6I1P: NADH-quinone oxidoreductase subunit 1

Respiratory complex I from Thermus thermophilus with bound NADH. Determined by X-ray diffraction at 3.21 Å resolution. Released 2 Sept 2020.

Method: X-ray diffraction
Resolution: 3.21 Å
Organism: Thermus thermophilus HB8
Chains: 32
Atoms: 74,174
Mol. weight: 1081.91 kDa
Ligands: SF4, FMN, NAI, FES
Released: 2 Sept 2020

Explore 6I1P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6I1P contains 470 α-helices and 309 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: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
α-helix	29-34	6
α-helix	39-47	9
α-helix	50-59	10
β-strand	63	1	2
β-strand	71	1	2
α-helix	72-77	6
β-strand	87-93	7	3
α-helix	102-109	8
α-helix	111-125	15
β-strand	127-134	8	3
α-helix	140-154	15
β-strand	170-175	6	3
α-helix	180-183	4
α-helix	185-193	9
α-helix	199-201	3
α-helix	211-213	3
β-strand	217-220	4	3
α-helix	221-232	12
α-helix	236-239	4
β-strand	241	1	1
β-strand	249-255	7	4
β-strand	258	1	5
β-strand	262-267	6	4
β-strand	271	1	6
α-helix	272-273	2
α-helix	274-279	6
β-strand	283	1	5
β-strand	287-291	5	4
α-helix	298-299	2
β-strand	300-301	2	4
α-helix	304-307	4
β-strand	310	1	6
α-helix	317-319	3
β-strand	327-332	6	4
α-helix	337-350	14
α-helix	357	1
α-helix	358-367	10
α-helix	368-375	8
β-strand	376	1	7
α-helix	381-390	10
α-helix	392-395	4
α-helix	402-426	25
β-strand	430	1	7
α-helix	431-432	2

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	4

Chain 3: 32 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	11
β-strand	9-13	5	11
β-strand	17	1	12
β-strand	18	1	13
α-helix	19-25	7
β-strand	49-50	2	14
β-strand	51-53	3	11
β-strand	75	1	11
β-strand	80-81	2	14
β-strand	86	1	13
β-strand	91-94	4	11
α-helix	98-112	15
α-helix	119-121	3
α-helix	129-137	9
α-helix	160-162	3
β-strand	168-171	4	15
β-strand	174-176	3	15
α-helix	186-193	8
β-strand	201-202	2	16
β-strand	211-212	2	16
α-helix	225-229	5
β-strand	235-237	3	15
α-helix	238-240	3
β-strand	250-255	6	17
β-strand	264-269	6	17
β-strand	272	1	18
β-strand	274-279	6	17
β-strand	282	1	19
β-strand	286	1	19
α-helix	292-296	5
β-strand	310-312	3	20
β-strand	317-319	3	20
α-helix	322-332	11
β-strand	341-345	5	20
α-helix	351-363	13
β-strand	369-371	3	20
β-strand	384	1	21
α-helix	387-392	6
β-strand	395-399	5	21
α-helix	402-405	4
α-helix	408-416	9
β-strand	426	1	22
β-strand	429	1	22
β-strand	434	1	12
β-strand	449-452	4	21
α-helix	457-460	4
β-strand	464-467	4	21
α-helix	473-481	9
α-helix	488-499	12
β-strand	503-507	5	21
α-helix	509-512	4
α-helix	515-527	13
β-strand	532-534	3	21
α-helix	541-547	7
β-strand	565-568	4	20
α-helix	574-577	4
β-strand	582-587	6	20
α-helix	592-597	6
β-strand	600-603	4	20
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	669-670	2
α-helix	674	1
β-strand	675	1	24
α-helix	676-677	2
β-strand	692-696	5	25
α-helix	701-703	3
β-strand	715-718	4	25
α-helix	720-726	7
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	774-776	3	25

