6I0D: NADH-quinone oxidoreductase subunit 1

Respiratory complex I from Thermus thermophilus with bound Decyl-Ubiquinone. Determined by X-ray diffraction at 3.6 Å resolution. Released 2 Sept 2020.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Thermus thermophilus HB8
Chains: 32
Atoms: 74,132
Mol. weight: 1081.22 kDa
Ligands: DCQ, FES, FMN, SF4
Released: 2 Sept 2020

Explore 6I0D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6I0D contains 485 α-helices and 312 β-strands across 32 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 1: 27 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
α-helix	18-20	3
α-helix	29-34	6
α-helix	39-47	9
α-helix	50-60	11
β-strand	63	1	2
β-strand	71	1	2
α-helix	72-77	6
β-strand	88-92	5	3
α-helix	102-109	8
α-helix	111-125	15
β-strand	129-134	6	3
α-helix	139-154	16
β-strand	171-175	5	3
α-helix	180-183	4
α-helix	185-193	9
α-helix	211-213	3
β-strand	217-220	4	3
α-helix	221-232	12
α-helix	238-240	3
β-strand	241	1	1
β-strand	242	1	4
β-strand	247	1	4
β-strand	249-255	7	5
β-strand	258	1	6
β-strand	262-267	6	5
β-strand	271	1	7
α-helix	272-273	2
α-helix	274-279	6
β-strand	283	1	6
β-strand	287-291	5	5
α-helix	298-299	2
β-strand	300-301	2	5
α-helix	304-307	4
β-strand	310	1	7
α-helix	317-319	3
β-strand	327-332	6	5
α-helix	337-350	14
α-helix	357	1
α-helix	358-367	10
α-helix	368-373	6
α-helix	374-378	5
α-helix	381-390	10
α-helix	392-395	4
α-helix	402-427	26
α-helix	430-432	3

Chain 2: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	23-26	4
α-helix	27-38	12
α-helix	43-53	11
α-helix	57-64	8
β-strand	78-83	6	9
α-helix	86-90	5
α-helix	93-104	12
β-strand	111	1	9
β-strand	117-122	6	9
β-strand	134-136	3	9
α-helix	140-141	2
β-strand	142	1	9
α-helix	147-158	12
β-strand	176	1	5

Chain 3: 38 helices, 50 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	10
β-strand	9-13	5	10
β-strand	17	1	11
β-strand	18	1	12
α-helix	19-25	7
β-strand	36	1	13
β-strand	39	1	13
β-strand	49-50	2	14
β-strand	51-53	3	10
β-strand	75	1	10
β-strand	80-81	2	14
β-strand	86	1	12
β-strand	91-94	4	10
α-helix	98-112	15
α-helix	119-121	3
α-helix	129-137	9
α-helix	160-162	3
β-strand	168-169	2	15
β-strand	174-176	3	15
α-helix	186-193	8
β-strand	201-202	2	16
α-helix	206-208	3
β-strand	211-212	2	16
α-helix	225-229	5
β-strand	236-237	2	15
α-helix	238-240	3
α-helix	246-248	3
β-strand	250-255	6	17
β-strand	264-270	7	17
β-strand	272	1	18
β-strand	273-279	7	17
β-strand	282	1	19
β-strand	286	1	19
α-helix	292-296	5
α-helix	299-302	4
β-strand	310-312	3	20
β-strand	317-319	3	20
α-helix	322-333	12
β-strand	341-345	5	20
α-helix	351-363	13
β-strand	369-371	3	20
α-helix	379-381	3
α-helix	383-384	2
α-helix	387-391	5
β-strand	396-399	4	21
α-helix	402-405	4
α-helix	407-417	11
α-helix	422-424	3
β-strand	426	1	22
β-strand	429	1	22
β-strand	434	1	11
β-strand	448-451	4	21
α-helix	457-460	4
β-strand	464-465	2	21
α-helix	473-481	9
α-helix	488-499	12
β-strand	504-507	4	21
α-helix	509-512	4
α-helix	515-527	13
β-strand	532-534	3	21
α-helix	541-546	6
β-strand	565-568	4	20
α-helix	574-577	4
β-strand	582-587	6	20
α-helix	594-597	4
β-strand	600-603	4	20
α-helix	607-609	3
β-strand	612-615	4	23
β-strand	620	1	24
β-strand	621-624	4	23
α-helix	625-627	3
β-strand	629	1	18
α-helix	637-646	10
α-helix	650-652	3
α-helix	657-666	10
α-helix	669-671	3
β-strand	675	1	24
β-strand	692-696	5	25
α-helix	701-703	3
α-helix	706-708	3
β-strand	714-718	5	25
α-helix	720-725	6
β-strand	733-738	6	25
β-strand	741-749	9	25
α-helix	754	1
β-strand	758-762	5	25
β-strand	770-771	2	25
β-strand	774	1	25

