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9tao

Local refinement of E. coli Complex I D79N NuoA mutant membrane domain in LMNG

Method: ELECTRON MICROSCOPY D_max: 175.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tao
deposition_date	2025-11-18
title	Local refinement of E. coli Complex I D79N NuoA mutant membrane domain in LMNG
keywords	PROTON TRANSPORT, bioenergetics; PROTON TRANSPORT
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	52.00 Å
rg_electron	52.48 Å
i0	726976000.00
molecular_weight	263730.0 kDa
excluded_volume	346240 Å³
envelope_volume	421350 Å³
shell_volume	71081 Å³
envelope_diameter	191.2 Å
shell_rg	49.89 Å
envelope_rg	53.29 Å
shape_rg	52.48 Å
total_rg	52.38 Å
total_atoms	18587
n_residues	2281
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	175.0 Å
rg_real	52.56 Å
rg_real_error	1.68 Å
i0_real	7.2700e+08
i0_real_error	1.3400e+07
rg_reciprocal	51.52 Å
i0_reciprocal	725900000.0000
total_estimate	0.7426
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	40.8 Å
skewness	0.609
kurtosis	-0.408
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	181900000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.566; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.847; Smooth: 0.103

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4. Crystallography & Experiment

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5. Entities & Polymer Info (12)

Entity 1 polymer

description	NADH-quinone oxidoreductase subunit H
formula_weight	36240.9 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H
atom_count	18764

MSWISPELIEILLTILKAVVILLVVVTCGAFMSFGERRLLGLFQNRYGPNRVGWGGSLQLVADMIKMFFKEDWIPKFSDRVIFTLAPMIAFTSLLLAFAIVPVSPGWVVADLNIGILFFLMMAGLAVYAVLFAGWSSNNKYSLLGAMRASAQTLSYEVFLGLSLMGVVAQAGSFNMTDIVNSQAHVWNVIPQFFGFITFAIAGVAVCHRHPFDQPEAEQELADGYHIEYSGMKFGLFFVGEYIGIVTISALMVTLFFGGWQGPLLPPFIWFALKTAFFMMMFILIRASLPRPRYDQVMSFGWKICLPLTLINLLVTAAVILWQAQ

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 2 polymer

description	NADH-quinone oxidoreductase subunit K
formula_weight	10853.0 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

MIPLQHGLILAAILFVLGLTGLVIRRNLLFMLIGLEIMINASALAFVVAGSYWGQTDGQVMYILAISLAAAEASIGLALLLQLHRRRQNLNIDSVSEMRG

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 3 polymer

description	NADH-quinone oxidoreductase subunit L
formula_weight	66483.6 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

MNMLALTIILPLIGFVLLAFSRGRWSENVSAIVGVGSVGLAALVTAFIGVDFFANGEQTYSQPLWTWMSVGDFNIGFNLVLDGLSLTMLSVVTGVGFLIHMYASWYMRGEEGYSRFFAYTNLFIASMVVLVLADNLLLMYLGWEGVGLCSYLLIGFYYTDPKNGAAAMKAFVVTRVGDVFLAFALFILYNELGTLNFREMVELAPAHFADGNNMLMWATLMLLGGAVGKSAQLPLQTWLADAMAGPTPVSALIHAATMVTAGVYLIARTHGLFLMTPEVLHLVGIVGAVTLLLAGFAALVQTDIKRVLAYSTMSQIGYMFLALGVQAWDAAIFHLMTHAFFKALLFLASGSVILACHHEQNIFKMGGLRKSIPLVYLCFLVGGAALSALPLVTAGFFSKDEILAGAMANGHINLMVAGLVGAFMTSLYTFRMIFIVFHGKEQIHAHAVKGVTHSLPLIVLLILSTFVGALIVPPLQGVLPQTTELAHGSMLTLEITSGVVAVVGILLAAWLWLGKRTLVTSIANSAPGRLLGTWWYNAWGFDWLYDKVFVKPFLGIAWLLKRDPLNSMMNIPAVLSRFAGKGLLLSENGYLRWYVASMSIGAVVVLALLMVLR

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 4 polymer

description	NADH-quinone oxidoreductase subunit A
formula_weight	16473.3 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MSMSTSTEVIAHHWAFAIFLIVAIGLCCLMLVGGWFLGGRARARSKNVPFESGIDSVGSARLRLSAKFYLVAMFFVIFNVEALYLFAWSTSIRESGWVGFVEAAIFIFVLLAGLVYLVRIGALDWTPARSRRERMNPETNSIANRQR

