1PPJ: PDB entry 1PPJ
Bovine cytochrome bc1 complex with stigmatellin and antimycin. Determined by X-ray diffraction at 2.1 Å resolution. Released 20 Jul 2004.
- Method
- X-ray diffraction
- Resolution
- 2.1 Å
- Organism
- Bos taurus
- Chains
- 20
- Atoms
- 33,549
- Mol. weight
- 488.11 kDa
- Ligands
- JZR, PO4, AZI, HEM
- Released
- 20 Jul 2004
Explore 1PPJ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1PPJ contains 234 α-helices and 116 β-strands across 20 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.
Chains A and N: 26 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-8 | 5 | |
| α-helix | 12-14 | 3 | |
| β-strand | 15-18 | 4 | 1 |
| β-strand | 24-29 | 6 | 1 |
| β-strand | 34-41 | 8 | 1 |
| α-helix | 45-47 | 3 | |
| α-helix | 55-62 | 8 | |
| β-strand | 67 | 1 | 2 |
| α-helix | 74-81 | 8 | |
| β-strand | 85-90 | 6 | 1 |
| β-strand | 95-102 | 8 | 1 |
| α-helix | 103-105 | 3 | |
| α-helix | 106-119 | 14 | |
| β-strand | 120 | 1 | 2 |
| α-helix | 124-141 | 18 | |
| α-helix | 145-157 | 13 | |
| α-helix | 162-164 | 3 | |
| α-helix | 171-176 | 6 | |
| α-helix | 179-189 | 11 | |
| α-helix | 192-194 | 3 | |
| β-strand | 195-201 | 7 | 1 |
| α-helix | 205-216 | 12 | |
| α-helix | 230-233 | 4 | |
| β-strand | 239-245 | 7 | 3 |
| β-strand | 251-259 | 9 | 3 |
| α-helix | 266-277 | 12 | |
| β-strand | 279-281 | 3 | 3 |
| α-helix | 287-289 | 3 | |
| α-helix | 293-300 | 8 | |
| β-strand | 306-313 | 8 | 3 |
| β-strand | 318-326 | 9 | 3 |
| α-helix | 331-348 | 18 | |
| α-helix | 351-368 | 18 | |
| α-helix | 372-385 | 14 | |
| α-helix | 389-391 | 3 | |
| α-helix | 392-400 | 9 | |
| α-helix | 404-414 | 11 | |
| β-strand | 421-426 | 6 | 3 |
| α-helix | 432-433 | 2 | |
| α-helix | 434-439 | 6 | |
Chain B: 25 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 22-24 | 3 | |
| β-strand | 25-28 | 4 | 4 |
| β-strand | 34-38 | 5 | 4 |
| β-strand | 44-51 | 8 | 4 |
| α-helix | 55-57 | 3 | |
| α-helix | 65-71 | 7 | |
| β-strand | 77 | 1 | 5 |
| α-helix | 82-91 | 10 | |
| β-strand | 95-100 | 6 | 4 |
| β-strand | 105-112 | 8 | 4 |
| α-helix | 113-115 | 3 | |
| α-helix | 116-128 | 13 | |
| β-strand | 130 | 1 | 5 |
| α-helix | 134-140 | 7 | |
| α-helix | 142-151 | 10 | |
| α-helix | 155-167 | 13 | |
| β-strand | 168 | 1 | 6 |
| α-helix | 171-173 | 3 | |
| α-helix | 180-182 | 3 | |
| α-helix | 188-198 | 11 | |
| α-helix | 201-203 | 3 | |
| β-strand | 204-209 | 6 | 4 |
| α-helix | 213-223 | 11 | |
| β-strand | 239 | 1 | 6 |
| β-strand | 242-247 | 6 | 7 |
| β-strand | 252-260 | 9 | 7 |
| α-helix | 267-279 | 13 | |
| β-strand | 285 | 1 | 1 |
| α-helix | 294-302 | 9 | |
| β-strand | 307-315 | 9 | 7 |
| β-strand | 320-329 | 10 | 7 |
| α-helix | 330-332 | 3 | |
| α-helix | 333-348 | 16 | |
| α-helix | 354-371 | 18 | |
| α-helix | 375-388 | 14 | |
| α-helix | 395-403 | 9 | |
| α-helix | 407-419 | 13 | |
| α-helix | 421 | 1 | |
| β-strand | 422-428 | 7 | 7 |
| α-helix | 433-435 | 3 | |
| α-helix | 436-438 | 3 | |
Chain C: 21 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-24 | 3 | 8 |
| α-helix | 29-31 | 3 | |
