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9q8i

Cryo-EM structure of E. coli complex I variant V96P/N142M (NuoE)

Method: ELECTRON MICROSCOPY D_max: 220.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q8i
deposition_date	2025-02-24
title	Cryo-EM structure of E. coli complex I variant V96P/N142M (NuoE)
keywords	Respiratory chain, Complex I, NADH ubiquinone oxidoreductase, electron transport, proton transport, 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	77.16 Å
rg_electron	78.84 Å
i0	3601260000.00
molecular_weight	534920.0 kDa
excluded_volume	679360 Å³
envelope_volume	939490 Å³
shell_volume	106140 Å³
envelope_diameter	275.5 Å
shell_rg	67.13 Å
envelope_rg	77.86 Å
shape_rg	78.86 Å
total_rg	78.62 Å
total_atoms	37532
n_residues	4746
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	220.0 Å
rg_real	75.27 Å
rg_real_error	1.38 Å
i0_real	3.5440e+09
i0_real_error	6.6800e+07
rg_reciprocal	73.74 Å
i0_reciprocal	3569000000.0000
total_estimate	0.7888
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	55.0 Å
skewness	0.442
kurtosis	-0.780
angular_range	— – 0.1000 Å⁻¹
current_alpha	0.0707
highest_alpha	83800000.0000
n_real_points	21
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 0.981; Sysdev: 1.000; Positv: 1.000; Valcen: 0.844; Smooth: 0.015

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4. Crystallography & Experiment

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5. Entities & Polymer Info (20)

Entity 1 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
atom_count	37648

MSMSTSTEVIAHHWAFAIFLIVAIGLCCLMLVGGWFLGGRARARSKNVPFESGIDSVGSARLRLSAKFYLVAMFFVIFDVEALYLFAWSTSIRESGWVGFVEAAIFIFVLLAGLVYLVRIGALDWTPARSRRERMNPETNSIANRQR

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BW25113

Entity 2 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
ncbi_taxonomy_id	562
host_organism	Escherichia coli BW25113

Entity 3 polymer

description	NADH-quinone oxidoreductase subunit C/D
formula_weight	68321.9 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MTDLTAQEPAWQTRDHLDDPVIGELRNRFGPDAFTVQATRTGVPVVWIKREQLLEVGDFLKKLPKPYVMLFDLHGMDERLRTHREGLPAADFSVFYHLISIDRNRDIMLKVALAENDLHVPTFTKLFPNANWYERETWDLFGITFDGHPNLRRIMMPQTWKGHPLRKDYPARATEFSPFELTKAKQDLEMEALTFKPEEWGMKRGTENEDFMFLNLGPNHPSAHGAFRIVLQLDGEEIVDCVPDIGYHHRGAEKMGERQSWHSYIPYTDRIEYLGGCVNEMPYVLAVEKLAGITVPDRVNVIRVMLSELFRINSHLLYISTFIQDVGAMTPVFFAFTDRQKIYDLVEAITGFRMHPAWFRIGGVAHDLPRGWDRLLREFLDWMPKRLASYEKAALQNTILKGRSQGVAAYGAKEALEWGTTGAGLRATGIDFDVRKARPYSGYENFDFEIPVGGGVSDCYTRVMLKVEELRQSLRILEQCLNNMPEGPFKADHPLTTPPPKERTLQHIETLITHFLQVSWGPVMPANESFQMIEATKGINSYYLTSDGSTMSYRTRVRTPSFAHLQQIPAAIRGSLVSDLIVYLGSIDFVMSDVDR

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BW25113

Entity 4 polymer

description	NADH-quinone oxidoreductase subunit E
formula_weight	18629.1 kDa
ec_number	7.1.1.-
mutation	V96P, N142M
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MHENQQPQTEAFELSAAEREAIEHEMHHYEDPRAASIEALKIVQKQRGWVPDGAIHAIADVLGIPASDVEGVATFYSQIFRQPVGRHVIRYCDSVPCHINGYQGIQAALEKKLNIKPGQTTFDGRFTLLPTCCLGNCDKGPMMMIDEDTHAHLTPEAIPELLERYK

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BW25113

Entity 5 polymer

description	NADH-quinone oxidoreductase subunit F
formula_weight	51208.4 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MRGSHHHHHHTDPALRAKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLKGRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNIMGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSKPPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNISKSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFLTEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDGLPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFEAGIKQPFSNTHLINGIQPNLLKERW

