3CXH: Cytochrome b-c1 complex subunit 1, mitochondrial
Structure of yeast complex III with isoform-2 cytochrome c bound and definition of a minimal core interface for electron transfer. Determined by X-ray diffraction at 2.5 Å resolution. Released 13 May 2008.
- Method
- X-ray diffraction
- Resolution
- 2.5 Å
- Organisms
- Saccharomyces cerevisiae, Mus musculus
- Chains
- 23
- Atoms
- 36,805
- Mol. weight
- 533.74 kDa
- Ligands
- 6PH, FES, 7PH, 9PE
- Released
- 13 May 2008
Explore 3CXH in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3CXH contains 237 α-helices and 163 β-strands across 23 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 22 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30-33 | 4 | 1 |
| β-strand | 37-42 | 6 | 1 |
| β-strand | 49-55 | 7 | 1 |
| α-helix | 59-61 | 3 | |
| α-helix | 69-77 | 9 | |
| α-helix | 80-88 | 9 | |
| β-strand | 92-97 | 6 | 1 |
| β-strand | 102-108 | 7 | 1 |
| α-helix | 113-123 | 11 | |
| α-helix | 134-154 | 21 | |
| α-helix | 156-168 | 13 | |
| α-helix | 173-175 | 3 | |
| α-helix | 182-185 | 4 | |
| α-helix | 190-200 | 11 | |
| α-helix | 203-205 | 3 | |
| β-strand | 206-212 | 7 | 1 |
| α-helix | 216-225 | 10 | |
| α-helix | 240-242 | 3 | |
| β-strand | 247-252 | 6 | 2 |
| β-strand | 259-266 | 8 | 2 |
| α-helix | 275-285 | 11 | |
| β-strand | 287-289 | 3 | 2 |
| α-helix | 293-296 | 4 | |
| α-helix | 302-307 | 6 | |
| β-strand | 314-321 | 8 | 2 |
| β-strand | 326-334 | 9 | 2 |
| α-helix | 340-356 | 17 | |
| α-helix | 360-378 | 19 | |
| α-helix | 383-397 | 15 | |
| α-helix | 400-402 | 3 | |
| α-helix | 403-412 | 10 | |
| α-helix | 415-425 | 11 | |
| β-strand | 432-437 | 6 | 2 |
| α-helix | 445-450 | 6 | |
Chain B: 20 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-22 | 5 | 3 |
| β-strand | 28-35 | 8 | 3 |
| α-helix | 39-41 | 3 | |
| α-helix | 47-54 | 8 | |
| β-strand | 59 | 1 | 4 |
| α-helix | 64-74 | 11 | |
| β-strand | 76-82 | 7 | 3 |
| β-strand | 87-94 | 8 | 3 |
| α-helix | 95-97 | 3 | |
| α-helix | 98-111 | 14 | |
| β-strand | 112 | 1 | 4 |
| α-helix | 116-118 | 3 | |
| α-helix | 119-123 | 5 | |
| α-helix | 124-135 | 12 | |
| α-helix | 138-150 | 13 | |
| α-helix | 169-179 | 11 | |
| α-helix | 182-184 | 3 | |
| β-strand | 185-190 | 6 | 3 |
| α-helix | 194-203 | 10 | |
| α-helix | 220-222 | 3 | |
| β-strand | 228-232 | 5 | 5 |
| β-strand | 237-245 | 9 | 5 |
| α-helix | 250-260 | 11 | |
| α-helix | 268-270 | 3 | |
| β-strand | 273-279 | 7 | 5 |
| β-strand | 282-291 | 10 | 5 |
| α-helix | 294-309 | 16 | |
| α-helix | 318-326 | 9 | |
| α-helix | 338-341 | 4 | |
| β-strand | 352-357 | 6 | 5 |
| α-helix | 359-361 | 3 | |
| α-helix | 365-367 | 3 | |
Chain C: 24 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 10-13 | 4 | |
| α-helix | 14-18 | 5 | |
| β-strand | 21-23 | 3 | 6 |
| α-helix | 28-31 | 4 | |
| α-helix | 32-51 | 20 | |
| α-helix | 61-70 | 10 | |
| α-helix | 75-103 | 29 | |
| α-helix | 111-135 | 25 | |
| β-strand | 137 | 1 | 7 |
| α-helix | 138-149 | 12 | |
| α-helix | 150-153 | 4 | |
| α-helix | 158-166 | 9 | |
| α-helix | 173-204 | 32 | |
| β-strand | 218-220 | 3 | 6 |
| α-helix | 221-225 | 5 | |
