2ibz

Yeast Cytochrome BC1 Complex with Stigmatellin

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquinol-cytochrome-c reductase complex core protein 1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Ubiquinol-cytochrome-c reductase complex core protein 2 × 1 （P07257） Cytochrome b × 1 （P00163） Cytochrome c1, heme protein, mitochondrial precursor × 1 （P07143） Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor × 1 （P08067） Ubiquinol-cytochrome c reductase complex 17 kDa protein × 1 （P00127） Ubiquinol-cytochrome c reductase complex 14 kDa protein × 1 （P00128） Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C × 1 （P08525） Ubiquinol-cytochrome c reductase complex 7.3 kDa protein × 1 （P22289） Variable Heavy chain of antibody fragment × 1 Variable Light chain of antibody fragment × 1 HEME C × 3 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 × 1 STIGMATELLIN A × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UQCR1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–431； UniProt 27–457

Ubiquinol-cytochrome-c reductase complex core protein 2

OrganismNot specified

UniProt P07257

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Ubiquinol-cytochrome-c reductase complex core protein 1 × 1 （P07256） Cytochrome b × 1 （P00163） Cytochrome c1, heme protein, mitochondrial precursor × 1 （P07143） Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor × 1 （P08067） Ubiquinol-cytochrome c reductase complex 17 kDa protein × 1 （P00127） Ubiquinol-cytochrome c reductase complex 14 kDa protein × 1 （P00128） Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C × 1 （P08525） Ubiquinol-cytochrome c reductase complex 7.3 kDa protein × 1 （P22289） Variable Heavy chain of antibody fragment × 1 Variable Light chain of antibody fragment × 1 HEME C × 3 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 × 1 STIGMATELLIN A × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UQCR2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–352； UniProt 17–368

Cytochrome b

OrganismNot specified

UniProt P00163

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Ubiquinol-cytochrome-c reductase complex core protein 1 × 1 （P07256） Ubiquinol-cytochrome-c reductase complex core protein 2 × 1 （P07257） Cytochrome c1, heme protein, mitochondrial precursor × 1 （P07143） Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor × 1 （P08067） Ubiquinol-cytochrome c reductase complex 17 kDa protein × 1 （P00127） Ubiquinol-cytochrome c reductase complex 14 kDa protein × 1 （P00128） Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C × 1 （P08525） Ubiquinol-cytochrome c reductase complex 7.3 kDa protein × 1 （P22289） Variable Heavy chain of antibody fragment × 1 Variable Light chain of antibody fragment × 1 HEME C × 3 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 × 1 STIGMATELLIN A × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYB_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–385； UniProt 1–385

Cytochrome c1, heme protein, mitochondrial precursor

OrganismNot specified

UniProt P07143

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Ubiquinol-cytochrome-c reductase complex core protein 1 × 1 （P07256） Ubiquinol-cytochrome-c reductase complex core protein 2 × 1 （P07257） Cytochrome b × 1 （P00163） Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor × 1 （P08067） Ubiquinol-cytochrome c reductase complex 17 kDa protein × 1 （P00127） Ubiquinol-cytochrome c reductase complex 14 kDa protein × 1 （P00128） Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C × 1 （P08525） Ubiquinol-cytochrome c reductase complex 7.3 kDa protein × 1 （P22289） Variable Heavy chain of antibody fragment × 1 Variable Light chain of antibody fragment × 1 HEME C × 3 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 × 1 STIGMATELLIN A × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CY1_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–248； UniProt 62–309

Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor

OrganismNot specified

UniProt P08067

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Ubiquinol-cytochrome-c reductase complex core protein 1 × 1 （P07256） Ubiquinol-cytochrome-c reductase complex core protein 2 × 1 （P07257） Cytochrome b × 1 （P00163） Cytochrome c1, heme protein, mitochondrial precursor × 1 （P07143） Ubiquinol-cytochrome c reductase complex 17 kDa protein × 1 （P00127） Ubiquinol-cytochrome c reductase complex 14 kDa protein × 1 （P00128） Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C × 1 （P08525） Ubiquinol-cytochrome c reductase complex 7.3 kDa protein × 1 （P22289） Variable Heavy chain of antibody fragment × 1 Variable Light chain of antibody fragment × 1 HEME C × 3 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 × 1 STIGMATELLIN A × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UCRI_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–185； UniProt 31–215