Chain 4: 24 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	27
β-strand	42-46	5	27
β-strand	54-58	5	27
α-helix	66-69	4
α-helix	70-72	3
α-helix	77-80	4
α-helix	82-84	3
α-helix	91-105	15
α-helix	111-139	29
α-helix	145-164	20
β-strand	173	1	28
β-strand	177	1	29
β-strand	178	1	28
α-helix	181-183	3
α-helix	186-208	23
α-helix	214-218	5
α-helix	226-231	6
α-helix	240-242	3
α-helix	248-251	4
α-helix	257-259	3
α-helix	272-295	24
β-strand	303	1	29
α-helix	311-313	3
α-helix	315-318	4
α-helix	321-332	12
α-helix	337-338	2
β-strand	340-342	3	30
β-strand	346-348	3	31
β-strand	351-353	3	31
β-strand	355-359	5	30
β-strand	367-370	4	30
α-helix	373-377	5
α-helix	378-380	3
α-helix	381-384	4
α-helix	392-400	9
α-helix	404-407	4

Chain 5: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
β-strand	17-20	4	36
β-strand	24-28	5	36
α-helix	31-43	13
β-strand	48-56	9	36
β-strand	68-75	8	36
β-strand	87-94	8	36
β-strand	102	1	37
α-helix	111-121	11
α-helix	124-126	3
β-strand	127	1	37
β-strand	157-158	2	38
β-strand	164-165	2	38
α-helix	167-170	4
α-helix	187-190	4

Chain 6: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	22-34	13
β-strand	38-42	5	43
α-helix	46-52	7
β-strand	54	1	44
β-strand	59	1	44
α-helix	72-74	3
β-strand	77-81	5	43
β-strand	85	1	45
α-helix	86-88	3
α-helix	89-97	9
β-strand	104-108	5	43
α-helix	110-113	4
β-strand	123	1	45
α-helix	127-129	3
β-strand	133-137	5	43
α-helix	142-143	2
α-helix	144-158	15
β-strand	163	1	46
α-helix	168	1
β-strand	169	1	46
α-helix	170-171	2

Chain 7: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-27	23
β-strand	30-36	7	54
α-helix	38-41	4
β-strand	54-60	7	54
β-strand	66-72	7	54
β-strand	82-86	5	54
β-strand	91-98	8	54
β-strand	102-105	4	54
β-strand	108-109	2	54
α-helix	112-126	15

Chain 9: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
α-helix	30	1
β-strand	31-32	2	48
β-strand	42-43	2	49
β-strand	45	1	50
β-strand	51	1	50
α-helix	58-61	4
β-strand	68-73	6	51
β-strand	76	1	52
β-strand	79	1	52
β-strand	87-94	8	51
α-helix	103-107	5
β-strand	113-114	2	49
β-strand	123	1	43
α-helix	126-128	3
β-strand	130-131	2	51
α-helix	133-135	3
β-strand	137	1	49
α-helix	144-153	10
β-strand	161-162	2	48
β-strand	163	1	53
α-helix	168-170	3
β-strand	177	1	53

24 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
NADH-quinone oxidoreductase subunit 1	1, B	protein	438	Thermus thermophilus HB8	Q56222 (AlphaFold model)
NADH-quinone oxidoreductase subunit 2	2, C	protein	181	Thermus thermophilus HB8	Q56221 (AlphaFold model)
NADH-quinone oxidoreductase subunit 3	3, D	protein	783	Thermus thermophilus HB8	Q56223 (AlphaFold model)
NADH-quinone oxidoreductase subunit 4	4, E	protein	409	Thermus thermophilus HB8	Q56220 (AlphaFold model)
NADH-quinone oxidoreductase subunit 5	5, F	protein	207	Thermus thermophilus HB8	Q56219
NADH-quinone oxidoreductase subunit 6	6, G	protein	181	Thermus thermophilus HB8	Q56218
NADH-quinone oxidoreductase subunit 9	9, O	protein	182	Thermus thermophilus HB8	Q56224
NADH-quinone oxidoreductase subunit 15	7, I	protein	129	Thermus thermophilus HB8	Q5SKZ7
NADH-quinone oxidoreductase subunit 16	W, X	protein	131	Thermus thermophilus HB8	Q5SI52
NADH-quinone oxidoreductase subunit 7	A, P	protein	119	Thermus thermophilus HB8	Q56217
NADH-quinone oxidoreductase subunit 10	J, R	protein	176	Thermus thermophilus HB8	Q56225
NADH-quinone oxidoreductase subunit 11	K, S	protein	95	Thermus thermophilus HB8	Q56226

4 more molecules are not listed.

