8BQ5
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete conformation 1 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 (PF10531) 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 (B5TM92) Pfam (PF00146) UniProt (by SIFTS) (P92558) | Arabidopsis thaliana (thale cress) | |
| 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 (A0A2P2CLG1) Pfam (PF00499) UniProt (by SIFTS) (P60497) | Arabidopsis thaliana (thale cress) | |
| 11 | K (K) | NADH dehydrogenase subunit 4L | polymer | 100 | 11193.6 | 1 | UniProt (A0A2P2CLH7) Pfam (PF00420) UniProt (by SIFTS) (Q04614) | Arabidopsis thaliana (thale cress) | |
| 12 | L (L) | NADH-ubiquinone oxidoreductase chain 5 | polymer | 669 | 74498.0 | 1 | UniProt (B5TM94) Pfam (PF00662) Pfam (PF00361) Pfam (PF06455) UniProt (by SIFTS) (P29388) | Arabidopsis thaliana (thale cress) | |
| 13 | M (M) | NADH-ubiquinone oxidoreductase chain 4 | polymer | 495 | 55995.7 | 1 | UniProt (B5TM93) Pfam (PF00361) UniProt (by SIFTS) (P93313) | Arabidopsis thaliana (thale cress) | |
| 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) | AT3G07480.1 | polymer | 159 | 17626.2 | 1 | UniProt (A0A384LA38) UniProt (by SIFTS) (Q9SRR8) | Arabidopsis thaliana (thale cress) | |
| 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) | P1 | polymer | 98 | 11808.2 | 1 | UniProt (A0A178W1I8) Pfam (PF17250) UniProt (by SIFTS) (Q9FYF8) | Arabidopsis thaliana (thale cress) | |
| 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) | B15 -- 1 beta subcomplex subunit 4 | polymer | 71 | 8305.5 | 1 | UniProt (A0A178VZI4) UniProt (by SIFTS) (Q9SIQ8) | Arabidopsis thaliana (thale cress) | |
| 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 (A0A2P2CLG2) Pfam (PF00033) Pfam (PF00032) UniProt (by SIFTS) (P42792) | Arabidopsis thaliana (thale cress) | |
| 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 | PB, SB, UB, VB, XB... (B, F, G, I) | IRON/SULFUR CLUSTER | non-polymer | 351.6 | 6 | Chemie (SF4) | |||
| 59 | LC, QB, SC, TB (AD, E, BD, G) | FE2/S2 (INORGANIC) CLUSTER | non-polymer | 175.8 | 4 | Chemie (FES) | |||
| 60 | RB (F) | FLAVIN MONONUCLEOTIDE | non-polymer | 456.3 | 1 | Chemie (FMN) | |||
| 61 | WB (H) | Ubiquinone-9 | non-polymer | 795.2 | 1 | Chemie (UQ9) | |||
| 62 | ZB (O) | FE (III) ION | non-polymer | 55.8 | 1 | Chemie (FE) | |||
| 63 | AC (P) | NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | non-polymer | 745.4 | 1 | Chemie (NDP) | |||
| 64 | BC, FC, GC, NC (R, y, AB, BB) | ZINC ION | non-polymer | 65.4 | 4 | Chemie (ZN) | |||
| 65 | CC, DC (W, n) | S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate | non-polymer | 540.7 | 2 | Chemie (8Q1) | |||
| 66 | EC (x) | CROTONYL COENZYME A | non-polymer | 835.6 | 1 | Chemie (COO) | |||
| 67 | HC, IC, MC, OC, PC... (AC, AE, BC, BE) | PROTOPORPHYRIN IX CONTAINING FE | non-polymer | 616.5 | 6 | Chemie (HEM) | |||
| 68 | JC, KC, QC (AC, BC) | 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 | 3 | Chemie (UQ5) | |||
| 69 | RC (BC) | UBIQUINONE-7 | non-polymer | 659.0 | 1 | Chemie (UQ7) |
Sequence modifications
D: 1 - 394 (UniProt: P93306)
L: 1 - 669 (UniProt: B5TM94)
M: 1 - 495 (UniProt: B5TM93)
| PDB | External Database | Details |
|---|---|---|
| Leu 70 | Ser 70 | conflict |
| Ser 227 | Pro 227 | conflict |
| Leu 309 | Ser 309 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Phe 91 | Ser 91 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Leu 326 | Pro 326 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 67 |
| Total formula weight | 1575182.7 | |
| Non-Polymers* | Number of molecules | 31 |
| Total formula weight | 12970.7 | |
| All* | Total formula weight | 1588153.4 |
