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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8BPX

Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete composition)

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1ANADH-ubiquinone oxidoreductase chain 3polymer11913969.41UniProt (P92533)
Pfam (PF00507)
In PDB		Arabidopsis thaliana (thale cress)NADH dehydrogenase subunit 3
2BNADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialpolymer21824071.91UniProt (Q42577)
Pfam (PF01058)
In PDB		Arabidopsis thaliana (thale cress)
3CNADH dehydrogenase [ubiquinone] iron-sulfur protein 3polymer19022910.91UniProt (Q95748)
Pfam (PF00329)
In PDB		Arabidopsis thaliana (thale cress)NADH dehydrogenase subunit 9
4DNADH dehydrogenase [ubiquinone] iron-sulfur protein 2polymer39445062.91UniProt (P93306)
Pfam (PF00346)
In PDB		Arabidopsis thaliana (thale cress)NADH dehydrogenase subunit 7
5ENADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialpolymer25528423.61UniProt (O22769)
Pfam (PF01257)
In PDB		Arabidopsis thaliana (thale cress)
6FNADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialpolymer48653522.41UniProt (Q9FNN5)
Pfam (PF01512)
Pfam (PF22461)
Pfam (PF10531)
Pfam (PF10589)
In PDB		Arabidopsis thaliana (thale cress)
7GNADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrialpolymer74881619.41UniProt (Q9FGI6)
Pfam (PF13510)
Pfam (PF10588)
Pfam (PF22117)
Pfam (PF22151)
Pfam (PF00384)
Pfam (PF09326)
In PDB		Arabidopsis thaliana (thale cress)Protein EMBRYO DEFECTIVE 1467
8HNADH-ubiquinone oxidoreductase chain 1polymer32536020.11UniProt (P92558)
Pfam (PF00146)
In PDB		Arabidopsis thaliana (thale cress)NADH dehydrogenase subunit 1
9INADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrialpolymer22225536.81UniProt (Q42599)
Pfam (PF12838)
In PDB		Arabidopsis thaliana (thale cress)
10JNADH-ubiquinone oxidoreductase chain 6polymer20523690.41UniProt (P60497)
Pfam (PF00499)
In PDB		Arabidopsis thaliana (thale cress)NADH dehydrogenase subunit 6
11KNADH-ubiquinone oxidoreductase chain 4Lpolymer10011193.61UniProt (Q04614)
Pfam (PF00420)
In PDB		Arabidopsis thaliana (thale cress)NADH dehydrogenase subunit 4L
12LNADH-ubiquinone oxidoreductase chain 5polymer66974498.01UniProt (P29388)
Pfam (PF00662)
Pfam (PF00361)
Pfam (PF06455)
In PDB		Arabidopsis thaliana (thale cress)NADH dehydrogenase subunit 5
13MNADH-ubiquinone oxidoreductase chain 4polymer49555995.71UniProt (P93313)
Pfam (PF00361)
In PDB		Arabidopsis thaliana (thale cress)NADH dehydrogenase subunit 4
14NNADH-ubiquinone oxidoreductase chain 2polymer49955486.81UniProt (O05000)
Pfam (PF00361)
In PDB		Arabidopsis thaliana (thale cress)NADH dehydrogenase subunit 2
15O2Fe-2S ferredoxin-like superfamily proteinpolymer15917626.21UniProt (Q9SRR8)
In PDB		Arabidopsis thaliana (thale cress)F21O3.19 protein,Uncharacterized protein At3g07480,Uncharacterized protein F21O3.19
16PNADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialpolymer40243988.71UniProt (Q9SK66)
Pfam (PF01370)
In PDB		Arabidopsis thaliana (thale cress)
17QNADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialpolymer15417160.41UniProt (Q9FJW4)
Pfam (PF04800)
In PDB		Arabidopsis thaliana (thale cress)Protein FROSTBITE1
18RNADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialpolymer11012251.11UniProt (Q9M9M6)
Pfam (PF10276)
In PDB		Arabidopsis thaliana (thale cress)
19SNADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2polymer9710865.81UniProt (Q9FIJ2)
Pfam (PF05047)
In PDB		Arabidopsis thaliana (thale cress)
20TAcyl carrier protein 1, mitochondrialpolymer12213735.61UniProt (P53665)
Pfam (PF00550)
In PDB		Arabidopsis thaliana (thale cress)MtACP-1,ACP,NADH-ubiquinone oxidoreductase 9.6 kDa subunit
21UAcyl carrier protein 2, mitochondrialpolymer12614183.11UniProt (O80800)
Pfam (PF00550)
In PDB		Arabidopsis thaliana (thale cress)MtACP-2,ACP,NADH-ubiquinone oxidoreductase 9.6 kDa subunit
22VProbable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrialpolymer16919201.91UniProt (Q9FLX7)
Pfam (PF04716)
In PDB		Arabidopsis thaliana (thale cress)
23WNADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6polymer13315102.31UniProt (Q9LHI0)
In PDB		Arabidopsis thaliana (thale cress)
24XNADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-Bpolymer10611986.01UniProt (Q8LGE7)
Pfam (PF06747)
In PDB		Arabidopsis thaliana (thale cress)
25YOuter envelope pore protein 16-3, chloroplastic/mitochondrialpolymer15917017.31UniProt (O48528)
Pfam (PF02466)
In PDB		Arabidopsis thaliana (thale cress)Chloroplastic outer envelope pore protein of 16 kDa 3,AtOEP16-3,OEP16-3,Mitochondrial complex I subunit B14.7
26ZNADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-Apolymer14316145.61UniProt (Q8RWA7)
Pfam (PF06212)
In PDB		Arabidopsis thaliana (thale cress)Protein MATERNAL EFFECT EMBRYO ARREST 4
27aNADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1polymer657349.61UniProt (Q9C9Z5)
Pfam (PF15879)
In PDB		Arabidopsis thaliana (thale cress)
28bAt2g46540/F11C10.23polymer656810.21UniProt (Q9ZPY5)
In PDB		Arabidopsis thaliana (thale cress)Expressed protein,F11C10.23/F11C10.23,Fiber
29cTransmembrane proteinpolymer889876.41UniProt (Q8VZT9)
In PDB		Arabidopsis thaliana (thale cress)
30dExcitatory amino acid transporterpolymer819220.71UniProt (Q94AL6)
In PDB		Arabidopsis thaliana (thale cress)
31eNADH dehydrogenase [ubiquinone] iron-sulfur protein 5-Bpolymer839914.11UniProt (Q9LZI6)
Pfam (PF10200)
In PDB		Arabidopsis thaliana (thale cress)
32fAt4g16450polymer10611383.01UniProt (Q84W12)
Pfam (PF10785)
In PDB		Arabidopsis thaliana (thale cress)NADH-ubiquinone oxidoreductase,Uncharacterized protein At4g16450
33gESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) proteinpolymer11412648.31UniProt (Q9SLC8)
In PDB		Arabidopsis thaliana (thale cress)
34iAt1g67350polymer9811808.21UniProt (Q9FYF8)
Pfam (PF17250)
In PDB		Arabidopsis thaliana (thale cress)F1N21.17,NADH-ubiquinone oxidoreductase
35jNADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2polymer697582.61UniProt (Q8LDK3)
In PDB		Arabidopsis thaliana (thale cress)
36kNADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-Apolymer728064.31UniProt (O64725)
Pfam (PF08122)
In PDB		Arabidopsis thaliana (thale cress)
37lNADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialpolymer12513225.21UniProt (Q9FGK0)
In PDB		Arabidopsis thaliana (thale cress)
38mAT2G31490 proteinpolymer718305.51UniProt (Q9SIQ8)
In PDB		Arabidopsis thaliana (thale cress)At2g31490,Expressed protein,Neuronal acetylcholine receptor subunit alpha-5,Uncharacterized protein At2g31490, B15 -- 1 beta subcomplex subunit 4
39nNADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9polymer11713638.31UniProt (Q945M1)
In PDB		Arabidopsis thaliana (thale cress)B22 subunit of eukaryotic mitochondrial complex I,Complex I-B22,CI-B22,NADH-ubiquinone oxidoreductase B22 subunit
40oNADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7polymer10311757.81UniProt (Q9SKC9)
Pfam (PF05676)
In PDB		Arabidopsis thaliana (thale cress)
41pNADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-Bpolymer10612462.31UniProt (Q94C12)
Pfam (PF10249)
In PDB		Arabidopsis thaliana (thale cress)
42qProbable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12polymer15918346.71UniProt (Q9M9M9)
Pfam (PF05071)
In PDB		Arabidopsis thaliana (thale cress)
43uUncharacterized protein At1g67785polymer637546.81UniProt (Q8VZ65)
In PDB		Arabidopsis thaliana (thale cress)
44vUncharacterized protein At2g27730, mitochondrialpolymer11311965.51UniProt (Q9ZUX4)
In PDB		Arabidopsis thaliana (thale cress)
45xGamma carbonic anhydrase-like 2, mitochondrialpolymer25627985.11UniProt (Q9SMN1)
In PDB		Arabidopsis thaliana (thale cress)GAMMA CAL2
46yGamma carbonic anhydrase 2, mitochondrialpolymer27830102.21UniProt (Q9C6B3)
Pfam (PF00132)
In PDB		Arabidopsis thaliana (thale cress)GAMMA CA2,Transcription factor APFI
47zGamma carbonic anhydrase 1, mitochondrialpolymer27530010.01UniProt (Q9FWR5)
In PDB		Arabidopsis thaliana (thale cress)GAMMA CA1
48AA, BAProbable mitochondrial-processing peptidase subunit alpha-1, mitochondrialpolymer50354459.82UniProt (Q9ZU25)
Pfam (PF00675)
Pfam (PF05193)
In PDB		Arabidopsis thaliana (thale cress)Alpha-MPP 1,Complex III subunit II,Core protein II,Cytochrome b-c1 complex subunit 2-1,mitochondrial,Inactive zinc metalloprotease alpha-1,Ubiquinol-cytochrome c oxidoreductase core protein 2-1
49AB, BBProbable mitochondrial-processing peptidase subunit beta, mitochondrialpolymer53159234.82UniProt (Q42290)
Pfam (PF00675)
Pfam (PF05193)
In PDB		Arabidopsis thaliana (thale cress)Beta-MPP,Complex III subunit I,Core protein I,Cytochrome b-c1 complex subunit 1,mitochondrial,Ubiquinol-cytochrome c oxidoreductase core protein 1
50AC, BCCytochrome bpolymer39344310.62UniProt (P42792)
Pfam (PF00033)
Pfam (PF00032)
In PDB		Arabidopsis thaliana (thale cress)Complex III subunit 3,Complex III subunit III,Cytochrome b-c1 complex subunit 3,Ubiquinol-cytochrome-c reductase complex cytochrome b subunit
51AD, BDCytochrome b-c1 complex subunit Rieske-1, mitochondrialpolymer27229645.62UniProt (Q94JS0)
Pfam (PF02921)
Pfam (PF00355)
In PDB		Arabidopsis thaliana (thale cress)Complex III subunit 5-1,Rieske iron-sulfur protein 1,RISP1,Ubiquinol-cytochrome c reductase iron-sulfur subunit 1
52AE, BECytochrome c1 2, heme protein, mitochondrialpolymer30733728.22UniProt (Q9FKS5)
Pfam (PF02167)
In PDB		Arabidopsis thaliana (thale cress)Complex III subunit 4-2,Complex III subunit IV-2,Cytochrome b-c1 complex subunit 4-2,Ubiquinol-cytochrome c reductase complex cytochrome c1 subunit 2,Cytochrome c-1 2
53AF, BFCytochrome b-c1 complex subunit 7-2, mitochondrialpolymer12214620.02UniProt (F4JWS8)
Pfam (PF02271)
In PDB		Arabidopsis thaliana (thale cress)Complex III subunit 7-2,Complex III subunit VII,Ubiquinol-cytochrome c oxidoreductase subunit 7-2
54AG, BGCytochrome b-c1 complex subunit 8-1, mitochondrialpolymer728518.02UniProt (Q9SG91)
Pfam (PF10890)
In PDB		Arabidopsis thaliana (thale cress)Complex III subunit 8-1,Complex III subunit VIII,Ubiquinol-cytochrome c oxidoreductase subunit 8-1,Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C
55AH, BHCytochrome b-c1 complex subunit 6-1, mitochondrialpolymer697997.32UniProt (Q0WWE3)
Pfam (PF02320)
In PDB		Arabidopsis thaliana (thale cress)Complex III subunit 6-1,Complex III subunit VI,Mitochondrial hinge protein,Ubiquinol-cytochrome c oxidoreductase subunit 6-1
56AI, BICytochrome b-c1 complex subunit 9, mitochondrialpolymer728461.62UniProt (Q9LXJ2)
Pfam (PF05365)
In PDB		Arabidopsis thaliana (thale cress)Complex III subunit 9,Complex III subunit X,Ubiquinol-cytochrome c oxidoreductase subunit 9
57AJ, BJCytochrome b-c1 complex subunit 10, mitochondrialpolymer575980.92UniProt (Q94K78)
In PDB		Arabidopsis thaliana (thale cress)Complex III subunit 10,Complex III subunit XI,Ubiquinol-cytochrome c oxidoreductase subunit 10
58L, AF, M, y, BC...(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATEnon-polymer751.010Chemie (PGT)
59I, B, F, GIRON/SULFUR CLUSTERnon-polymer351.66Chemie (SF4)
60d, m, L, BB, M...PHOSPHATIDYLETHANOLAMINEnon-polymer734.014Chemie (PTY)
61AD, E, BD, GFE2/S2 (INORGANIC) CLUSTERnon-polymer175.84Chemie (FES)
62FFLAVIN MONONUCLEOTIDEnon-polymer456.31Chemie (FMN)
63HUbiquinone-9non-polymer795.21Chemie (UQ9)
64K, M, BC, H, a2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosidenon-polymer1165.36Chemie (Q7G)
65BJ, f, L, l, AI...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATEnon-polymer705.011Chemie (3PH)
66AC, d, f, AG, L...(7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDEnon-polymer763.19Chemie (PC7)
67L, BC, AC2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONEnon-polymer522.84Chemie (UQ5)
68OFE (III) IONnon-polymer55.81Chemie (FE)
69PNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATEnon-polymer745.41Chemie (NDP)
70BB, y, AB, RZINC IONnon-polymer65.44Chemie (ZN)
71T, WS-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioatenon-polymer540.72Chemie (8Q1)
72AE, u, BC, BE, AC...CARDIOLIPINnon-polymer1464.09Chemie (CDL)
73yCROTONYL COENZYME Anon-polymer835.61Chemie (COO)
74AE, BC, AC, BEPROTOPORPHYRIN IX CONTAINING FEnon-polymer616.56Chemie (HEM)
75BCUBIQUINONE-7non-polymer659.01Chemie (UQ7)
76waterwater18.04834Chemie (HOH)
Sequence modifications
D: 1 - 394 (UniProt: P93306)
PDBExternal DatabaseDetails
Leu 70Ser 70conflict
Ser 227Pro 227conflict
Leu 309Ser 309conflict
H: 1 - 325 (UniProt: P92558)
PDBExternal DatabaseDetails
Arg 126Trp 126conflict
J: 1 - 205 (UniProt: P60497)
PDBExternal DatabaseDetails
Ser 155Pro 155conflict
K: 1 - 100 (UniProt: Q04614)
PDBExternal DatabaseDetails
Leu 44Ser 44conflict
L: 1 - 669 (UniProt: P29388)
PDBExternal DatabaseDetails
Phe 91Ser 91variant
Phe 288Ser 288variant
Leu 537Pro 537variant
M: 1 - 495 (UniProt: P93313)
PDBExternal DatabaseDetails
Phe 146Pro 146variant
Leu 326Pro 326variant
Phe 383Ser 383variant
AC, BC: 1 - 393 (UniProt: P42792)
PDBExternal DatabaseDetails
Ser 40Pro 40variant
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains67
Total formula weight1575182.7
Non-Polymers*Number of molecules91
Total formula weight66071.4
All*Total formula weight1641254.1
*Water molecules are not included.

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PDB entries from 2024-07-24

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