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9tak

Local refinement of E. coli Complex I WT membrane domain in LMNG

Method: ELECTRON MICROSCOPY D_max: 181.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tak
deposition_date	2025-11-18
title	Local refinement of E. coli Complex I WT 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	54.13 Å
rg_electron	54.70 Å
i0	776826000.00
molecular_weight	273270.0 kDa
excluded_volume	358830 Å³
envelope_volume	448130 Å³
shell_volume	72506 Å³
envelope_diameter	198.5 Å
shell_rg	50.82 Å
envelope_rg	56.01 Å
shape_rg	54.68 Å
total_rg	54.65 Å
total_atoms	19260
n_residues	2358
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	181.0 Å
rg_real	54.81 Å
rg_real_error	2.13 Å
i0_real	7.7680e+08
i0_real_error	1.7110e+07
rg_reciprocal	53.55 Å
i0_reciprocal	775400000.0000
total_estimate	0.7322
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	43.7 Å
skewness	0.606
kurtosis	-0.430
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	133400000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.568; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.754; Smooth: 0.056

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4. Crystallography & Experiment

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5. Entities & Polymer Info (14)

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	19437

MSWISPELIEILLTILKAVVILLVVVTCGAFMSFGERRLLGLFQNRYGPNRVGWGGSLQLVADMIKMFFKEDWIPKFSDRVIFTLAPMIAFTSLLLAFAIVPVSPGWVVADLNIGILFFLMMAGLAVYAVLFAGWSSNNKYSLLGAMRASAQTLSYEVFLGLSLMGVVAQAGSFNMTDIVNSQAHVWNVIPQFFGFITFAIAGVAVCHRHPFDQPEAEQELADGYHIEYSGMKFGLFFVGEYIGIVTISALMVTLFFGGWQGPLLPPFIWFALKTAFFMMMFILIRASLPRPRYDQVMSFGWKICLPLTLINLLVTAAVILWQAQ

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 2 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 3 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 4 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 5 polymer

description	NADH-quinone oxidoreductase subunit A
formula_weight	16474.3 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MSMSTSTEVIAHHWAFAIFLIVAIGLCCLMLVGGWFLGGRARARSKNVPFESGIDSVGSARLRLSAKFYLVAMFFVIFDVEALYLFAWSTSIRESGWVGFVEAAIFIFVLLAGLVYLVRIGALDWTPARSRRERMNPETNSIANRQR

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 6 polymer

description	NADH-quinone oxidoreductase subunit B
formula_weight	25081.8 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MDYTLTRIDPNGENDRYPLQKQEIVTDPLEQEVNKNVFMGKLNDMVNWGRKNSIWPYNFGLSCCYVEMVTSFTAVHDVARFGAEVLRASPRQADLMVVAGTCFTKMAPVIQRLYDQMLEPKWVISMGACANSGGMYDIYSVVQGVDKFIPVDVYIPGCPPRPEAYMQALMLLQESIGKERRPLSWVVGDQGVYRANMQSERERKRGERIAVTNLRTPDEI

Source

organism	Escherichia coli BW25113
ncbi_taxonomy_id	679895
host_organism	Escherichia coli BW25113

Entity 7 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 8 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 9 non-polymer

description	1,2-Distearoyl-sn-glycerophosphoethanolamine
formula_weight	748.1 kDa
src_method	syn
entity_count	16

Entity 10 non-polymer

description	EICOSANE
formula_weight	282.5 kDa
src_method	syn
entity_count	2

Entity 11 non-polymer

description	CARDIOLIPIN
formula_weight	1464.0 kDa
src_method	syn
entity_count	1

Entity 12 non-polymer

description	TRIDECANE
formula_weight	184.4 kDa
src_method	syn
entity_count	3

Entity 13 non-polymer

description	Ubiquinone-8
formula_weight	727.1 kDa
src_method	syn
entity_count	2

Entity 14 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	166

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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	triclinic

resolution	2.80 Å
resolution_method	—
num_particles	70502

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

Local refinement of E. coli Complex I WT 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 (14)

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 polymer

Polymer

Source

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

Entity 14 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)