Ubiquinol-cytochrome c reductase complex 17 kDa protein

OrganismNot specified

UniProt P00127

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Ubiquinol-cytochrome-c reductase complex core protein 1 × 1 （P07256） Ubiquinol-cytochrome-c reductase complex core protein 2 × 1 （P07257） Cytochrome b × 1 （P00163） Cytochrome c1, heme protein, mitochondrial precursor × 1 （P07143） Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor × 1 （P08067） Ubiquinol-cytochrome c reductase complex 14 kDa protein × 1 （P00128） Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C × 1 （P08525） Ubiquinol-cytochrome c reductase complex 7.3 kDa protein × 1 （P22289） Variable Heavy chain of antibody fragment × 1 Variable Light chain of antibody fragment × 1 HEME C × 3 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 × 1 STIGMATELLIN A × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UCRH_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain H； PDBConstruct 1–74； UniProt 74–147

Ubiquinol-cytochrome c reductase complex 14 kDa protein

OrganismNot specified

UniProt P00128

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Ubiquinol-cytochrome-c reductase complex core protein 1 × 1 （P07256） Ubiquinol-cytochrome-c reductase complex core protein 2 × 1 （P07257） Cytochrome b × 1 （P00163） Cytochrome c1, heme protein, mitochondrial precursor × 1 （P07143） Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor × 1 （P08067） Ubiquinol-cytochrome c reductase complex 17 kDa protein × 1 （P00127） Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C × 1 （P08525） Ubiquinol-cytochrome c reductase complex 7.3 kDa protein × 1 （P22289） Variable Heavy chain of antibody fragment × 1 Variable Light chain of antibody fragment × 1 HEME C × 3 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 × 1 STIGMATELLIN A × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UCR7_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain F； PDBConstruct 1–127； UniProt 1–127

Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C

OrganismNot specified

UniProt P08525

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Ubiquinol-cytochrome-c reductase complex core protein 1 × 1 （P07256） Ubiquinol-cytochrome-c reductase complex core protein 2 × 1 （P07257） Cytochrome b × 1 （P00163） Cytochrome c1, heme protein, mitochondrial precursor × 1 （P07143） Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor × 1 （P08067） Ubiquinol-cytochrome c reductase complex 17 kDa protein × 1 （P00127） Ubiquinol-cytochrome c reductase complex 14 kDa protein × 1 （P00128） Ubiquinol-cytochrome c reductase complex 7.3 kDa protein × 1 （P22289） Variable Heavy chain of antibody fragment × 1 Variable Light chain of antibody fragment × 1 HEME C × 3 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 × 1 STIGMATELLIN A × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UCRQ_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain G； PDBConstruct 1–94； UniProt 1–94

Ubiquinol-cytochrome c reductase complex 7.3 kDa protein

OrganismNot specified

UniProt P22289

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Ubiquinol-cytochrome-c reductase complex core protein 1 × 1 （P07256） Ubiquinol-cytochrome-c reductase complex core protein 2 × 1 （P07257） Cytochrome b × 1 （P00163） Cytochrome c1, heme protein, mitochondrial precursor × 1 （P07143） Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor × 1 （P08067） Ubiquinol-cytochrome c reductase complex 17 kDa protein × 1 （P00127） Ubiquinol-cytochrome c reductase complex 14 kDa protein × 1 （P00128） Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C × 1 （P08525） Variable Heavy chain of antibody fragment × 1 Variable Light chain of antibody fragment × 1 HEME C × 3 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 × 1 STIGMATELLIN A × 1 FE2/S2 (INORGANIC) CLUSTER × 1 water × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UCR9_YEAST
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain I； PDBConstruct 1–66； UniProt 0–65

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ibz
Deposition date deposition_date	2006-09-12
Structure title title	Yeast Cytochrome BC1 Complex with Stigmatellin
Keywords keywords	multisubunit membrane protein complex, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2ibz__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ibz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ibz__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	55.13 Å
Rg (electron density)	54.75 Å
Total Rg	54.77 Å
Atom count	17439
Residues	2179
Excluded volume	312290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ibz__assembly_1__model_1`	undecameric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (16)