Sequence of entity 1 (1, B), FASTA

>6I0D_1 NADH-quinone oxidoreductase subunit 1 (chains 1, B)
MTGPILSGLDPRFERTLYAHVGKEGSWTLDYYLRHGGYETAKRVLKEKTPDEVIEEVKRS
GLRGRGGAGFPTGLKWSFMPKDDGKQHYLICNADESEPGSFKDRYILEDVPHLLIEGMIL
AGYAIRATVGYIYVRGEYRRAADRLEQAIKEARARGYLGKNLFGTDFSFDLHVHRGAGAY
ICGEETALMNSLEGLRANPRLKPPFPAQSGLWGKPTTINNVETLASVVPIMERGADWFAQ
MGTEQSKGMKLYQISGPVKRPGVYELPMGTTFRELIYEWAGGPLEPIQAIIPGGSSTPPL
PFTEEVLDTPMSYEHLQAKGSMLGTGGVILIPERVSMVDAMWNLTRFYAHESCGKCTPCR
EGVAGFMVNLFAKIGTGQGEEKDVENLEALLPLIEGRSFCPLADAAVWPVKGSLRHFKDQ
YLALAREKRPVPRPSLWR

Sequence of entity 2 (2, C), FASTA

>6I0D_2 NADH-quinone oxidoreductase subunit 2 (chains 2, C)
MGFFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEV
MGVASFYSYYQFVPTGKYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQ
KVECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRAGKRLEEIELPGKCGHHVHEVE
V

Sequence of entity 3 (3, D), FASTA

>6I0D_3 NADH-quinone oxidoreductase subunit 3 (chains 3, D)
MVRVKVNDRIVEVPPGTSVMDAVFHAGYDVPLFCSEKHLSPIGACRMCLVRIGLPKKGPD
GKPLLNEKGEPEIQWQPKLAASCVTAVADGMVVDTLSDVVREAQAGMVEFTLLNHPLDCP
TCDKGGACELQDRTVEYGLYEKYYQKGPLELPVYTRFEFTRRHVDKHHPLSPFVILDRER
CIHCKRCVRYFEEVPGDEVLDFIERGVHTFIGTMDFGLPSGFSGNITDICPVGALLDLTA
RFRARNWEMEETPTTCALCPVGCGITADTRSGELLRIRAREVPEVNEIWICDAGRFGHEW
ADQNRLKTPLVRKEGRLVEATWEEAFLALKEGLKEARGEEVGLYLAHDATLEEGLLASEL
AKALKTPHLDFQGRTAAPASLFPPASLEDLLQADFALVLGDPTEEAPILHLRLSEFVRDL
KPPHRYNHGTPFADLQIKERMPRRTDKMALFAPYRAPLMKWAAIHEVHRPGEEREILLAL
LGDKEGSEMVAKAKEAWEKAKNPVLILGAGVLQDTVAAERARLLAERKGAKVLAMTPAAN
ARGLEAMGVLPGAKGASWDEPGALYAYYGFVPPEEALKGKRFVVMHLSHLHPLAERYAHV
VLPAPTFYEKRGHLVNLEGRVLPLSPAPIENGEAEGALQVLALLAEALGVRPPFRLHLEA
QKALKARKVPEAMGRLSFRLKELRPKERKGAFYLRPTMWKAHQAVGKAQEAARAELWAHP
ETARAEALPEGAQVAVETPFGRVEARVVHREDVPKGHLYLSALGPAAGLRVEGRVLVPAG
GEA

Sequence of entity 4 (4, E), FASTA

>6I0D_4 NADH-quinone oxidoreductase subunit 4 (chains 4, E)
MREEFLEEIPLDAPPEEAKELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIG
YLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAETIRVIL
NELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKE
DLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLR
ASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLEPG
PVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSD
GGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR

Sequence of entity 5 (5, F), FASTA

>6I0D_5 NADH-quinone oxidoreductase subunit 5 (chains 5, F)
MRLERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKAMGFNFLADIVGLDYLTY
PDPRPERFAVVYELVSLPGWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYD
LFGIVFEGHPDLRKILTPEDLEGHPLRKDYPLGETPTLFREGRYIIPAEFRAALTGKDPG
LTFYKGGSRKGYRSLWADLKKAREVKG