| α-helix | 226-246 | 21 | |
| α-helix | 254-257 | 4 | |
| β-strand | 259 | 1 | 7 |
| α-helix | 273-275 | 3 | |
| α-helix | 276-283 | 8 | |
| α-helix | 288-300 | 13 | |
| α-helix | 301-304 | 4 | |
| α-helix | 305-308 | 4 | |
| α-helix | 320-341 | 22 | |
| α-helix | 346-361 | 16 | |
| α-helix | 362-366 | 5 | |
| α-helix | 367-380 | 14 | |
Chain D: 13 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-67 | 4 | |
| α-helix | 69-72 | 4 | |
| α-helix | 87-96 | 10 | |
| α-helix | 97-101 | 5 | |
| β-strand | 111 | 1 | 8 |
| α-helix | 112-114 | 3 | |
| β-strand | 116 | 1 | 9 |
| β-strand | 120 | 1 | 9 |
| α-helix | 122-130 | 9 | |
| β-strand | 133-135 | 3 | 10 |
| β-strand | 146-148 | 3 | 10 |
| β-strand | 154 | 1 | 8 |
| α-helix | 155-157 | 3 | |
| α-helix | 162-167 | 6 | |
| α-helix | 188-196 | 9 | |
| α-helix | 202-203 | 2 | |
| β-strand | 210 | 1 | 11 |
| β-strand | 212 | 1 | 11 |
| β-strand | 213-214 | 2 | 12 |
| β-strand | 222-223 | 2 | 12 |
| α-helix | 226-227 | 2 | |
| α-helix | 244-259 | 16 | |
| α-helix | 263-296 | 34 | |
| β-strand | 299-302 | 4 | 2 |
Chain E: 8 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-38 | 3 | |
| β-strand | 43 | 1 | 13 |
| α-helix | 44-45 | 2 | |
| α-helix | 51-81 | 31 | |
| β-strand | 94-97 | 4 | 14 |
| α-helix | 98-100 | 3 | |
| β-strand | 105-111 | 7 | 15 |
| β-strand | 114-120 | 7 | 15 |
| α-helix | 123-130 | 8 | |
| α-helix | 134-136 | 3 | |
| β-strand | 152-156 | 5 | 15 |
| α-helix | 164-166 | 3 | |
| β-strand | 167-168 | 2 | 16 |
| β-strand | 176-177 | 2 | 16 |
| β-strand | 184-185 | 2 | 16 |
| β-strand | 191-193 | 3 | 16 |
| α-helix | 199-201 | 3 | |
| β-strand | 205-208 | 4 | 14 |
| β-strand | 211-214 | 4 | 14 |
Chains F and Q: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 77-86 | 10 | |
| α-helix | 89-110 | 22 | |
| α-helix | 124-142 | 19 | |
| α-helix | 143-145 | 3 | |
Chain G: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-17 | 13 | |
| α-helix | 19-36 | 18 | |
| α-helix | 38-41 | 4 | |
| α-helix | 45-48 | 4 | |
| α-helix | 54-62 | 9 | |
| α-helix | 65-84 | 20 | |
| α-helix | 90-92 | 3 | |
| α-helix | 94-95 | 2 | |
| α-helix | 104-120 | 17 | |
Chain H: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-7 | 5 | |
| β-strand | 12 | 1 | 17 |
| β-strand | 15 | 1 | 17 |
| α-helix | 19-21 | 3 | |
| β-strand | 24-29 | 6 | 2 |
| α-helix | 31-33 | 3 | |
| β-strand | 34 | 1 | 13 |
| α-helix | 51-53 | 3 | |
| α-helix | 56-80 | 25 | |
| α-helix | 83-85 | 3 | |
| α-helix | 86-92 | 7 | |
13 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cytochrome b-c1 complex subunit 1, mitochondrial | A, L | protein | 431 | Saccharomyces cerevisiae | P07256 (AlphaFold model) |
| Cytochrome b-c1 complex subunit 2, mitochondrial | B, M | protein | 352 | Saccharomyces cerevisiae | P07257 (AlphaFold model) |
| Cytochrome b | C, N | protein | 385 | Saccharomyces cerevisiae | P00163 (AlphaFold model) |
| Cytochrome c1, heme protein, mitochondrial | D, O | protein | 248 | Saccharomyces cerevisiae | P07143 (AlphaFold model) |
| Cytochrome b-c1 complex subunit Rieske, mitochondrial | E, P | protein | 185 | Saccharomyces cerevisiae | P08067 |
