← Back to search

9qef

Respiratory supercomplex from Mycobacterium smegmatis with decylubiquinone

Method: ELECTRON MICROSCOPY D_max: 256.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qef
deposition_date	2025-03-09
title	Respiratory supercomplex from Mycobacterium smegmatis with decylubiquinone
keywords	RESPIRATORY SUPERCOMPLEX, MEMBRANE PROTEIN, ACTINOBACTERIA, ELECTRON TRANSPORT; ELECTRON TRANSPORT
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	65.77 Å
rg_electron	65.51 Å
i0	5386150000.00
molecular_weight	688260.0 kDa
excluded_volume	887160 Å³
envelope_volume	1139900 Å³
shell_volume	143920 Å³
envelope_diameter	220.8 Å
shell_rg	65.03 Å
envelope_rg	65.28 Å
shape_rg	65.57 Å
total_rg	65.26 Å
total_atoms	48551
n_residues	5797
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

▼

3. P(r) Analysis (GNOM)

dmax	256.4 Å
rg_real	70.91 Å
rg_real_error	2.02 Å
i0_real	5.4560e+09
i0_real_error	1.1110e+08
rg_reciprocal	65.36 Å
i0_reciprocal	5378000000.0000
total_estimate	0.8440
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.1 Å
skewness	0.661
kurtosis	0.033
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.9998
highest_alpha	474600000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.592; Stabil: 0.832; Sysdev: 1.000; Positv: 1.000; Valcen: 0.904; Smooth: 0.835

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (33)

Entity 1 polymer

description	Cytochrome bc1 complex cytochrome c subunit
formula_weight	29109.9 kDa
ec_number	7.1.1.8
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	O,C
atom_count	49157

MHHHHHHMGSMTSKSRRRLRRRLSAGLLLLIGLAVAGGVAATLTPQPQVAVADESQSALLRTGKQLFETSCVSCHGANLQGVPDRGPSLIGTGEAAVYFQVSTGRMPAMRGEAQAPSKPPHFDESQIDALGAYVQANGGGPTVPRDDHGAVAQESLIGGDVARGGDLFRLNCASCHNFTGKGGALSSGKYAPDLGDANPAQIYTAMLTGPQNMPKFSDRQLTPDEKRDIVAYVRESAETPSYGGYGLGGFGPAPEGMAMWIIGMVAAIGVAMWIGSRA

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 2 polymer

description	Cytochrome bc1 complex cytochrome c subunit
formula_weight	44869.4 kDa
ec_number	7.1.1.8
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	M,G

MDRIASMSQDSPDIKGTDAPGQTGVPGQPTDAELAEMSREELVKLGGKIDGVETIFKEPRWPVPGTKAEKRTERLVAYWLMLGGLSGLALLLVFLFWPWEYQPFGSEGEFLYSLATPLYGLTFGLSILSIGIGAVLFQKKFIPEEISVQDRHDGRSPEVHRKTVAANLTDALEGSTLKRRKVIGLSLGIGLGAFGAGTLVAFIGGLIKNPWKPVVPTAEGKKAVLWTSGWTPRFKGETIYLARATGRPGESPFVKMRPEDIDAGGMETVFPWRESDGDGTTVESEHKLTEIAMGVRNPVMLIRIKPADMHRVIKRKGQESFNFGELFAYTKVCSHLGCPSSLYEQQTYRILCPCHQSQFDALEFAKPIFGPAARALAQLPITIDEDGYLVANGDFVEPVGPAFWERKS

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 3 polymer

description	Cytochrome bc1 complex cytochrome b subunit
formula_weight	61514.3 kDa
ec_number	7.1.1.8
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	N,H

MSPDFAKLAAAQGDAIDSRYHPSAAVRRQLNKVFPTHWSFLLGEIALYSFIILLLTGVWLTLFFDPSMAHVTYDGVYQPLRGVQMSRAYETALDISFEVRGGLFVRQVHHWAALMFAASIMVHLARIFFTGAFRRPREANWVIGSLLLILAMFEGFFGYSLPDDLLSGTGIRAALSGITMGIPVIGTWMHWALFGGDFPGEILIPRLYALHILLIPGIILALIGAHLALVWFQKHTQFPGPGRTETNVVGVRVMPVFAVKSGAFFAMITGVLGLMGGLLTINPIWNLGPYKPSQVSAGSQPDFYMMWTDGLIRLWPAWEFYPFGHTIPQGVWVAVGMGLVFALLIAYPFIEKKVTGDDAHHNLLQRPRDVPVRTAIGSMAIALYLLLTFACMNDIIALKFHISLNATTWIGRIGMVVLPAIVYFVAYRWAISLQRSDREVLEHGVETGIIKRLPHGAYVELHQPLGPVDEHGHPIPLEYAGAPLPKRMNKLGSGGAPGTGSFLFPDPAVEHEALTEAAHASEHKSLTALKEHQDRIHGNGETNGHHKLDYKDDDDK