| α-helix | 33-52 | 20 | |
| α-helix | 62-72 | 11 | |
| α-helix | 76-104 | 29 | |
| α-helix | 106-108 | 3 | |
| α-helix | 110-132 | 23 | |
| β-strand | 136 | 1 | 9 |
| α-helix | 137-147 | 11 | |
| α-helix | 148-152 | 5 | |
| α-helix | 157-165 | 9 | |
| α-helix | 172-203 | 32 | |
| β-strand | 217-219 | 3 | 8 |
| α-helix | 220-245 | 26 | |
| α-helix | 253-256 | 4 | |
| β-strand | 258 | 1 | 9 |
| α-helix | 272-274 | 3 | |
| α-helix | 275-282 | 8 | |
| α-helix | 287-299 | 13 | |
| α-helix | 300-302 | 3 | |
| α-helix | 304-307 | 4 | |
| α-helix | 319-339 | 21 | |
| α-helix | 347-360 | 14 | |
| α-helix | 361-365 | 5 | |
| α-helix | 366-376 | 11 | |
Chains D and Q: 14 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| α-helix | 19-21 | 3 | |
| α-helix | 23-35 | 13 | |
| α-helix | 37-39 | 3 | |
| β-strand | 47 | 1 | 10 |
| α-helix | 48-51 | 4 | |
| β-strand | 52 | 1 | 11 |
| β-strand | 56 | 1 | 11 |
| α-helix | 58-65 | 8 | |
| β-strand | 69-72 | 4 | 12 |
| β-strand | 81-84 | 4 | 12 |
| β-strand | 90 | 1 | 10 |
| α-helix | 91-93 | 3 | |
| α-helix | 98-103 | 6 | |
| α-helix | 110-112 | 3 | |
| α-helix | 123-131 | 9 | |
| α-helix | 136-138 | 3 | |
| α-helix | 143-144 | 2 | |
| β-strand | 148-149 | 2 | 13 |
| β-strand | 157-158 | 2 | 13 |
| α-helix | 179-194 | 16 | |
| α-helix | 198-231 | 34 | |
| β-strand | 234-237 | 4 | 3 |
Chain E: 11 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-4 | 3 | |
| α-helix | 7-9 | 3 | |
| β-strand | 14 | 1 | 14 |
| α-helix | 16-18 | 3 | |
| α-helix | 26-61 | 36 | |
| α-helix | 64-65 | 2 | |
| α-helix | 68-70 | 3 | |
| β-strand | 74-76 | 3 | 15 |
| α-helix | 78-80 | 3 | |
| β-strand | 86-91 | 6 | 16 |
| β-strand | 94-100 | 7 | 16 |
| α-helix | 103-110 | 8 | |
| α-helix | 123-125 | 3 | |
| β-strand | 132-136 | 5 | 16 |
| α-helix | 146 | 1 | |
| β-strand | 147-148 | 2 | 17 |
| β-strand | 154-158 | 5 | 17 |
| β-strand | 163-166 | 4 | 17 |
| β-strand | 171-173 | 3 | 17 |
| α-helix | 179-181 | 3 | |
| β-strand | 185-187 | 3 | 15 |
| β-strand | 193-195 | 3 | 15 |
Chain F: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-24 | 12 | |
| α-helix | 26-29 | 4 | |
| α-helix | 33-36 | 4 | |
| α-helix | 41-48 | 8 | |
| α-helix | 52-70 | 19 | |
| α-helix | 77-79 | 3 | |
| α-helix | 81-82 | 2 | |
| α-helix | 83-85 | 3 | |
| α-helix | 91-109 | 19 | |
Chains G and T: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-18 | 8 | 3 |
| α-helix | 20-22 | 3 | |
| β-strand | 23 | 1 | 14 |
| α-helix | 33-70 | 38 | |
Chain H: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-24 | 9 | |
| α-helix | 28-45 | 18 | |
| α-helix | 55-72 | 18 | |
| α-helix | 73-76 | 4 | |
9 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 |
|---|
| Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial | A, N | protein | 446 | Bos taurus | P31800 (AlphaFold model) |
| Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial | B, O | protein | 439 | Bos taurus | P23004 (AlphaFold model) |
| Cytochrome b | C, P | protein | 379 | Bos taurus | P00157 (AlphaFold model) |
| Cytochrome c1, heme protein, mitochondrial | D, Q | protein | 241 | Bos taurus | P00125 (AlphaFold model) |
| Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial | E, R | protein | 196 | Bos taurus | P13272 |
| Ubiquinol-cytochrome C reductase complex 14 kDa protein | F, S | protein | 110 | Bos taurus | P00129 |
| Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C | G, T | protein | 81 | Bos taurus | P13271 |
| Ubiquinol-cytochrome C reductase complex 11 kDa protein | H, U | protein | 78 | Bos taurus | P00126 |
| Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial | I, V | protein | 78 | Bos taurus | P13272 |
| Ubiquinol-cytochrome C reductase complex 7.2 kDa protein | J, W | protein | 62 | Bos taurus | P00130 |
Sequence of entity 1 (A, N), FASTA
>1PPJ_1 Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial (chains A, N)
TATYAQALQSVPETQVSQLDNGLRVASEQSSQPTCTVGVWIDAGSRYESEKNNGAGYFVE
HLAFKGTKNRPGNALEKEVESMGAHLNAYSTREHTAYYIKALSKDLPKAVELLADIVQNC
SLEDSQIEKERDVILQELQENDTSMRDVVFNYLHATAFQGTPLAQSVEGPSENVRKLSRA
DLTEYLSRHYKAPRMVLAAAGGLEHRQLLDLAQKHFSGLSGTYDEDAVPTLSPCRFTGSQ
ICHREDGLPLAHVAIAVEGPGWAHPDNVALQVANAIIGHYDCTYGGGAHLSSPLASIAAT
NKLCQSFQTFNICYADTGLLGAHFVCDHMSIDDMMFVLQGQWMRLCTSATESEVLRGKNL
LRNALVSHLDGTTPVCEDIGRSLLTYGRRIPLAEWESRIAEVDARVVREVCSKYFYDQCP
AVAGFGPIEQLPDYNRIRSGMFWLRF
Sequence of entity 2 (B, O), FASTA
>1PPJ_2 Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial (chains B, O)
SLKVAPKVKATEAPAGVPPHPQDLEFTRLPNGLVIASLENYAPASRIGLFIKAGSRYENS
NNLGTSHLLRLASSLTTKGASSFKITRGIEAVGGKLSVTSTRENMAYTVECLRDDVDILM
EFLLNVTTAPEFRRWEVAALQPQLRIDKAVALQNPQAHVIENLHAAAYRNALANSLYCPD
YRIGKVTPVELHDYVQNHFTSARMALIGLGVSHPVLKQVAEQFLNIRGGLGLSGAKAKYH
GGEIREQNGDSLVHAALVAESAAIGSAEANAFSVLQHVLGAGPHVKRGSNATSSLYQAVA
KGVHQPFDVSAFNASYSDSGLFGFYTISQAASAGDVIKAAYNQVKTIAQGNLSNPDVQAA
KNKLKAGYLMSVESSEGFLDEVGSQALAAGSYTPPSTVLQQIDAVADADVINAAKKFVSG
RKSMAASGNLGHTPFIDEL
Sequence of entity 3 (C, P), FASTA
>1PPJ_3 Cytochrome b (chains C, P)
MTNIRKSHPLMKIVNNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTT
TAFSSVTHICRDVNYGWIIRYMHANGASMFFICLYMHVGRGLYYGSYTFLETWNIGVILL
LTVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFA
FHFILPFIIMAIAMVHLLFLHETGSNNPTGISSDVDKIPFHPYYTIKDILGALLLILALM
LLVLFAPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALAFSILI
LALIPLLHTSKQRSMMFRPLSQCLFWALVADLLTLTWIGGQPVEHPYITIGQLASVLYFL
LILVLMPTAGTIENKLLKW
Sequence of entity 4 (D, Q), FASTA
>1PPJ_4 Cytochrome c1, heme protein, mitochondrial (chains D, Q)
SDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQVCSSCHSMDYVAYRHLVGVCYTEDE
AKALAEEVEVQDGPNEDGEMFMRPGKLSDYFPKPYPNPEAARAANNGALPPDLSYIVRAR
HGGEDYVFSLLTGYCEPPTGVSLREGLYFNPYFPGQAIGMAPPIYNEVLEFDDGTPATMS
QVAKDVCTFLRWAAEPEHDHRKRMGLKMLLMMGLLLPLVYAMKRHKWSVLKSRKLAYRPP
K
Sequence of entity 5 (E, R), FASTA
>1PPJ_5 Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial (chains E, R)
SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS
SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDP
QHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL
EVPSYEFTSDDMVIVG
Sequence of entity 6 (F, S), FASTA
>1PPJ_6 Ubiquinol-cytochrome C reductase complex 14 kDa protein (chains F, S)