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BW25113

Entity 6 polymer

description	NADH-quinone oxidoreductase subunit G
formula_weight	100419.2 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MATIHVDGKEYEVNGADNLLEACLSLGLDIPYFCWHPALGSVGACRQCAVKQYQNAEDTRGRLVMSCMTPASDGTFISIDDEEAKQFRESVVEWLMTNHPHDCPVCEEGGNCHLQDMTVMTGHSFRRYRFTKRTHRNQDLGPFISHEMNRCIACYRCVRYYKDYADGTDLGVYGAHDNVYFGRPEDGTLESEFSGNLVEICPTGVFTDKTHSERYNRKWDMQFAPSICQQCSIGCNISPGERYGELRRIENRYNGTVNHYFLCDRGRFGYGYVNLKDRPRQPVQRRGDDFITLNAEQAMQGAADILRQSKKVIGIGSPRASVESNFALRELVGEENFYTGIAHGEQERLQLALKVLREGGIYTPALREIESYDAVLVLGEDVTQTGARVALAVRQAVKGKAREMAAAQKVADWQIAAILNIGQRAKHPLFVTNVDDTRLDDIAAWTYRAPVEDQARLGFAIAHALDNSAPAVDGIEPELQSKIDVIVQALAGAKKPLIISGTNAGSLEVIQAAANVAKALKGRGADVGITMIARSVNSMGLGIMGGGSLEEALTELETGRADAVVVLENDLHRHASAIRVNAALAKAPLVMVVDHQRTAIMENAHLVLSAASFAESDGTVINNEGRAQRFFQVYDPAYYDSKTVMLESWRWLHSLHSTLLSREVDWTQLDHVIDAVVAKIPELAGIKDAAPDATFRIRGQKLAREPHRYSGRTAMRANISVHEPRQPQDIDTMFTFSMEGNNQPTAHRSQVPFAWAPGWNSPQAWNKFQDEVGGKLRFGDPGVRLFETSENGLDYFTSVPARFQPQDGKWRIAPYYHLFGSDELSQRAPVFQSRMPQPYIKLNPADAAKLGVNAGTRVSFSYDGNTVTLPVEIAEGLTAGQVGLPMGMSGIAPVLAGAHLEDLKEAQQ

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BW25113

Entity 7 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

MSWISPELIEILLTILKAVVILLVVVTCGAFMSFGERRLLGLFQNRYGPNRVGWGGSLQLVADMIKMFFKEDWIPKFSDRVIFTLAPMIAFTSLLLAFAIVPVSPGWVVADLNIGILFFLMMAGLAVYAVLFAGWSSNNKYSLLGAMRASAQTLSYEVFLGLSLMGVVAQAGSFNMTDIVNSQAHVWNVIPQFFGFITFAIAGVAVCHRHPFDQPEAEQELADGYHIEYSGMKFGLFFVGEYIGIVTISALMVTLFFGGWQGPLLPPFIWFALKTAFFMMMFILIRASLPRPRYDQVMSFGWKICLPLTLINLLVTAAVILWQAQ

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BW25113

Entity 8 polymer

description	NADH-quinone oxidoreductase subunit I
formula_weight	20562.8 kDa
ec_number	7.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MTLKELLVGFGTQVRSIWMIGLHAFAKRETRMYPEEPVYLPPRYRGRIVLTRDPDGEERCVACNLCAVACPVGCISLQKAETKDGRWYPEFFRINFSRCIFCGLCEEACPTTAIQLTPDFEMGEYKRQDLVYEKEDLLISGPGKYPEYNFYRMAGMAIDGKDKGEAENEAKPIDVKSLLP

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BW25113

Entity 9 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
ncbi_taxonomy_id	562
host_organism	Escherichia coli BW25113

Entity 10 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
ncbi_taxonomy_id	562
host_organism	Escherichia coli BW25113

Entity 11 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
ncbi_taxonomy_id	562
host_organism	Escherichia coli BW25113

Entity 12 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
ncbi_taxonomy_id	562
host_organism	Escherichia coli BW25113

Entity 13 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
ncbi_taxonomy_id	562
host_organism	Escherichia coli BW25113

Entity 14 non-polymer

description	1,2-Distearoyl-sn-glycerophosphoethanolamine
formula_weight	748.1 kDa
src_method	syn
entity_count	10

Entity 15 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	7

Entity 16 non-polymer

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

Entity 17 non-polymer

description	FLAVIN MONONUCLEOTIDE
formula_weight	456.3 kDa
src_method	syn
entity_count	1

Entity 18 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 19 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 20 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	116

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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	2.350 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

fit	/app/data/saxs_computation/q8/9q8i/9q8i.fit
pddf	/app/data/pr_computation/q8/9q8i/9q8i.pr.out
profile	/app/data/saxs_computation/q8/9q8i/9q8i.dat

Cryo-EM structure of E. coli complex I variant V96P/N142M (NuoE)

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

5. Entities & Polymer Info (20)

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 polymer

Polymer

Source

Entity 10 polymer

Polymer

Source

Entity 11 polymer

Polymer

Source

Entity 12 polymer

Polymer

Source

Entity 13 polymer

Polymer

Source

Entity 14 non-polymer

Entity 15 non-polymer

Entity 16 non-polymer

Entity 17 non-polymer

Entity 18 non-polymer

Entity 19 non-polymer

Entity 20 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)