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 4 polymer

description	Transmembrane protein
formula_weight	11329.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	P,I

MSSTQDRSQLDPEEQPVANTEVERHTGVDVEDVPSAEWGWSHMPIGVMHIGGLLSAAFLLVMMRGNHVGHVEDWFLIGFAAVIVALVGRNWWLRRRGWIR

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 5 polymer

description	Probable cytochrome c oxidase subunit 3
formula_weight	22196.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	S,J

MTSAVGTSGTAITSRVHSLNRPNMVSVGTIVWLSSELMFFAGLFAMYFTARAQAGGAWPPEPTELNLALAVPVTLVLIASSFTCQMGVFAAERGDVFGLRRWYVITFLMGLFFVLGQGYEYIHLVEHGTTIPGSAYGSVFYLATGFHGLHVIGGLVAFVLLLARTKMSKFTPAQATAAIVVSYYWHFVDIVWIALFATIYFVR

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 6 polymer

description	Cytochrome c oxidase polypeptide 4
formula_weight	15177.4 kDa
ec_number	7.1.1.9
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	T,K

MHIEARLFEILTAFFALAAVVYAVLTAMFATGGVEWAGTTALVLTTGLTLITGTFFRFVARRLDTRPEDYEDAEISDGAGELGFFAPHSWWPILISLSFSTAAVGAALWLPWLIAAGVAFVITSVCGLVFEYYWGPEKH

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 7 polymer

description	Cytochrome c oxidase subunit 1
formula_weight	64163.0 kDa
ec_number	7.1.1.9
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	R,L

MVAEAPPIGELEARRPFPERMGPKGNLIYKLITTTDHKLIGIMYCVVCFAFFLVGGLMALFMRTELAMPGLQFLSNEQFNQLFTMHGTVMLLFYATPIVFGFANLVLPLQIGAPDVAFPRLNALSFWLFLFGALIAIAGFITPGGAADFGWTAYSPLTDAIHSPGAGGDLWIMGLAVGGLGTILGGVNMITTVVCMRAPGMTMFRMPIFTWNILVTSILVLIAFPILTAALFGLAADRHLGAHIYDPANGGVLLWQHLFWFFGHPEVYIIALPFFGIVSEIFPVFSRKPIFGYTTLIYATLAIAALSVAVWAHHMYATGAVLLPFFSFMTFLIAVPTGIKFFNWIGTMWKGQLTFETPMLFSVGFLITFLLGGLSGVLLASPPLDFHVTDSYFVIAHFHYVLFGTIVFATYAGIYFWFPKMTGRLLDERLGKLHFWLTFIGFHTTFLVQHWLGDEGMPRRYADYLPTDGFTTLNVISTVGAFILGVSMLPFVWNVFKSWRYGEPVTVDDPWGYGNSLEWATSCPPPRHNFTELPRIRSERPAFELHYPHMVERMRAEAHVGRAHHPELETADKSS

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 8 polymer

description	cytochrome-c oxidase
formula_weight	38077.5 kDa
ec_number	7.1.1.9
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	Q,X

MTPRGFRVVALSIVLGGSALLLSGCSWSDALALGWPTGITPEAKLNRELWIGSVIASFAVGAIVWGLIFWTSAFHRKKATDTELPRQFGYNMPLELTLTVIPFLIISVLFYFTVVVQERMMHKDPNPEVVIDVTAFQWNWKFGYQKIAFADGSFDYDGADPERKEAMTSRPEGKDEHGIEKVGPIRGMTPEDRTYLNFDKIETLGTSSEIPVLVLPAGKRIEFVLNSADVIHGFWVPEFLFKRDVLPEPKANNSDNVFQVSEIQQTGAFVGRCTEMCGTFHAMMNFEVRVVEPNDFKAYIDQRNAGKTNAEALAAINQPPLAITTEPFESRRGELVPQASK

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 9 polymer

description	Cytochrome c oxidase subunit
formula_weight	8365.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	U,Z

MSTALTHGLIGGVPLVLFAVLALIFLTRKGPHPDTYKMSDPWTHAPILWAAEEPREHGHGGHGHDSHGVVIGGGASGKW

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 10 polymer

description	Uncharacterized protein MSMEG_4692/MSMEI_4575
formula_weight	15911.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	V,a

MASGDIATVANAELDLPYGSALTSSGRISAVTEPGELSVHYPFPTMDLVVLDDALKYGSRAAKARFAVYIGPLGADTAATAREILANVPTPENAVLLAVSPDQRAIEVVYGADVKGRGIESAAPLGVSAAAASFKEGNLIDGLISAVRVMSAGVSPA

