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9w2z

Cryo-EM structure of complex IV on the bovine heart submitochondrial particles, IV-A

Method: ELECTRON MICROSCOPY D_max: 128.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w2z
deposition_date	2025-07-28
title	Cryo-EM structure of complex IV on the bovine heart submitochondrial particles, IV-A
keywords	respiratory chain complex, supercomplex, submitochondrial particles, MOTOR PROTEIN, OXIDOREDUCTASE; OXIDOREDUCTASE
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	39.78 Å
rg_electron	38.60 Å
i0	577450000.00
molecular_weight	210140.0 kDa
excluded_volume	267980 Å³
envelope_volume	341990 Å³
shell_volume	70927 Å³
envelope_diameter	137.0 Å
shell_rg	46.36 Å
envelope_rg	38.68 Å
shape_rg	38.60 Å
total_rg	39.07 Å
total_atoms	14825
n_residues	1816
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	128.3 Å
rg_real	39.62 Å
rg_real_error	0.89 Å
i0_real	5.7740e+08
i0_real_error	8.8700e+06
rg_reciprocal	39.72 Å
i0_reciprocal	577500000.0000
total_estimate	0.8928
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	48.1 Å
skewness	0.242
kurtosis	-0.433
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	119700000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.909

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4. Crystallography & Experiment

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5. Entities & Polymer Info (23)

Entity 1 polymer

description	Cytochrome c oxidase subunit 1
formula_weight	57093.9 kDa
ec_number	7.1.1.9
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	14825

MFINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQTPLFVWSVMITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMMWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNDTWAKIHFAIMFVGVNMTFFPQHFLGLSGMPRRYSDYPDAYTMWNTISSMGSFISLTAVMLMVFIIWEAFASKREVLTVDLTTTNLEWLNGCPPPYHTFEEPTYVNLK

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 2 polymer

description	Cytochrome c oxidase subunit 2
formula_weight	25909.2 kDa
ec_number	7.1.1.9
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

AYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 3 polymer

description	Cytochrome c oxidase subunit 3
formula_weight	29443.1 kDa
ec_number	7.1.1.9
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

QTHAYHMVNPSPWPLTGALSALLMTSGLTMWFHFNSMTLLMIGLTTNMLTMYQWWRDVIRESTFQGHHTPAVQKGLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIHPLNPLEVPLLNTSVLLASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYYEAPFTISDGVYGSTFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYWHFVDVVWLFLYVSIYWW

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 4 polymer

description	Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
formula_weight	16038.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

YALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVELYRLKFKESFAEMNRSTNEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYDKNEWK

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 5 polymer

description	Cytochrome c oxidase subunit 5A, mitochondrial
formula_weight	11717.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

TDEEFDARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEELGLDK

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 6 polymer

description	Cytochrome c oxidase subunit 5B, mitochondrial
formula_weight	9937.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

GGGVPTDEEQATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTHYKLVP

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 7 polymer

description	Cytochrome c oxidase subunit 6A2, mitochondrial
formula_weight	8368.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

GARTWRFLTFGLALPSVALCTLNSWLHSGHRERPAFIPYHHLRIRTKPFSWGDGNHTFFHNPRVNPLPTGYE

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 8 polymer

description	Cytochrome c oxidase subunit 6B1
formula_weight	9610.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QAKIKNYQTAPFDSRFPNQNQTRNCWQNYLDFHRCEKAMTAKGGDVSVCEWYRRVYKSLCPISWVSTWDDRRAEGTFPGKI

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 9 polymer

description	Cytochrome c oxidase subunit 6C
formula_weight	8177.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

ALAKPQMRGLLARRLRFHIVGAFMVSLGFATFYKFAVAEKRKKAYADFYRNYDSMKDFEEMRKAGIFQSA

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 10 polymer

description	Cytochrome c oxidase subunit 7A1, mitochondrial
formula_weight	6189.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

FENRVAEKQKLFQEDNGLPVHLKGGATDNILYRVTMTLCLGGTLYSLYCLGWASF

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 11 polymer

description	Cytochrome c oxidase subunit 7B, mitochondrial
formula_weight	5442.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

APDFHDKYGNAVLASGATFCVAVWVYMATQIGIEWNPSPVGRVTPKEWR

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 12 polymer

description	Cytochrome c oxidase subunit 7C, mitochondrial
formula_weight	5095.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

YEEGPGKNIPFSVENKWRLLAMMTLFFGSGFAAPFFIVRHQLLK

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 13 polymer

description	Cytochrome c oxidase subunit 8B, mitochondrial
formula_weight	4393.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

ITAKPAKTPTSPKEQAIGLSVTFLSFLLPAGWVLYHLDNY

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 14 polymer

description	Cytochrome c oxidase subunit NDUFA4
formula_weight	9205.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

LRQIIGQAKRHPSLIPLFIFIGAGGTGAALYVTRLALFNPDVSWDRKNNPEPWNKLGPNDQYKFYSVNVDYSKLKKEGPDF

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Bos taurus

Entity 15 non-polymer

description	HEME-A
formula_weight	852.8 kDa
src_method	syn
entity_count	2

Entity 16 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	1

Entity 17 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 18 non-polymer

description	PEROXIDE ION
formula_weight	32.0 kDa
src_method	syn
entity_count	1

Entity 19 non-polymer

description	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
formula_weight	749.0 kDa
src_method	syn
entity_count	2

Entity 20 non-polymer

description	DINUCLEAR COPPER ION
formula_weight	127.1 kDa
src_method	syn
entity_count	1

Entity 21 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 22 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 23 non-polymer

description	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
formula_weight	768.1 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	2.61 Å
resolution_method	—
num_particles	227858

fit	/app/data/saxs_computation/w2/9w2z/9w2z.fit
pddf	/app/data/pr_computation/w2/9w2z/9w2z.pr.out
profile	/app/data/saxs_computation/w2/9w2z/9w2z.dat

Cryo-EM structure of complex IV on the bovine heart submitochondrial particles, IV-A

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (23)

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

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)