AGRPAVSASSRWLEGIRKWYYNAAGFNKLGLMRDDTIHENDDVKEAIRRLPENLYDDRVF
RIKRALDLSMRQQILPKEQWTKYEEDKSYLEPYLKEVIRERKEREEWAKK
Sequence of entity 7 (G, T), FASTA
>1PPJ_7 Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C (chains G, T)
GRQFGHLTRVRHVITYSLSPFEQRAFPHYFSKGIPNVLRRTRACILRVAPPFVAFYLVYT
WGTQEFEKSKRKNPAAYENDR
Sequence of entity 8 (H, U), FASTA
>1PPJ_8 Ubiquinol-cytochrome C reductase complex 11 kDa protein (chains H, U)
GDPKEEEEEEEELVDPLTTVREQCEQLEKCVKARERLELCDERVSSRSQTEEDCTEELLD
FLHARDHCVAHKLFNSLK
Sequence of entity 9 (I, V), FASTA
>1PPJ_9 Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial (chains I, V)
MLSVAARSGPFAPVLSATSRGVAGALRPLVQAAVPATSESPVLDLKLSVLCRESLRGQAA
GRPLVASVSLNVPASVRY
Sequence of entity 10 (J, W), FASTA
>1PPJ_10 Ubiquinol-cytochrome C reductase complex 7.2 kDa protein (chains J, W)
VAPTLTARLYSLLFRRTSTFALTIVVGALFFERAFDQGADAIYEHINEGKLWKHIKHKYE
NK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| JZR | hexyl beta-D-glucopyranoside | C12 H24 O6 | 9 |
| PO4 | Phosphate ion | O4 P | 5 |
| AZI | Azide ion | N3 | 5 |
| HEM | Protoporphyrin IX containing FE | C34 H32 Fe N4 O4 | 4 |
| SMA | Stigmatellin a | C30 H42 O7 | 2 |
| PEE | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine | C41 H78 N O8 P | 4 |
| ANY | 2-methyl-butyric acid 3-(3-formylamino-2-hydroxy-benzoylamino)-8-heptyl-2,6-dim… | C29 H42 N2 O9 | 2 |
| HEC | Heme C | C34 H36 Fe N4 O4 | 2 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 4 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 2 |
Water and common crystallization additives (GOL) are not listed.
Primary citation
Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial bc(1) Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-bonding Pattern. Huang, L.S., Cobessi, D., Tung, E.Y. et al. J Mol Biol (2005) 351:573-597. DOI 10.1016/j.jmb.2005.05.053 · PubMed
Other PDB entries of the same protein (UniProt P31800 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1PP9 2.1 Å, Bovine cytochrome bc1 complex with stigmatellin bound
- 2A06 2.1 Å, Bovine cytochrome bc1 complex with stigmatellin bound
- 9W2X 2.2 Å, Cryo-EM structure of complex III on the bovine heart submitochondrial particles, III-1
- 2FYU 2.26 Å, Crystal structure of bovine heart mitochondrial bc1 with jg144 inhibitor
- 1L0L 2.35 Å, structure of bovine mitochondrial cytochrome bc1 complex with a bound fungicide famoxadone
- 1NTM 2.4 Å, Crystal Structure of Mitochondrial Cytochrome bc1 Complex at 2.4 Angstrom
- 9W2Y 2.4 Å, Cryo-EM structure of complex III on the bovine heart submitochondrial particles, III-2
- 1L0N 2.6 Å, native structure of bovine mitochondrial cytochrome bc1 complex
- 1NTK 2.6 Å, Crystal Structure of Mitochondrial Cytochrome bc1 in Complex with Antimycin A1
- 1NTZ 2.6 Å, Crystal Structure of Mitochondrial Cytochrome bc1 Complex Bound with Ubiquinone
- 1SQX 2.6 Å, Crystal Structure Analysis of Bovine Bc1 with Stigmatellin A
- 5KLV 2.65 Å, Structure of bos taurus cytochrome bc1 with fenamidone inhibited
Browse structure collections
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