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 11 polymer

description	LpqE protein
formula_weight	19119.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	W,b

MNRFSSRAGLAVCGLATAVALTACSAGQISQTTTQEPAVNGVNAQAGQVSLRNVHLRAPQQTDYVEPGTTVELLFVAANDSTEGSNKLKSITSDVGEVTLTGDSTVPADGVLIVGEPDGQIQAVENAEAADAVTAEVELTKPITNGLLYDFTFTFEDGETTVAVPISAGEQPRRPVPPAGPGSSEH

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 12 polymer

description	Superoxide dismutase [Cu-Zn]
formula_weight	23232.4 kDa
ec_number	1.15.1.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	Y,c

MLKPVSVAVLFATPVLALSACSPPGETASSEPGTTPAIWTGSPSPAAPSGEDHGGGHGAGAAGAGETLTAELKTADGTSVATADFQFADGFATVTIETTTPGRLTPGFHGVHIHSVGKCEANSVAPTGGAPGDFNSAGGHFQVSGHSGHPASGDLSSLQVRADGSGKLVTTTDAFTAEDLLDGAKTAIIIHEKADNFANIPPERYQQVNGAPGPDQTTMATGDAGSRVACGVISAG

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 13 polymer

description	Co-purified transmembrane protein
formula_weight	13027.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,A

MRHRLERTAVPYVSYVLVLVGFVAFGALVASLAYGSHIPAGIAGAVLAGSLTGAVIGFRAAARRLRADRGDAHNVSIFDTPLEPEMVDRYARRYRATGTDAEESAVAVLPAAETAAARERRAA

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 14 polymer

description	Co-purified peptide
formula_weight	7075.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,B

MWGVADKKKKQYVDNGWPTLSGDDDHAVTELASDRTGALSPFGDVVFPLPAEQLPFLPAVTVVNR

Source

organism	Mycolicibacterium smegmatis
ncbi_taxonomy_id	1772
host_organism	Mycolicibacterium smegmatis

Entity 15 non-polymer

description	HEME C
formula_weight	618.5 kDa
src_method	syn
entity_count	4

Entity 16 non-polymer

description	MENAQUINONE-9
formula_weight	785.2 kDa
src_method	syn
entity_count	7

Entity 17 non-polymer

description	acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2)
formula_weight	1415.8 kDa
src_method	syn
entity_count	4

Entity 18 non-polymer

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

Entity 19 non-polymer

description	;[(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{R})-10-methyldodecanoate ;
formula_weight	1677.8 kDa
src_method	syn
entity_count	2

Entity 20 non-polymer

description	;(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate ;
formula_weight	853.1 kDa
src_method	syn
entity_count	4

Entity 21 non-polymer

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

Entity 22 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	4

Entity 23 non-polymer

description	CARDIOLIPIN
formula_weight	1464.0 kDa
src_method	syn
entity_count	17

Entity 24 non-polymer

description	PALMITIC ACID
formula_weight	256.4 kDa
src_method	syn
entity_count	4

Entity 25 non-polymer

description	(2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
formula_weight	595.0 kDa
src_method	syn
entity_count	4

Entity 26 non-polymer

description	TRIDECANE
formula_weight	184.4 kDa
src_method	syn
entity_count	10

Entity 27 non-polymer

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

Entity 28 non-polymer

description	HEME-A
formula_weight	852.8 kDa
src_method	syn
entity_count	4

Entity 29 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	6

Entity 30 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 31 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 32 non-polymer

description	2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
formula_weight	322.4 kDa
src_method	syn
entity_count	1

Entity 33 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	606

▶

6. Citations (1)

▶

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	2.50 Å
resolution_method	—
num_particles	79

fit	/app/data/saxs_computation/qe/9qef/9qef.fit
pddf	/app/data/pr_computation/qe/9qef/9qef.pr.out
profile	/app/data/saxs_computation/qe/9qef/9qef.dat

Respiratory supercomplex from Mycobacterium smegmatis with decylubiquinone

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 (33)

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 polymer

Polymer

Source

Entity 15 non-polymer

Entity 16 non-polymer

Entity 17 non-polymer

Entity 18 non-polymer

Entity 19 non-polymer

Entity 20 non-polymer

Entity 21 non-polymer

Entity 22 non-polymer

Entity 23 non-polymer

Entity 24 non-polymer

Entity 25 non-polymer

Entity 26 non-polymer

Entity 27 non-polymer

Entity 28 non-polymer

Entity 29 non-polymer

Entity 30 non-polymer

Entity 31 non-polymer

Entity 32 non-polymer

Entity 33 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)