6T15: PDB entry 6T15

The III2-IV(5B)1 respiratory supercomplex from S. cerevisiae. Determined by electron microscopy at 3.29 Å resolution. Released 22 Apr 2020.

Method
Electron microscopy
Resolution
3.29 Å
Organisms
Saccharomyces cerevisiae S288C, Saccharomyces cerevisiae S288c
Chains
33
Atoms
48,966
Mol. weight
741.48 kDa
Ligands
ZN, CUA, MG, HEA
Released
22 Apr 2020

Explore 6T15 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T15 contains 294 α-helices and 143 β-strands across 33 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: 28 helices, 3 β-strands

ElementResiduesLengthSheet
α-helix21
α-helix3-75
α-helix15-3925
α-helix52-6615
α-helix67-715
α-helix721
α-helix73-808
α-helix81-877
α-helix98-11619
α-helix143-17028
α-helix184-21431
α-helix230-26132
α-helix270-28314
α-helix288-2914
α-helix299-32729
α-helix336-35823
α-helix363-3653
β-strand370140
α-helix371-3777
α-helix378-3869
α-helix387-40014
α-helix407-42519
α-helix427-4348
α-helix4361
β-strand437140
α-helix450-47728
α-helix479-4846
α-helix501-5044
α-helix514-5163
α-helix5191
β-strand533141
Chain A: 19 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand30-3231
β-strand37-4261
β-strand50-5561
α-helix69-779
α-helix80-878
β-strand91-9771
β-strand102-10871
α-helix114-1207
α-helix121-1255
α-helix136-15318
α-helix156-16813
α-helix182-1843
α-helix190-20011
β-strand206-21271
α-helix216-22510
α-helix235-2373
β-strand247-25372
β-strand261-26772
α-helix268-2692
α-helix275-28511
β-strand287-28932
α-helix302-3043
β-strand314-31852
β-strand326-33382
α-helix340-35617
α-helix361-37818
α-helix385-39612
α-helix404-4118
α-helix415-42511
β-strand432-43762
α-helix445-4506
Chain b: 4 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix31-6434
α-helix79-10628
β-strand115-122842
β-strand125-130642
β-strand141-144442
α-helix146-1494
β-strand167-170443
β-strand175-179542
β-strand181142
β-strand186-190544
β-strand195-199544
β-strand205-209542
β-strand215-220643
β-strand233-239743
α-helix241-25010
Chain B: 15 helices, 15 β-strands
ElementResiduesLengthSheet
β-strand1913
β-strand2213
β-strand28-3583
α-helix39-413
α-helix47-548
β-strand5914
α-helix64-7411
β-strand76-8273
β-strand87-9483
α-helix95-973
α-helix98-11013
β-strand11214
α-helix116-1183
α-helix119-1235
α-helix124-13613
α-helix138-15013
α-helix169-17911
β-strand186-19053
α-helix195-2017
β-strand228-23255
β-strand237-24595
α-helix250-26011
β-strand273-27865
β-strand283-29195
α-helix295-30814
β-strand311-31336
α-helix318-32912
β-strand345-34736
β-strand352-35765
α-helix359-3613
Chain c: 9 helices, 1 β-strand
ElementResiduesLengthSheet
β-strand2145
α-helix24-3916
α-helix40-423
α-helix49-7426
α-helix81-11333
α-helix131-1333
α-helix140-16122
α-helix164-19027
α-helix199-23133
α-helix241-26525
Chain C: 21 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix3-64
α-helix8-136
α-helix14-185
β-strand21-2337
α-helix32-5120
α-helix61-688
α-helix75-10228
α-helix111-13424
α-helix138-15114
α-helix158-1658
α-helix173-18513
α-helix187-20216
β-strand218-22037
α-helix225-24521
α-helix248-2503
α-helix273-2753
α-helix276-2827
α-helix288-29912
β-strand31318
α-helix316-3183
α-helix321-33919
α-helix348-36114
α-helix362-3665
α-helix367-38216
Chain d: 5 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix37-393
α-helix49-513
α-helix56-583
α-helix59-624
α-helix66-7611
β-strand98-102546
β-strand106147
β-strand109-111341
β-strand122-124341
β-strand127147
β-strand132-133246
β-strand140-145646
Chain D: 15 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix64-674
α-helix69-713
α-helix87-9913
α-helix101-1033
β-strand11119
β-strand116110
β-strand120110
α-helix122-1287
α-helix129-1313
β-strand133-136411
α-helix137-1382
β-strand145-148411
β-strand15419
α-helix155-1573
α-helix162-1676
α-helix172-1765
α-helix177-1793
α-helix188-1958
β-strand204112
β-strand206112
β-strand213-214213
β-strand222-223213
α-helix244-25916
α-helix263-29634
β-strand299-30242
α-helix303-3075