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 5 polymer

description	NADH-quinone oxidoreductase subunit J
formula_weight	19889.6 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MEFAFYICGLIAILATLRVITHTNPVHALLYLIISLLAISGVFFSLGAYFAGALEIIVYAGAIMVLFVFVVMMLNLGGSEIEQERQWLKPQVWIGPAILSAIMLVVIVYAILGVNDQGIDGTPISAKAVGITLFGPYVLAVELASMLLLAGLVVAFHVGREERAGEVLSNRKDDSAKRKTEEHA

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 6 polymer

description	NADH-quinone oxidoreductase subunit M
formula_weight	56560.1 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

MLLPWLILIPFIGGFLCWQTERFGVKVPRWIALITMGLTLALSLQLWLQGGYSLTQSAGIPQWQSEFDMPWIPRFGISIHLAIDGLSLLMVVLTGLLGVLAVLCSWKEIEKYQGFFHLNLMWILGGVIGVFLAIDMFLFFFFWEMMLVPMYFLIALWGHKASDGKTRITAATKFFIYTQASGLVMLIAILALVFVHYNATGVWTFNYEELLNTPMSSGVEYLLMLGFFIAFAVKMPVVPLHGWLPDAHSQAPTAGSVDLAGILLKTAAYGLLRFSLPLFPNASAEFAPIAMWLGVIGIFYGAWMAFAQTDIKRLIAYTSVSHMGFVLIAIYTGSQLAYQGAVIQMIAHGLSAAGLFILCGQLYERIHTRDMRMMGGLWSKMKWLPALSLFFAVATLGMPGTGNFVGEFMILFGSFQVVPVITVISTFGLVFASVYSLAMLHRAYFGKAKSQIASQELPGMSLRELFMILLLVVLLVLLGFYPQPILDTSHSAIGNIQQWFVNSVTTTRP

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 7 polymer

description	NADH-quinone oxidoreductase subunit N
formula_weight	52072.7 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

MTITPQNLIALLPLLIVGLTVVVVMLSIAWRRNHFLNATLSVIGLNAALVSLWFVGQAGAMDVTPLMRVDGFAMLYTGLVLLASLATCTFAYPWLEGYNDNKDEFYLLVLIAALGGILLANANHLASLFLGIELISLPLFGLVGYAFRQKRSLEASIKYTILSAAASSFLLFGMALVYAQSGDLSFVALGKNLGDGMLNEPLLLAGFGLMIVGLGFKLSLVPFHLWTPDVYQGAPAPVSTFLATASKIAIFGVVMRLFLYAPVGDSEAIRVVLAIIAFASIIFGNLMALSQTNIKRLLGYSSISHLGYLLVALIALQTGEMSMEAVGVYLAGYLFSSLGAFGVVSLMSSPYRGPDADSLFSYRGLFWHRPILAAVMTVMMLSLAGIPMTLGFIGKFYVLAVGVQAHLWWLVGAVVVGSAIGLYYYLRVAVSLYLHAPEQPGRDAPSNWQYSAGGIVVLISALLVLVLGVWPQPLISIVRLAMPLM

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 8 non-polymer

description	1,2-Distearoyl-sn-glycerophosphoethanolamine
formula_weight	748.1 kDa
src_method	syn
entity_count	12

Entity 9 non-polymer

description	(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
formula_weight	564.7 kDa
src_method	syn
entity_count	5

Entity 10 non-polymer

description	CARDIOLIPIN
formula_weight	1464.0 kDa
src_method	syn
entity_count	1

Entity 11 non-polymer

description	Ubiquinone-8
formula_weight	727.1 kDa
src_method	syn
entity_count	2

Entity 12 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	177

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6. Citations (2)

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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	triclinic

resolution	2.61 Å
resolution_method	—
num_particles	86927

fit	/app/data/saxs_computation/ta/9tao/9tao.fit
pddf	/app/data/pr_computation/ta/9tao/9tao.pr.out
profile	/app/data/saxs_computation/ta/9tao/9tao.dat

Local refinement of E. coli Complex I D79N NuoA mutant membrane domain in LMNG

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 polymer

Polymer

Source

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)