Entity 1 Entity 1 polymer

Description description	Ubiquinol-cytochrome-c reductase complex core protein 1
Molecular weight formula_weight	47445.2 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	17779

AEVTQLSNGIVVATEHNPSAHTASVGVVFGSGAANENPYNNGVSNLWKNIFLSKENSAVAAKEGLALSSNISRDFQSYIVSSLPGSTDKSLDFLNQSFIQQKANLLSSSNFEATKKSVLKQVQDFEDNDHPNRVLEHLHSTAFQNTPLSLPTRGTLESLENLVVADLESFANNHFLNSNAVVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKKKAAFLGSEVRLRDDTLPKAWISLAVEGEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGIKLLDNIQEYQLCDNFNHFSLSYKDSGLWGFSTATRNVTMIDDLIHFTLKQWNRLTISVTDTEVERAKSLLKLQLGQLYESGNPVNDANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRLWDQDIAIAGTGQIEGLLDYMRIRSDMSMMRW

Entity 2 Entity 2 polymer

Description description	Ubiquinol-cytochrome-c reductase complex core protein 2
Molecular weight formula_weight	38751.9 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

LTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGGTFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQCPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVYTKENLEVSGENVVEADLKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVLANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKKGKDLSPAINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVSNLPYLDEL

Entity 3 Entity 3 polymer

Description description	Cytochrome b
Molecular weight formula_weight	43674.5 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIELAFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVIIFTLTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFFALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLILALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAILVLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYFAYFLIIVPVISTIENVLFYIGRVNK

Entity 4 Entity 4 polymer

Description description	Cytochrome c1, heme protein, mitochondrial precursor
Molecular weight formula_weight	27807.4 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSHTNEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIVKARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGTPATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFVFNPPKPRK

Entity 5 Entity 5 polymer

Description description	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor
Molecular weight formula_weight	20123.0 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

KSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLAMAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDPQWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGDKVIVG

Entity 6 Entity 6 polymer

Description description	Ubiquinol-cytochrome c reductase complex 17 kDa protein
Molecular weight formula_weight	8854.8 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

VTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHKEDCVEEFFHLQHYLDTATAPRLFDKLK

Entity 7 Entity 7 polymer

Description description	Ubiquinol-cytochrome c reductase complex 14 kDa protein
Molecular weight formula_weight	14583.8 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MPQSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTALRRLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDELDNIEVSK

Entity 8 Entity 8 polymer

Description description	Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C
Molecular weight formula_weight	10987.5 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MGPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVLIPAGIYWYWWKNGNEYNEFLYSKAGREELERVNV

Entity 9 Entity 9 polymer

Description description	Ubiquinol-cytochrome c reductase complex 7.3 kDa protein
Molecular weight formula_weight	7485.3 kDa
EC 编号 ec_number	1.10.2.2
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MSFSSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAAGDGDDDDE

Entity 10 Entity 10 polymer

Description description	Variable Heavy chain of antibody fragment
Molecular weight formula_weight	14365.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

EVKLQESGAGLVQPSQSLSLTCSVTGYSITSGYYWNWIRLFPGNKLEWVGYISNVGDNNYNPSLKDRLSITRDTSKNQFFLKLNSVTTEDTATYYCARSEYYSVTGYAMDYWGQGTTVTVSSAWRHP

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 11 Entity 11 polymer

Description description	Variable Light chain of antibody fragment
Molecular weight formula_weight	11926.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

DIELTQTPVSLAASLGDRVTISCRASQDINNFLNWYQQKPDGTIKLLIYYTSRLHAGVPSRFSGSGSGTDYSLTISNLEPEDIATYFCQHHIKFPWTFGAGTKLEIK

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 12 Entity 12 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 13 Entity 13 non-polymer

Description 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
Molecular weight formula_weight	592.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 14 Entity 14 non-polymer

Description description	STIGMATELLIN A
Molecular weight formula_weight	514.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 15 Entity 15 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 16 Entity 16 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	340