25 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Cytochrome B-C1 complex subunit 1, mitochondrial; synonym: complex III subunit 1, core protein I,…A, Lprotein431Saccharomyces cerevisiae S288CP07256 (AlphaFold model)
Cytochrome B-C1 complex subunit 2, mitochondrial; synonym: complex III subunit 2, core protein II,…B, Mprotein352Saccharomyces cerevisiae S288CP07257 (AlphaFold model)
Cytochrome B-C1 complex subunit 2, mitochondrial; synonym: complex III subunit 2, core protein II,…C, Nprotein385Saccharomyces cerevisiae S288CP00163 (AlphaFold model)
Cytochrome C1, heme protein, mitochondrial; synonym: complex III subunit 4, complex III subunit…D, Oprotein248Saccharomyces cerevisiae S288CP07143 (AlphaFold model)
Cytochrome B-C1 complex subunit rieske, mitochondrial; synonym: complex III subunit 5, rieske…E, Pprotein185Saccharomyces cerevisiae S288CP08067
Cytochrome B-C1 complex subunit 6; synonym: complex III subunit 6,COMPLEX III subunit…F, Qprotein147Saccharomyces cerevisiae S288CP00127
Cytochrome B-C1 complex subunit 7; synonym: complex III subunit 7,COMPLEX III subunit…G, Rprotein127Saccharomyces cerevisiae S288CP00128
Cytochrome B-C1 complex subunit 8; synonym: complex III subunit 8,COMPLEX III subunit…H, Sprotein94Saccharomyces cerevisiae S288CP08525
Cytochrome B-C1 complex subunit 9; synonym: complex III subunit 9, complex III subunit X,…I, Tprotein66Saccharomyces cerevisiae S288CP22289
Cytochrome B-C1 complex subunit 10; synonym: complex III subunit 10,COMPLEX III subunit XI,…J, Uprotein77Saccharomyces cerevisiae S288CP37299
Cytochrome C oxidase subunit 1; synonym: cytochrome C oxidase polypeptide I, COX1aprotein534Saccharomyces cerevisiae S288CP00401
Cytochrome C oxidase subunit 2; synonym: cytochrome C oxidase polypeptide II, COX2bprotein236Saccharomyces cerevisiae S288CP00410

11 more molecules are not listed.

Sequence of entity 1 (A, L), FASTA
>6T15_1 CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 1, CORE PROTEIN I, UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 1 (chains A, L)
AEVTQLSNGIVVATEHNPSAHTASVGVVFGSGAANENPYNNGVSNLWKNIFLSKENSAVA
AKEGLALSSNISRDFQSYIVSSLPGSTDKSLDFLNQSFIQQKANLLSSSNFEATKKSVLK
QVQDFEENDHPNRVLEHLHSTAFQNTPLSLPTRGTLESLENLVVADLESFANNHFLNSNA
VVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKKKAAFLGSEVRLRDDTLPKAWISLAVE
GEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGIKLLDNIQEYQLCDNFNHFSLSYKDSG
LWGFSTATRNVTMIDDLIHFTLKQWNRLTISVTDTEVERAKSLLKLQLGQLYESGNPVND
ANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRLWDQDIAIAGTGQIEGLLDYM
RIRSDMSMMRW
Sequence of entity 2 (B, M), FASTA
>6T15_2 CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 2, CORE PROTEIN II, UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2 (chains B, M)
LTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGG
TFKSTLDREYITLKATFLKDDLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQ
CPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFADKVYTKENLEVSGENVVEAD
LKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVL
ANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKKGKDLSP
AINYTKLKNAVQNESVSSPIELNFDAVKDFKLGKFNYVAVGDVSNLPYLDEL
Sequence of entity 3 (C, N), FASTA
>6T15_3 CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 2, CORE PROTEIN II, UBIQUINOL-CYTOCHROME-C COMPLEX CORE PROTEIN 2 (chains C, N)
MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIEL
AFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVII
FILTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFF
ALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL
ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAIL
VLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYF
AYFLIIVPVISTIENVLFYIGRVNK
Sequence of entity 4 (D, O), FASTA
>6T15_4 CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 4, COMPLEX III SUBUNIT IV, CYTOCHROME B-C1 COMPLEX SUBUNIT 4, UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CYTOCHROME C1 SUBUNIT, CYTOCHROME C-1 (chains D, O)
MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSHT
NEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIV
KARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGGSIAMARVLFDDMVEYEDGTP
ATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFV
FNPPKPRK
Sequence of entity 5 (E, P), FASTA
>6T15_5 CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 5, RIESKE IRON-SULFUR PROTEIN, RISP, UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT (chains E, P)
KSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLA
MAKVEVNLAAIPLGKNVVVKWQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDP
QWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGRIRKGPAPLNLEIPAYEFDGD
KVIVG
Sequence of entity 6 (F, Q), FASTA
>6T15_6 CYTOCHROME B-C1 COMPLEX SUBUNIT 6; SYNONYM: COMPLEX III SUBUNIT 6,COMPLEX III SUBUNIT VI,CYTOCHROME C1 NON-HEME 17 KDA PROTEIN,MITOCHONDRIAL HINGE PROTEIN,UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KDA PROTEIN (chains F, Q)
MGMLELVGEYWEQLKITVVPVVAAAEDDDNEQHEEKAAEGEEKEEENGDEDEDEDEDEDD
DDDDDEDEEEEEEVTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHK
EDCVEEFFHLQHYLDTATAPRLFDKLK
Sequence of entity 7 (G, R), FASTA
>6T15_7 CYTOCHROME B-C1 COMPLEX SUBUNIT 7; SYNONYM: COMPLEX III SUBUNIT 7,COMPLEX III SUBUNIT VII,UBIQUINOL-CYTOCHROME C REDUCTASE C REDUCTASE COMPLEX 14 KDA PROTEIN (chains G, R)
MPQSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTAL
RRLPEDESYARAYRIIRAHQTELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDEL
DNIEVSK
Sequence of entity 8 (H, S), FASTA
>6T15_8 CYTOCHROME B-C1 COMPLEX SUBUNIT 8; SYNONYM: COMPLEX III SUBUNIT 8,COMPLEX III SUBUNIT VII,UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 11 KDA PROTEIN,UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C (chains H, S)
MGPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVL
IPAGIYWYWWKNGNEYNEFLYSKAGREELERVNV
Sequence of entity 9 (I, T), FASTA
>6T15_9 CYTOCHROME B-C1 COMPLEX SUBUNIT 9; SYNONYM: COMPLEX III SUBUNIT 9, COMPLEX III SUBUNIT X, CYTOCHROME C1 NON-HEME 7.3 KDA PROTEIN, UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KDA PROTEIN (chains I, T)
MSFSSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAAGD
GDDDDE
Sequence of entity 10 (J, U), FASTA
>6T15_10 CYTOCHROME B-C1 COMPLEX SUBUNIT 10; SYNONYM: COMPLEX III SUBUNIT 10,COMPLEX III SUBUNIT XI, UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 8.5 KDA PROTEIN (chains J, U)
MAYTSHLSSKTGLHFGRLSLRSLTAYAPNLMLWGGASMLGLFVFTEGWPKFQDTLYKKIP
LLGPTLEDHTPPEDKPN
Sequence of entity 11 (a), FASTA
>6T15_11 CYTOCHROME C OXIDASE SUBUNIT 1; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE I, COX1 (chains a)
MVQRWLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVV
GHAVLMIFFLVMPALIGGFGNYLLPLMIGATDTAFPRINNIAFWVLPMGLVCLVTSTLVE
SGAGTGWTVYPPLSSIQAHSGPSVDLAIFALHLTSISSLLGAINFIVTTLNMRTNGMTMH
KLPLFVWSIFITAFLLLLSLPVLSAGITMLLLDRNFNTSFFEVSGGGDPILYEHLFWFFG
HPEVYILIIPGFGIISHVVSTYSKKPVFGEISMVYAMASIGLLGFLVWSHHMYIVGLDAD
TRAYFTSATMIIAIPTGIKIFSWLATIHGGSIRLATPMLYAIAFLFLFTMGGLTGVALAN
ASLDVAFHDTYYVVGHFHYVLSMGAIFSLFAGYYYWSPQILGLNYNEKLAQIQFWLIFIG
ANVIFFPMHFLGINGMPRRIPDYPDAFAGWNYVASIGSFIATLSLFLFIYILYDQLVNGL
NNKVNNKSVIYNKAPDFVESNTIFNLNTVKSSSIEFLLTSPPAVHSFNTPAVQS
Sequence of entity 12 (b), FASTA
>6T15_12 CYTOCHROME C OXIDASE SUBUNIT 2; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE II, COX2 (chains b)
DVPTPYACYFQDSATPNQEGILELHDNIMFYLLVILGLVSWMLYTIVMTYSKNPIAYKYI
KHGQTIEVIWTIFPAVILLIIAFPSFILLYLCDEVISPAMTIKAIGYQWYWKYEYSDFIN
DSGETVEFESYVIPDELLEEGQLRLLDTDTSMVVPVDTHIRFVVTAADVIHDFAIPSLGI
KVDATPGRLNQVSALIQREGVFYGACSELCGTGHANMPIKIEAVSLPKFLEWLNEQ

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn1
CUADinuclear copper ionCu21
MGMagnesium ionMg1
HEAHeme-aC49 H56 Fe N4 O62
CUCopper (II) ionCu1
FESFE2/S2 (inorganic) clusterFe2 S22
HECHeme CC34 H36 Fe N4 O42
PCF1,2-diacyl-sn-glycero-3-phoshocholineC40 H80 N O8 P6
CDLCardiolipinC81 H156 O17 P27
HEMProtoporphyrin IX containing FEC34 H32 Fe N4 O44
PEFDi-palmitoyl-3-sn-phosphatidylethanolamineC37 H74 N O8 P18

Primary citation

Rcf2 revealed in cryo-EM structures of hypoxic isoforms of mature mitochondrial III-IV supercomplexes. Hartley, A.M., Meunier, B., Pinotsis, N. et al. Proc Natl Acad Sci U S A (2020) 117:9329-9337. DOI 10.1073/pnas.1920612117 · PubMed

Other PDB entries of the same protein (UniProt P07256 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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