52.6 Å
skewness	0.260
kurtosis	-0.477
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	97210000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.936

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4. Crystallography & Experiment

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5. Entities & Polymer Info (15)

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	15132

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	Aurachin D
formula_weight	363.5 kDa
src_method	syn
entity_count	1

Entity 10 non-polymer

description	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
formula_weight	744.0 kDa
src_method	syn
entity_count	2

Entity 11 non-polymer

description	DODECYL-BETA-D-MALTOSIDE
formula_weight	510.6 kDa
src_method	syn
entity_count	2

Entity 12 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 13 non-polymer

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

Entity 14 non-polymer

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

Entity 15 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	61

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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	3.180 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.18 Å
resolution_method	—
num_particles	390000

fit	/app/data/saxs_computation/ud/9udg/9udg.fit
pddf	/app/data/pr_computation/ud/9udg/9udg.pr.out
profile	/app/data/saxs_computation/ud/9udg/9udg.dat

;Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, with bound aurachin D-42 ;

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

Refinement

EM 3D

5. Entities & Polymer Info (15)

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

Entity 13 non-polymer

Entity 14 non-polymer

Entity 15 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)