| Cytochrome b-c1 complex subunit 6 | F, Q | protein | 146 | Saccharomyces cerevisiae | P00127 |
| Cytochrome b-c1 complex subunit 7 | G, R | protein | 126 | Saccharomyces cerevisiae | P00128 |
| Cytochrome b-c1 complex subunit 8 | H, S | protein | 93 | Saccharomyces cerevisiae | P08525 |
| Cytochrome b-c1 complex subunit 9 | I, T | protein | 65 | Saccharomyces cerevisiae | P22289 |
| Heavy chain (VH) of fv-fragment | J, U | protein | 127 | Mus musculus | |
| Light chain (VL) of fv-fragment | K, V | protein | 107 | Mus musculus | |
| Cytochrome c iso-2 | W | protein | 112 | Saccharomyces cerevisiae | P00045 |
Sequence of entity 1 (A, L), FASTA
>3CXH_1 Cytochrome b-c1 complex subunit 1, mitochondrial (chains A, L)
AEVTQLSNGIVVATEHNPSAHTASVGVVFGSGAANENPYNNGVSNLWKNIFLSKENSAVA
AKEGLALSSNISRDFQSYIVSSLPGSTDKSLDFLNQSFIQQKANLLSSSNFEATKKSVLK
QVQDFEDNDHPNRVLEHLHSTAFQNTPLSLPTRGTLESLENLVVADLESFANNHFLNSNA
VVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKKKAAFLGSEVRLRDDTLPKAWISLAVE
GEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGIKLLDNIQEYQLCDNFNHFSLSYKDSG
LWGFSTATRNVTMIDDLIHFTLKQWNRLTISVTDTEVERAKSLLKLQLGQLYESGNPVND
ANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRLWDQDIAIAGTGQIEGLLDYM
RIRSDMSMMRW
Sequence of entity 2 (B, M), FASTA
>3CXH_2 Cytochrome b-c1 complex subunit 2, mitochondrial (chains B, M)
LTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGG
TFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQ
CPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVYTKENLEVSGENVVEAD
LKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVL
ANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKKGKDLSP
AINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVSNLPYLDEL
Sequence of entity 3 (C, N), FASTA
>3CXH_3 Cytochrome b (chains C, N)
MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIEL
AFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVII
FILTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFF
ALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL
ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAIL
VLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYF
AYFLIIVPVISTIENVLFYIGRVNK
Sequence of entity 4 (D, O), FASTA
>3CXH_4 Cytochrome c1, heme protein, mitochondrial (chains D, O)
MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSHT
NEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIV
KARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGTP
ATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFV
FNPPKPRK
Sequence of entity 5 (E, P), FASTA
>3CXH_5 Cytochrome b-c1 complex subunit Rieske, mitochondrial (chains E, P)
KSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLA
MAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDP
QWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGD
KVIVG
Sequence of entity 6 (F, Q), FASTA
>3CXH_6 Cytochrome b-c1 complex subunit 6 (chains F, Q)
GMLELVGEYWEQLKITVVPVVAAAEDDDNEQHEEKAAEGEEKEEENGDEDEDEDEDEDDD
DDDDEDEEEEEEVTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHKE
DCVEEFFHLQHYLDTATAPRLFDKLK
Sequence of entity 7 (G, R), FASTA
>3CXH_7 Cytochrome b-c1 complex subunit 7 (chains G, R)
PQSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTALR
RLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDELD
NIEVSK
Sequence of entity 8 (H, S), FASTA
>3CXH_8 Cytochrome b-c1 complex subunit 8 (chains H, S)
GPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVLI
PAGIYWYWWKNGNEYNEFLYSKAGREELERVNV
Sequence of entity 9 (I, T), FASTA
>3CXH_9 Cytochrome b-c1 complex subunit 9 (chains I, T)
SFSSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAAGDG
DDDDE
Sequence of entity 10 (J, U), FASTA
>3CXH_10 HEAVY CHAIN (VH) OF FV-FRAGMENT (chains J, U)
EVKLQESGAGLVQPSQSLSLTCSVTGYSITSGYYWNWIRLFPGNKLEWVGYISNVGDNNY
NPSLKDRLSITRDTSKNQFFLKLNSVTTEDTATYYCARSEYYSVTGYAMDYWGQGTTVTV
SSAWRHP
Sequence of entity 11 (K, V), FASTA
>3CXH_11 LIGHT CHAIN (VL) OF FV-FRAGMENT (chains K, V)
DIELTQTPVSLAASLGDRVTISCRASQDINNFLNWYQQKPDGTIKLLIYYTSRLHAGVPS
RFSGSGSGTDYSLTISNLEPEDIATYFCQHHIKFPWTFGAGTKLEIK
Sequence of entity 12 (W), FASTA
>3CXH_12 Cytochrome c iso-2 (chains W)
AKESTGFKPGSAKKGATLFKTRCQQCHTIEEGGPNKVGPNLHGIFGRHSGQVKGYSYTDA
NINKNVKWDEDSMSEYLTNPKKYIPGTKMAFAGLKKEKDRNDLITYMTKAAK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| 6PH | (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate | C31 H61 O8 P | 2 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 2 |
| 7PH | (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate | C29 H57 O8 P | 2 |
| 9PE | (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]et… | C30 H60 N O8 P | 2 |
| CN6 | (2R,5R,11S,14R)-2-(butanoyloxy)-5,8,11-trihydroxy-5,11-dioxido-16-oxo-14-[(prop… | C31 H58 O17 P2 | 2 |
| 8PE | (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl… | C37 H74 N O8 P | 2 |
| SMA | Stigmatellin a | C30 H42 O7 | 2 |
| HEM | Protoporphyrin IX containing FE | C34 H32 Fe N4 O4 | 7 |
| UMQ | Undecyl-maltoside | C23 H44 O11 | 2 |
Primary citation
Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer. Solmaz, S.R., Hunte, C. J Biol Chem (2008) 283:17542-17549. DOI 10.1074/jbc.M710126200 · PubMed
Other PDB entries of the same protein (UniProt P07256 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3CX5 1.9 Å, Structure of complex III with bound cytochrome c in reduced state and definition of a…
- 1EZV 2.3 Å, Structure of the yeast cytochrome BC1 complex co-crystallized with an antibody fv-fragment
- 1KB9 2.3 Å, Yeast cytochrome BC1 complex
- 2IBZ 2.3 Å, Yeast Cytochrome BC1 Complex with Stigmatellin
- 8YIO 2.35 Å, Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in azoxystrobin-bound state
- 9ETZ 2.4 Å, III2IV respiratory supercomplex from Saccharomyces cerevisiae
- 8YHQ 2.42 Å, Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in pyraclostrobin-bound state
- 1P84 2.5 Å, HDBT inhibited Yeast Cytochrome bc1 Complex
- 8ZJC 2.5 Å, Cryo-EM structure of Saccharomyces cerevisiae bc1 complex
- 8ZMT 2.52 Å, Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in Metyltetraprole-bound state
- 9BPB 2.57 Å, Tethered respiratory III2IV2 supercomplex from Saccharomyces cerevisiae
- 8YIL 2.58 Å, Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF24228-bound state
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