Sequence of entity 6 (6, G), FASTA

>6I0D_6 NADH-quinone oxidoreductase subunit 6 (chains 6, G)
MALKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDL
ARFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFNN
YAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAYNERGERLPPVAAWKRTR
G

Sequence of entity 7 (9, O), FASTA

>6I0D_7 NADH-quinone oxidoreductase subunit 9 (chains 9, O)
MTLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCA
AACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFE
MADYEYSDLVYGKEDMLVDVVGTKPQRREAKRTGKPVKVGYVVPYVRPELEGFKAPTEGG
KR

Sequence of entity 8 (7, I), FASTA

>6I0D_8 NADH-quinone oxidoreductase subunit 15 (chains 7, I)
MSASSERELYEAWVELLSWMREYAQAKGVRFEKEADFPDFIYRMERPYDLPTTIMTASLS
DGLGEPFLLADVSPRHAKLKRIGLRLPRAHIHLHAHYEPGKGLVTGKIPLTKERFFALAD
RAREALAFA

Sequence of entity 9 (W, X), FASTA

>6I0D_9 NADH-quinone oxidoreductase subunit 16 (chains W, X)
MVRVGMRAAPRVSLEALKAALGGLKLSEAKVYLITDWQDKRDQARYALLLHTGKKDLLVP
DAFGPAFPGGEEALSELVGLLLAQGARRFYEAVVSPGEMTALLDLPPEELLKRVMAIANP
TDPGIYLKRAA

Sequence of entity 10 (A, P), FASTA

>6I0D_10 NADH-quinone oxidoreductase subunit 7 (chains A, P)
MAPIQEYVGTLIYVGVALFIGVAALLVGALLGPKKPGRAKLMPYESGNDPAGEVKRFPVH
FYVVAMLFILFDVEVAFLWPYAVSAGGLGLYGFLGVLAFTLLLFVGFLYEWWKGVMRWH

Sequence of entity 11 (J, R), FASTA

>6I0D_11 NADH-quinone oxidoreductase subunit 10 (chains J, R)
MSLLEGLALFLLLLSGVLVVTLRNAIHAALALILNFLVLAGVYVALDARFLGFIQVIVYA
GAIVVLFLFVIMLLFAAQGEIGFDPLVRSRPLAALLALGVAGILAAGLWGLDLAFTQDLK
GGLPQALGPLLYGDWLFVLLAVGFLLMAATVVAVALVEPGKASRAKEAEKREEVAR

Sequence of entity 12 (K, S), FASTA

>6I0D_12 NADH-quinone oxidoreductase subunit 11 (chains K, S)
MSYLLTSALLFALGVYGVLTRRTAILVFLSIELMLNAANLSLVGFARAYGLDGQVAALMV
IAVAAAEVAVGLGLIVAIFRHRESTAVDDLSELRG

Ligands and cofactors

ID	Name	Formula	Copies
DCQ	2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione	C19 H30 O4	2
FES	FE2/S2 (inorganic) cluster	Fe2 S2	4
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	2
SF4	Iron/sulfur cluster	Fe4 S4	14

Primary citation

Key role of quinone in the mechanism of respiratory complex I. Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G.S. et al. Nat Commun (2020) 11:4135-4135. DOI 10.1038/s41467-020-17957-0 · PubMed

Other PDB entries of the same protein (UniProt Q56222 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3I9V 3.1 Å, Crystal structure of the hydrophilic domain of respiratory complex I from Thermus…
3IAM 3.1 Å, Crystal structure of the hydrophilic domain of respiratory complex I from Thermus…
6Y11 3.11 Å, Respiratory complex I from Thermus thermophilus
3IAS 3.15 Å, Crystal structure of the hydrophilic domain of respiratory complex I from Thermus…
6I1P 3.21 Å, Respiratory complex I from Thermus thermophilus with bound NADH
2FUG 3.3 Å, Crystal structure of the hydrophilic domain of respiratory complex I from Thermus…
4HEA 3.3 Å, Crystal structure of the entire respiratory complex I from Thermus thermophilus
6Q8W 3.4 Å, Respiratory complex I from Thermus thermophilus with bound Aureothin.
6Q8X 3.51 Å, Respiratory complex I from Thermus thermophilus with bound Pyridaben.
6Q8O 3.6 Å, Respiratory complex I from Thermus thermophilus with bound Piericidin A
6ZIY 4.25 Å, Respiratory complex I from Thermus thermophilus, NADH dataset, major state
6ZJL 4.3 Å, Respiratory complex I from Thermus thermophilus, NAD+ dataset, major state

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