Chain 4: 23 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	28
β-strand	42-46	5	28
β-strand	54-58	5	28
α-helix	66-69	4
α-helix	70-72	3
α-helix	75-78	4
α-helix	91-105	15
α-helix	111-139	29
α-helix	144-163	20
β-strand	173	1	29
β-strand	178	1	29
α-helix	181-183	3
α-helix	186-209	24
α-helix	215-218	4
β-strand	224	1	30
α-helix	226-231	6
α-helix	240-242	3
α-helix	248-251	4
α-helix	257-259	3
β-strand	270	1	30
α-helix	272-295	24
α-helix	311-313	3
α-helix	314-317	4
α-helix	321-332	12
α-helix	337-338	2
β-strand	339-342	4	31
β-strand	346-348	3	32
β-strand	351-353	3	32
β-strand	354-360	7	31
β-strand	367-371	5	31
α-helix	373-376	4
α-helix	378-380	3
α-helix	381-384	4
α-helix	392-399	8
α-helix	404-407	4

Chain 5: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	2-11	10
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	88-94	7	36
β-strand	100-102	3	37
α-helix	111-121	11
β-strand	125-127	3	37
β-strand	157-158	2	38
β-strand	164-165	2	38
α-helix	167-169	3
α-helix	187-190	4

Chain 6: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	22-34	13
β-strand	38-42	5	43
α-helix	45-51	7
α-helix	52-54	3
α-helix	72-74	3
β-strand	77-81	5	43
β-strand	85	1	44
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	44
α-helix	127-129	3
β-strand	135-137	3	43
α-helix	142-143	2
α-helix	144-158	15
β-strand	163	1	45
α-helix	168	1
β-strand	169	1	45
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	52
α-helix	38-41	4
β-strand	54-60	7	52
β-strand	66-72	7	52
β-strand	82-86	5	52
β-strand	91-98	8	52
β-strand	102-105	4	52
β-strand	108-109	2	52
α-helix	112-125	14

Chain 9: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	4-18	15
β-strand	31-32	2	47
β-strand	39-43	5	48
β-strand	45	1	49
β-strand	51	1	49
α-helix	58-61	4
β-strand	68-74	7	50
β-strand	86-94	9	50
α-helix	103-107	5
β-strand	113-116	4	48
β-strand	123	1	43
α-helix	126-128	3
β-strand	130-131	2	50
α-helix	133-135	3
β-strand	137	1	48
α-helix	144-153	10
β-strand	161-162	2	47
β-strand	163	1	51
α-helix	168-170	3
β-strand	177	1	51

23 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

>6I1P_1 NADH-quinone oxidoreductase subunit 1 (chains 1, B)
MTGPILSGLDPRFERTLYAHVGKEGSWTLDYYLRHGGYETAKRVLKEKTPDEVIEEVKRS
GLRGRGGAGFPTGLKWSFMPKDDGKQHYLICNADESEPGSFKDRYILEDVPHLLIEGMIL
AGYAIRATVGYIYVRGEYRRAADRLEQAIKEARARGYLGKNLFGTDFSFDLHVHRGAGAY
ICGEETALMNSLEGLRANPRLKPPFPAQSGLWGKPTTINNVETLASVVPIMERGADWFAQ
MGTEQSKGMKLYQISGPVKRPGVYELPMGTTFRELIYEWAGGPLEPIQAIIPGGSSTPPL
PFTEEVLDTPMSYEHLQAKGSMLGTGGVILIPERVSMVDAMWNLTRFYAHESCGKCTPCR
EGVAGFMVNLFAKIGTGQGEEKDVENLEALLPLIEGRSFCPLADAAVWPVKGSLRHFKDQ
YLALAREKRPVPRPSLWR

Sequence of entity 2 (2, C), FASTA

>6I1P_2 NADH-quinone oxidoreductase subunit 2 (chains 2, C)
MGFFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEV
MGVASFYSYYQFVPTGKYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQ
KVECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRAGKRLEEIELPGKCGHHVHEVE
V

Sequence of entity 3 (3, D), FASTA

>6I1P_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

>6I1P_4 NADH-quinone oxidoreductase subunit 4 (chains 4, E)
MREEFLEEIPLDAPPEEAKELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIG
YLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAETIRVIL
NELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKE
DLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLR
ASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLEPG
PVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSD
GGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR

Sequence of entity 5 (5, F), FASTA

>6I1P_5 NADH-quinone oxidoreductase subunit 5 (chains 5, F)
MRLERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKAMGFNFLADIVGLDYLTY
PDPRPERFAVVYELVSLPGWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYD
LFGIVFEGHPDLRKILTPEDLEGHPLRKDYPLGETPTLFREGRYIIPAEFRAALTGKDPG
LTFYKGGSRKGYRSLWADLKKAREVKG

Sequence of entity 6 (6, G), FASTA

>6I1P_6 NADH-quinone oxidoreductase subunit 6 (chains 6, G)
MALKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDL
ARFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFNN
YAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAYNERGERLPPVAAWKRTR
G

Sequence of entity 7 (9, O), FASTA

>6I1P_7 NADH-quinone oxidoreductase subunit 9 (chains 9, O)
MTLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCA
AACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFE
MADYEYSDLVYGKEDMLVDVVGTKPQRREAKRTGKPVKVGYVVPYVRPELEGFKAPTEGG
KR

Sequence of entity 8 (7, I), FASTA

>6I1P_8 NADH-quinone oxidoreductase subunit 15 (chains 7, I)
MSASSERELYEAWVELLSWMREYAQAKGVRFEKEADFPDFIYRMERPYDLPTTIMTASLS
DGLGEPFLLADVSPRHAKLKRIGLRLPRAHIHLHAHYEPGKGLVTGKIPLTKERFFALAD
RAREALAFA

Sequence of entity 9 (W, X), FASTA

>6I1P_9 NADH-quinone oxidoreductase subunit 16 (chains W, X)
MVRVGMRAAPRVSLEALKAALGGLKLSEAKVYLITDWQDKRDQARYALLLHTGKKDLLVP
DAFGPAFPGGEEALSELVGLLLAQGARRFYEAVVSPGEMTALLDLPPEELLKRVMAIANP
TDPGIYLKRAA

Sequence of entity 10 (A, P), FASTA

>6I1P_10 NADH-quinone oxidoreductase subunit 7 (chains A, P)
MAPIQEYVGTLIYVGVALFIGVAALLVGALLGPKKPGRAKLMPYESGNDPAGEVKRFPVH
FYVVAMLFILFDVEVAFLWPYAVSAGGLGLYGFLGVLAFTLLLFVGFLYEWWKGVMRWH

Sequence of entity 11 (J, R), FASTA

>6I1P_11 NADH-quinone oxidoreductase subunit 10 (chains J, R)
MSLLEGLALFLLLLSGVLVVTLRNAIHAALALILNFLVLAGVYVALDARFLGFIQVIVYA
GAIVVLFLFVIMLLFAAQGEIGFDPLVRSRPLAALLALGVAGILAAGLWGLDLAFTQDLK
GGLPQALGPLLYGDWLFVLLAVGFLLMAATVVAVALVEPGKASRAKEAEKREEVAR

Sequence of entity 12 (K, S), FASTA

>6I1P_12 NADH-quinone oxidoreductase subunit 11 (chains K, S)
MSYLLTSALLFALGVYGVLTRRTAILVFLSIELMLNAANLSLVGFARAYGLDGQVAALMV
IAVAAAEVAVGLGLIVAIFRHRESTAVDDLSELRG

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	14
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	2
NAI	1,4-dihydronicotinamide adenine dinucleotide	C21 H29 N7 O14 P2	2
FES	FE2/S2 (inorganic) cluster	Fe2 S2	4

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…
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.
6I0D 3.6 Å, Respiratory complex I from Thermus thermophilus with bound Decyl-Ubiquinone
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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