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1ezv

STRUCTURE OF THE YEAST CYTOCHROME BC1 COMPLEX CO-CRYSTALLIZED WITH AN ANTIBODY FV-FRAGMENT

Method: X-RAY DIFFRACTION D_max: 189.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ezv
deposition_date	2000-05-12
title	STRUCTURE OF THE YEAST CYTOCHROME BC1 COMPLEX CO-CRYSTALLIZED WITH AN ANTIBODY FV-FRAGMENT
keywords	;cytochrome bc1 complex, complex III, QCR, mitochondria, yeast, antibody Fv-fragment, stigmatellin, coenzyme Q6, matrix processing peptidases, ubiquinone, electron transfer, proton transfer, Q-cycle, OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX ;; OXIDOREDUCTASE/ELECTRON TRANSPORT
method	X-RAY DIFFRACTION

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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	55.12 Å
rg_electron	54.74 Å
i0	814823000.00
molecular_weight	246850.0 kDa
excluded_volume	312200 Å³
envelope_volume	467500 Å³
shell_volume	74033 Å³
envelope_diameter	187.1 Å
shell_rg	54.43 Å
envelope_rg	53.89 Å
shape_rg	54.73 Å
total_rg	54.76 Å
total_atoms	17435
n_residues	2178
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	189.0 Å
rg_real	55.28 Å
rg_real_error	2.60 Å
i0_real	8.1480e+08
i0_real_error	1.8060e+07
rg_reciprocal	54.94 Å
i0_reciprocal	814400000.0000
total_estimate	0.8635
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	45.6 Å
skewness	0.274
kurtosis	-0.790
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	61500000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.928; Smooth: 0.857

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4. Crystallography & Experiment

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5. Entities & Polymer Info (17)

Entity 1 polymer

description	UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I
formula_weight	47358.2 kDa
ec_number	1.10.2.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	17781

AEVTQLSNGIVVATEHNPAHTASVGVVFGSGAANENPYNNGVSNLWKNIFLSKENSAVAAKEGLALSSNISRDFQSYIVSSLPGSTDKSLDFLNQSFIQQKANLLSSSNFEATKKSVLKQVQDFEDNDHPNRVLEHLHSTAFQNTPLSLPTRGTLESLENLVVADLESFANNHFLNSNAVVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKKKAAFLGSEVRLRDDTLPKAWISLAVEGEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGIKLLDNIQEYQLCDNFNHFSLSYKDSGLWGFSTATRNVTMIDDLIHFTLKQWNRLTISVTDTEVERAKSLLKLQLGQLYESGNPVNDANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRLWDQDIAIAGTGQIEGLLDYMRIRSDMSMMRW

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932

Entity 2 polymer

description	UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2
formula_weight	38751.9 kDa
ec_number	1.10.2.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

LTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGGTFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQCPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVYTKENLEVSGENVVEADLKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVLANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKKGKDLSPAINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVSNLPYLDEL

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932

Entity 3 polymer

description	CYTOCHROME B
formula_weight	43674.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIELAFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVIIFTLTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFFALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLILALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAILVLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYFAYFLIIVPVISTIENVLFYIGRVNK

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932

Entity 4 polymer

description	CYTOCHROME C1
formula_weight	27423.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSHTNEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIVKARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGTPATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFVFNPPK

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932

Entity 5 polymer

description	UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
formula_weight	20123.0 kDa
ec_number	1.10.2.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

KSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLAMAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDPQWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGDKVIVG

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932

Entity 6 polymer

description	UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN
formula_weight	8854.8 kDa
ec_number	1.10.2.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

VTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHKEDCVEEFFHLQHYLDTATAPRLFDKLK

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932

Entity 7 polymer

description	UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN
formula_weight	14355.4 kDa
ec_number	1.10.2.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

QSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTALRRLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDELDNIEVSK

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932

Entity 8 polymer

description	UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C
formula_weight	10856.3 kDa
ec_number	1.10.2.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

GPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVLIPAGIYWYWWKNGNEYNEFLYSKAGREELERVNV

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932

Entity 9 polymer

description	UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN
formula_weight	6301.2 kDa
ec_number	1.10.2.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

SSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAA

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932

Entity 10 polymer

description	HEAVY CHAIN (VH) OF FV-FRAGMENT
formula_weight	14365.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	X

EVKLQESGAGLVQPSQSLSLTCSVTGYSITSGYYWNWIRLFPGNKLEWVGYISNVGDNNYNPSLKDRLSITRDTSKNQFFLKLNSVTTEDTATYYCARSEYYSVTGYAMDYWGQGTTVTVSSAWRHP

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 11 polymer

description	LIGHT CHAIN (VL) OF FV-FRAGMENT
formula_weight	11926.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Y

DIELTQTPVSLAASLGDRVTISCRASQDINNFLNWYQQKPDGTIKLLIYYTSRLHAGVPSRFSGSGSGTDYSLTISNLEPEDIATYFCQHHIKFPWTFGAGTKLEIK

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 12 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	2

Entity 13 non-polymer

description	STIGMATELLIN A
formula_weight	514.6 kDa
src_method	syn
entity_count	1

Entity 14 non-polymer

description	5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
formula_weight	592.9 kDa
src_method	syn
entity_count	1

Entity 15 non-polymer

description	HEME C
formula_weight	618.5 kDa
src_method	syn
entity_count	1

Entity 16 non-polymer

description	FE2/S2 (INORGANIC) CLUSTER
formula_weight	175.8 kDa
src_method	syn
entity_count	1

Entity 17 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	346

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6. Citations (1)

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length_a	214.470 Å
length_b	163.920 Å
length_c	147.270 Å
angle_alpha	90.00 °
angle_beta	117.50 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.300 Å
resolution_low	15.000 Å
r_factor	0.2530
r_work	0.2220
r_free	0.2540

fit	/app/data/saxs_computation/ez/1ezv/1ezv.fit
pddf	/app/data/pr_computation/ez/1ezv/1ezv.pr.out
profile	/app/data/saxs_computation/ez/1ezv/1ezv.dat

STRUCTURE OF THE YEAST CYTOCHROME BC1 COMPLEX CO-CRYSTALLIZED WITH AN ANTIBODY FV-FRAGMENT

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 (17)

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 non-polymer

Entity 13 non-polymer

Entity 14 non-polymer

Entity 15 non-polymer

Entity 16 non-polymer

Entity 17 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)