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6. Fold Classification (SCOP + CATH) 31 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d2ibza1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
Family Family family	d.185.1.1 — MPP-like

Domain ID domain_id	d2ibza2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
Family Family family	d.185.1.1 — MPP-like

Domain ID domain_id	d2ibzb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
Family Family family	d.185.1.1 — MPP-like

Domain ID domain_id	d2ibzb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
Family Family family	d.185.1.1 — MPP-like

Domain ID domain_id	d2ibzc1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.32 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Superfamily Superfamily superfamily	f.32.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Family Family family	f.32.1.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Domain ID domain_id	d2ibzc2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.21 — Heme-binding four-helical bundle
Superfamily Superfamily superfamily	f.21.1 — Transmembrane di-heme cytochromes
Family Family family	f.21.1.2 — Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Domain ID domain_id	d2ibzd1
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.3 — Cytochrome bc1 domain

Domain ID domain_id	d2ibzd2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.11 — Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
Family Family family	f.23.11.1 — Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor

Domain ID domain_id	d2ibze1
Class class	b — All beta proteins
Fold Fold fold	b.33 — ISP domain
Superfamily Superfamily superfamily	b.33.1 — ISP domain
Family Family family	b.33.1.1 — Rieske iron-sulfur protein (ISP)

Domain ID domain_id	d2ibze2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.12 — ISP transmembrane anchor
Family Family family	f.23.12.1 — ISP transmembrane anchor

Domain ID domain_id	d2ibzf_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.27 — 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Superfamily Superfamily superfamily	f.27.1 — 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Family Family family	f.27.1.1 — 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Domain ID domain_id	d2ibzg_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.13 — Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Family Family family	f.23.13.1 — Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Domain ID domain_id	d2ibzh_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.28 — Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Superfamily Superfamily superfamily	f.28.1 — Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Family Family family	f.28.1.1 — Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Domain ID domain_id	d2ibzi_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.14 — Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Family Family family	f.23.14.1 — Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Domain ID domain_id	d2ibzx_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ibzy_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (15 domains)

Domain ID domain_id	2ibzA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	2ibzA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	2ibzB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	2ibzB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	2ibzC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	810 — Cytochrome Bc1 Complex; Chain C
Homologous superfamily homologous superfamily	10 — Cytochrome Bc1 Complex; Chain C

Domain ID domain_id	2ibzD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	2ibzD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	100 — Cytochrome c1, transmembrane anchor, C-terminal

Domain ID domain_id	2ibzE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	270 — Ubiquinol cytochrome reductase, transmembrane domain

Domain ID domain_id	2ibzE02
Class class	2 — Mainly Beta
Architecture architecture	102 — 3-layer Sandwich
Topology topology	10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily	10 — Rieske [2Fe-2S] iron-sulphur domain

Domain ID domain_id	2ibzF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1090 — Cytochrome Bc1 Complex; Chain F
Homologous superfamily homologous superfamily	10 — Cytochrome b-c1 complex subunit 7

Domain ID domain_id	2ibzG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	210 — Cytochrome b-c1 complex subunit 8

Domain ID domain_id	2ibzH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	20 — Ubiquinol-cytochrome C reductase hinge domain

Domain ID domain_id	2ibzI00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	260 — Cytochrome b-c1 complex subunit 9

Domain ID domain_id	2ibzX00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ibzY00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

Unit-cell length a length_a	214.473 Å
Unit-cell length b length_b	163.921 Å
Unit-cell length c length_c	147.276 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	14.960 Å
R factor r_factor	—
R_work r_work	0.2220
R_free r_free	0.2560

Yeast Cytochrome BC1 Complex with Stigmatellin

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquinol-cytochrome-c reductase complex core protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquinol-cytochrome-c reductase complex core protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome b

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome c1, heme protein, mitochondrial precursor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquinol-cytochrome c reductase complex 17 kDa protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquinol-cytochrome c reductase complex 14 kDa protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquinol-cytochrome c reductase complex 7.3 kDa protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ibz__assembly_1__model_1

2ibz__assembly_1__model_1 | I(q)

2ibz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment