8BPX
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete composition)
This is a non-PDB format compatible entry.
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | NADH-ubiquinone oxidoreductase chain 3 | polymer | 119 | 13969.4 | 1 | UniProt (P92533) Pfam (PF00507) | Arabidopsis thaliana (thale cress) | NADH dehydrogenase subunit 3 |
| 2 | B (B) | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial | polymer | 218 | 24071.9 | 1 | UniProt (Q42577) Pfam (PF01058) | Arabidopsis thaliana (thale cress) | |
| 3 | C (C) | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 | polymer | 190 | 22910.9 | 1 | UniProt (Q95748) Pfam (PF00329) | Arabidopsis thaliana (thale cress) | NADH dehydrogenase subunit 9 |
| 4 | D (D) | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 | polymer | 394 | 45062.9 | 1 | UniProt (P93306) Pfam (PF00346) | Arabidopsis thaliana (thale cress) | NADH dehydrogenase subunit 7 |
| 5 | E (E) | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial | polymer | 255 | 28423.6 | 1 | UniProt (O22769) Pfam (PF01257) | Arabidopsis thaliana (thale cress) | |
| 6 | F (F) | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial | polymer | 486 | 53522.4 | 1 | UniProt (Q9FNN5) Pfam (PF01512) Pfam (PF22461) Pfam (PF10589) | Arabidopsis thaliana (thale cress) | |
| 7 | G (G) | NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial | polymer | 748 | 81619.4 | 1 | UniProt (Q9FGI6) Pfam (PF13510) Pfam (PF10588) Pfam (PF22117) Pfam (PF22151) Pfam (PF00384) Pfam (PF09326) | Arabidopsis thaliana (thale cress) | Protein EMBRYO DEFECTIVE 1467 |
| 8 | H (H) | NADH-ubiquinone oxidoreductase chain 1 | polymer | 325 | 36020.1 | 1 | UniProt (P92558) Pfam (PF00146) | Arabidopsis thaliana (thale cress) | NADH dehydrogenase subunit 1 |
| 9 | I (I) | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial | polymer | 222 | 25536.8 | 1 | UniProt (Q42599) Pfam (PF12838) | Arabidopsis thaliana (thale cress) | |
| 10 | J (J) | NADH-ubiquinone oxidoreductase chain 6 | polymer | 205 | 23690.4 | 1 | UniProt (P60497) Pfam (PF00499) | Arabidopsis thaliana (thale cress) | NADH dehydrogenase subunit 6 |
| 11 | K (K) | NADH-ubiquinone oxidoreductase chain 4L | polymer | 100 | 11193.6 | 1 | UniProt (Q04614) Pfam (PF00420) | Arabidopsis thaliana (thale cress) | NADH dehydrogenase subunit 4L |
| 12 | L (L) | NADH-ubiquinone oxidoreductase chain 5 | polymer | 669 | 74498.0 | 1 | UniProt (P29388) Pfam (PF00662) Pfam (PF00361) Pfam (PF06455) | Arabidopsis thaliana (thale cress) | NADH dehydrogenase subunit 5 |
| 13 | M (M) | NADH-ubiquinone oxidoreductase chain 4 | polymer | 495 | 55995.7 | 1 | UniProt (P93313) Pfam (PF00361) | Arabidopsis thaliana (thale cress) | NADH dehydrogenase subunit 4 |
| 14 | N (N) | NADH-ubiquinone oxidoreductase chain 2 | polymer | 499 | 55486.8 | 1 | UniProt (O05000) Pfam (PF00361) | Arabidopsis thaliana (thale cress) | NADH dehydrogenase subunit 2 |
| 15 | O (O) | 2Fe-2S ferredoxin-like superfamily protein | polymer | 159 | 17626.2 | 1 | UniProt (Q9SRR8) | Arabidopsis thaliana (thale cress) | F21O3.19 protein,Uncharacterized protein At3g07480,Uncharacterized protein F21O3.19 |
| 16 | P (P) | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial | polymer | 402 | 43988.7 | 1 | UniProt (Q9SK66) Pfam (PF01370) | Arabidopsis thaliana (thale cress) | |
| 17 | Q (Q) | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | polymer | 154 | 17160.4 | 1 | UniProt (Q9FJW4) Pfam (PF04800) | Arabidopsis thaliana (thale cress) | Protein FROSTBITE1 |
| 18 | R (R) | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial | polymer | 110 | 12251.1 | 1 | UniProt (Q9M9M6) Pfam (PF10276) | Arabidopsis thaliana (thale cress) | |
| 19 | S (S) | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 | polymer | 97 | 10865.8 | 1 | UniProt (Q9FIJ2) Pfam (PF05047) | Arabidopsis thaliana (thale cress) | |
| 20 | T (T) | Acyl carrier protein 1, mitochondrial | polymer | 122 | 13735.6 | 1 | UniProt (P53665) Pfam (PF00550) | Arabidopsis thaliana (thale cress) | MtACP-1,ACP,NADH-ubiquinone oxidoreductase 9.6 kDa subunit |
| 21 | U (U) | Acyl carrier protein 2, mitochondrial | polymer | 126 | 14183.1 | 1 | UniProt (O80800) Pfam (PF00550) | Arabidopsis thaliana (thale cress) | MtACP-2,ACP,NADH-ubiquinone oxidoreductase 9.6 kDa subunit |
| 22 | V (V) | Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial | polymer | 169 | 19201.9 | 1 | UniProt (Q9FLX7) Pfam (PF04716) | Arabidopsis thaliana (thale cress) | |
| 23 | W (W) | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 | polymer | 133 | 15102.3 | 1 | UniProt (Q9LHI0) | Arabidopsis thaliana (thale cress) | |
| 24 | X (X) | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B | polymer | 106 | 11986.0 | 1 | UniProt (Q8LGE7) Pfam (PF06747) | Arabidopsis thaliana (thale cress) | |
| 25 | Y (Y) | Outer envelope pore protein 16-3, chloroplastic/mitochondrial | polymer | 159 | 17017.3 | 1 | UniProt (O48528) Pfam (PF02466) | Arabidopsis thaliana (thale cress) | Chloroplastic outer envelope pore protein of 16 kDa 3,AtOEP16-3,OEP16-3,Mitochondrial complex I subunit B14.7 |
| 26 | Z (Z) | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A | polymer | 143 | 16145.6 | 1 | UniProt (Q8RWA7) Pfam (PF06212) | Arabidopsis thaliana (thale cress) | Protein MATERNAL EFFECT EMBRYO ARREST 4 |
| 27 | AA (a) | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 | polymer | 65 | 7349.6 | 1 | UniProt (Q9C9Z5) Pfam (PF15879) | Arabidopsis thaliana (thale cress) | |
| 28 | BA (b) | At2g46540/F11C10.23 | polymer | 65 | 6810.2 | 1 | UniProt (Q9ZPY5) | Arabidopsis thaliana (thale cress) | Expressed protein,F11C10.23/F11C10.23,Fiber |
| 29 | CA (c) | Transmembrane protein | polymer | 88 | 9876.4 | 1 | UniProt (Q8VZT9) | Arabidopsis thaliana (thale cress) | |
| 30 | DA (d) | Excitatory amino acid transporter | polymer | 81 | 9220.7 | 1 | UniProt (Q94AL6) | Arabidopsis thaliana (thale cress) | |
| 31 | EA (e) | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B | polymer | 83 | 9914.1 | 1 | UniProt (Q9LZI6) Pfam (PF10200) | Arabidopsis thaliana (thale cress) | |
| 32 | FA (f) | At4g16450 | polymer | 106 | 11383.0 | 1 | UniProt (Q84W12) Pfam (PF10785) | Arabidopsis thaliana (thale cress) | NADH-ubiquinone oxidoreductase,Uncharacterized protein At4g16450 |
| 33 | GA (g) | ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein | polymer | 114 | 12648.3 | 1 | UniProt (Q9SLC8) | Arabidopsis thaliana (thale cress) | |
| 34 | HA (i) | At1g67350 | polymer | 98 | 11808.2 | 1 | UniProt (Q9FYF8) Pfam (PF17250) | Arabidopsis thaliana (thale cress) | F1N21.17,NADH-ubiquinone oxidoreductase |
| 35 | IA (j) | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 | polymer | 69 | 7582.6 | 1 | UniProt (Q8LDK3) | Arabidopsis thaliana (thale cress) | |
| 36 | JA (k) | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A | polymer | 72 | 8064.3 | 1 | UniProt (O64725) Pfam (PF08122) | Arabidopsis thaliana (thale cress) | |
| 37 | KA (l) | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial | polymer | 125 | 13225.2 | 1 | UniProt (Q9FGK0) | Arabidopsis thaliana (thale cress) | |
| 38 | LA (m) | AT2G31490 protein | polymer | 71 | 8305.5 | 1 | UniProt (Q9SIQ8) | Arabidopsis thaliana (thale cress) | At2g31490,Expressed protein,Neuronal acetylcholine receptor subunit alpha-5,Uncharacterized protein At2g31490, B15 -- 1 beta subcomplex subunit 4 |
| 39 | MA (n) | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 | polymer | 117 | 13638.3 | 1 | UniProt (Q945M1) | Arabidopsis thaliana (thale cress) | B22 subunit of eukaryotic mitochondrial complex I,Complex I-B22,CI-B22,NADH-ubiquinone oxidoreductase B22 subunit |
| 40 | NA (o) | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 | polymer | 103 | 11757.8 | 1 | UniProt (Q9SKC9) Pfam (PF05676) | Arabidopsis thaliana (thale cress) | |
| 41 | OA (p) | NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B | polymer | 106 | 12462.3 | 1 | UniProt (Q94C12) Pfam (PF10249) | Arabidopsis thaliana (thale cress) | |
| 42 | PA (q) | Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 | polymer | 159 | 18346.7 | 1 | UniProt (Q9M9M9) Pfam (PF05071) | Arabidopsis thaliana (thale cress) | |
| 43 | QA (u) | Uncharacterized protein At1g67785 | polymer | 63 | 7546.8 | 1 | UniProt (Q8VZ65) | Arabidopsis thaliana (thale cress) | |
| 44 | RA (v) | Uncharacterized protein At2g27730, mitochondrial | polymer | 113 | 11965.5 | 1 | UniProt (Q9ZUX4) | Arabidopsis thaliana (thale cress) | |
| 45 | SA (x) | Gamma carbonic anhydrase-like 2, mitochondrial | polymer | 256 | 27985.1 | 1 | UniProt (Q9SMN1) | Arabidopsis thaliana (thale cress) | GAMMA CAL2 |
| 46 | TA (y) | Gamma carbonic anhydrase 2, mitochondrial | polymer | 278 | 30102.2 | 1 | UniProt (Q9C6B3) Pfam (PF00132) | Arabidopsis thaliana (thale cress) | GAMMA CA2,Transcription factor APFI |
| 47 | UA (z) | Gamma carbonic anhydrase 1, mitochondrial | polymer | 275 | 30010.0 | 1 | UniProt (Q9FWR5) | Arabidopsis thaliana (thale cress) | GAMMA CA1 |
| 48 | FB, VA (AA, BA) | Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial | polymer | 503 | 54459.8 | 2 | UniProt (Q9ZU25) Pfam (PF00675) Pfam (PF05193) | 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 |
| 49 | GB, WA (AB, BB) | Probable mitochondrial-processing peptidase subunit beta, mitochondrial | polymer | 531 | 59234.8 | 2 | UniProt (Q42290) Pfam (PF00675) Pfam (PF05193) | 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 |
| 50 | HB, XA (AC, BC) | Cytochrome b | polymer | 393 | 44310.6 | 2 | UniProt (P42792) Pfam (PF00033) Pfam (PF00032) | 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 |
| 51 | IB, YA (AD, BD) | Cytochrome b-c1 complex subunit Rieske-1, mitochondrial | polymer | 272 | 29645.6 | 2 | UniProt (Q94JS0) Pfam (PF02921) Pfam (PF00355) | Arabidopsis thaliana (thale cress) | Complex III subunit 5-1,Rieske iron-sulfur protein 1,RISP1,Ubiquinol-cytochrome c reductase iron-sulfur subunit 1 |
| 52 | JB, ZA (AE, BE) | Cytochrome c1 2, heme protein, mitochondrial | polymer | 307 | 33728.2 | 2 | UniProt (Q9FKS5) Pfam (PF02167) | 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 |
| 53 | AB, KB (AF, BF) | Cytochrome b-c1 complex subunit 7-2, mitochondrial | polymer | 122 | 14620.0 | 2 | UniProt (F4JWS8) Pfam (PF02271) | Arabidopsis thaliana (thale cress) | Complex III subunit 7-2,Complex III subunit VII,Ubiquinol-cytochrome c oxidoreductase subunit 7-2 |
| 54 | BB, LB (AG, BG) | Cytochrome b-c1 complex subunit 8-1, mitochondrial | polymer | 72 | 8518.0 | 2 | UniProt (Q9SG91) Pfam (PF10890) | 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 |
| 55 | CB, MB (AH, BH) | Cytochrome b-c1 complex subunit 6-1, mitochondrial | polymer | 69 | 7997.3 | 2 | UniProt (Q0WWE3) Pfam (PF02320) | Arabidopsis thaliana (thale cress) | Complex III subunit 6-1,Complex III subunit VI,Mitochondrial hinge protein,Ubiquinol-cytochrome c oxidoreductase subunit 6-1 |
| 56 | DB, NB (AI, BI) | Cytochrome b-c1 complex subunit 9, mitochondrial | polymer | 72 | 8461.6 | 2 | UniProt (Q9LXJ2) Pfam (PF05365) | Arabidopsis thaliana (thale cress) | Complex III subunit 9,Complex III subunit X,Ubiquinol-cytochrome c oxidoreductase subunit 9 |
| 57 | EB, OB (AJ, BJ) | Cytochrome b-c1 complex subunit 10, mitochondrial | polymer | 57 | 5980.9 | 2 | UniProt (Q94K78) | Arabidopsis thaliana (thale cress) | Complex III subunit 10,Complex III subunit XI,Ubiquinol-cytochrome c oxidoreductase subunit 10 |
| 58 | EC, EE, FC, GC, LC... (L, AF, M, y, BC...) | (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE | non-polymer | 751.0 | 10 | Chemie (PGT) PubChem (25267633) PubChem (449008) PubChem (102447212) PubChem (16040248) PubChem (172432040) | |||
| 59 | AC, BC, QB, UB, WB... (I, B, F, G) | IRON/SULFUR CLUSTER | non-polymer | 351.6 | 6 | Chemie (SF4) | |||
| 60 | AD, GD, HC, IE, MC... (d, m, L, BB, M...) | PHOSPHATIDYLETHANOLAMINE | non-polymer | 734.0 | 14 | Chemie (PTY) PubChem (446872) PubChem (3330137) | |||
| 61 | BE, SB, UE, VB (AD, E, BD, G) | FE2/S2 (INORGANIC) CLUSTER | non-polymer | 175.8 | 4 | Chemie (FES) | |||
| 62 | TB (F) | FLAVIN MONONUCLEOTIDE | non-polymer | 456.3 | 1 | Chemie (FMN) PubChem (710) PubChem (23585816) PubChem (8965) PubChem (51435500) PubChem (51435503) PubChem (643976) PubChem (5702760) PubChem (7048779) PubChem (7048781) PubChem (15559251) | |||
| 63 | YB (H) | Ubiquinone-9 | non-polymer | 795.2 | 1 | Chemie (UQ9) PubChem (99490) PubChem (5280473) PubChem (97038296) PubChem (97038294) PubChem (97038295) PubChem (125181414) PubChem (137350099) | |||
| 64 | CC, OC, SE, TE, ZB... (K, M, BC, H, a) | 2-{[(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-glucopyranoside | non-polymer | 1165.3 | 6 | Chemie (Q7G) | |||
| 65 | AF, BF, CD, DC, DD... (BJ, f, L, l, AI...) | 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE | non-polymer | 705.0 | 11 | Chemie (3PH) PubChem (447938) PubChem (86641) PubChem (16211043) | |||
| 66 | AE, BD, ED, FE, IC... (AC, 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-OXIDE | non-polymer | 763.1 | 9 | Chemie (PC7) PubChem (14389436) PubChem (449006) PubChem (5313171) | |||
| 67 | JC, LE, TD, UD (L, BC, AC) | 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE | non-polymer | 522.8 | 4 | Chemie (UQ5) PubChem (78410906) PubChem (6451986) PubChem (12832984) | |||
| 68 | SC (O) | FE (III) ION | non-polymer | 55.8 | 1 | Chemie (FE) PubChem (29936) | |||
| 69 | TC (P) | NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | non-polymer | 745.4 | 1 | Chemie (NDP) | |||
| 70 | HE, KD, OD, UC (BB, y, AB, R) | ZINC ION | non-polymer | 65.4 | 4 | Chemie (ZN) | |||
| 71 | VC, WC (T, W) | S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate | non-polymer | 540.7 | 2 | Chemie (8Q1) PubChem (119058169) PubChem (122362359) PubChem (162826280) | |||
| 72 | DE, HD, ID, PE, QE... (AE, u, BC, BE, AC...) | CARDIOLIPIN | non-polymer | 1464.0 | 9 | Chemie (CDL) PubChem (17753886) PubChem (5287898) | |||
| 73 | LD (y) | CROTONYL COENZYME A | non-polymer | 835.6 | 1 | Chemie (COO) PubChem (92856) PubChem (49858428) PubChem (44129625) PubChem (644064) PubChem (592) PubChem (87657467) PubChem (5280381) PubChem (5462197) PubChem (5497143) PubChem (125032976) PubChem (125032975) PubChem (135071021) PubChem (137349110) PubChem (11535197) PubChem (124929931) PubChem (124929932) PubChem (171391426) PubChem (129316461) PubChem (136212782) PubChem (163337851) | |||
| 74 | CE, JE, KE, RD, SD... (AE, BC, AC, BE) | PROTOPORPHYRIN IX CONTAINING FE | non-polymer | 616.5 | 6 | Chemie (HEM) | |||
| 75 | ME (BC) | UBIQUINONE-7 | non-polymer | 659.0 | 1 | Chemie (UQ7) PubChem (176478930) PubChem (9347) PubChem (57501260) PubChem (5289538) PubChem (5289540) PubChem (94937190) PubChem (94937186) PubChem (94937188) | |||
| 76 | AG, AH, BG, BH, CF... (Y, AD, Z, AE, A...) | water | water | 18.0 | 4834 | Chemie (HOH) |
Sequence modifications
D: 1 - 394 (UniProt: P93306)
H: 1 - 325 (UniProt: P92558)
J: 1 - 205 (UniProt: P60497)
K: 1 - 100 (UniProt: Q04614)
L: 1 - 669 (UniProt: P29388)
M: 1 - 495 (UniProt: P93313)
AC, BC: 1 - 393 (UniProt: P42792)
| PDB | External Database | Details |
|---|---|---|
| Leu 70 | Ser 70 | conflict |
| Ser 227 | Pro 227 | conflict |
| Leu 309 | Ser 309 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Arg 126 | Trp 126 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ser 155 | Pro 155 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Leu 44 | Ser 44 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Phe 91 | Ser 91 | variant |
| Phe 288 | Ser 288 | variant |
| Leu 537 | Pro 537 | variant |
| PDB | External Database | Details |
|---|---|---|
| Phe 146 | Pro 146 | variant |
| Leu 326 | Pro 326 | variant |
| Phe 383 | Ser 383 | variant |
| PDB | External Database | Details |
|---|---|---|
| Ser 40 | Pro 40 | variant |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 67 |
| Total formula weight | 1575182.7 | |
| Non-Polymers* | Number of molecules | 91 |
| Total formula weight | 66071.4 | |
| All* | Total formula weight | 1641254.1 |
