6ZIY: NADH-quinone oxidoreductase subunit 1

Respiratory complex I from Thermus thermophilus, NADH dataset, major state. Determined by electron microscopy at 4.25 Å resolution. Released 2 Sept 2020.

Method: Electron microscopy
Resolution: 4.25 Å
Organism: Thermus thermophilus
Chains: 15
Atoms: 36,101
Mol. weight: 526.75 kDa
Ligands: FES, NAI, FMN, SF4
Released: 2 Sept 2020

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

Secondary structure: helices and β-sheets

6ZIY contains 234 α-helices and 143 β-strands across 15 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
β-strand	21	1	2
β-strand	23	1	2
α-helix	29-33	5
α-helix	39-46	8
α-helix	50-60	11
α-helix	72-75	4
β-strand	87-93	7	3
α-helix	103-109	7
α-helix	111-124	14
β-strand	127-134	8	3
α-helix	140-155	16
β-strand	159	1	4
β-strand	169	1	4
β-strand	171-175	5	3
α-helix	180-183	4
α-helix	185-193	9
α-helix	211-213	3
β-strand	216-220	5	3
α-helix	221-225	5
α-helix	227-233	7
α-helix	235-239	5
β-strand	241	1	1
β-strand	249-254	6	5
β-strand	262-267	6	5
β-strand	271	1	6
α-helix	272-273	2
α-helix	274-279	6
α-helix	286	1
β-strand	287-291	5	7
β-strand	300-301	2	7
α-helix	304-307	4
β-strand	310	1	6
α-helix	311	1
α-helix	317-319	3
β-strand	327	1	5
β-strand	329-332	4	7
α-helix	337-351	15
α-helix	357-360	4
α-helix	362-367	6
α-helix	368-374	7
α-helix	382-390	9
α-helix	392-395	4
α-helix	402-416	15
α-helix	419-426	8

Chain 2: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	8-16	9
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	8
α-helix	86-90	5
α-helix	93-104	12
β-strand	117-122	6	8
α-helix	128-130	3
β-strand	134-136	3	8
β-strand	139-142	4	8
α-helix	147-158	12
β-strand	176	1	5

Chain 3: 34 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
β-strand	9-12	4	9
β-strand	18	1	10
α-helix	19-25	7
β-strand	49	1	11
β-strand	51-53	3	9
β-strand	75	1	9
β-strand	81	1	11
α-helix	82-84	3
β-strand	86	1	10
β-strand	92-94	3	9
α-helix	98-112	15
α-helix	129-137	9
β-strand	168-171	4	12
β-strand	174-176	3	12
α-helix	178-180	3
α-helix	186-193	8
β-strand	201-202	2	13
α-helix	206-208	3
β-strand	211-212	2	13
α-helix	223-225	3
α-helix	226-229	4
β-strand	235-237	3	12
α-helix	238-240	3
α-helix	246-248	3
β-strand	250-255	6	14
β-strand	264-270	7	14
β-strand	273-279	7	14
β-strand	282	1	15
β-strand	286	1	15
α-helix	292-295	4
α-helix	299-301	3
β-strand	310-312	3	16
β-strand	317-319	3	16
α-helix	322-332	11
β-strand	341-345	5	16
α-helix	351-363	13
β-strand	369-371	3	16
α-helix	388-391	4
β-strand	396-399	4	17
α-helix	402-405	4
α-helix	409-417	9
α-helix	421-423	3
β-strand	426	1	18
β-strand	429	1	18
β-strand	448-451	4	17
α-helix	457-461	5
β-strand	464-465	2	17
α-helix	468-469	2
α-helix	473-481	9
α-helix	488-499	12
β-strand	504-507	4	17
α-helix	509-512	4
α-helix	515-527	13
β-strand	532-534	3	17
α-helix	541-546	6
β-strand	565-568	4	16
α-helix	574-577	4
β-strand	583-587	5	16
β-strand	600-603	4	16
α-helix	607-609	3
β-strand	612-615	4	19
β-strand	620	1	20
β-strand	621-624	4	19
α-helix	637-647	11
α-helix	657-667	11
β-strand	675	1	20
β-strand	692-696	5	21
α-helix	701-703	3
α-helix	708-711	4
β-strand	714-718	5	21
α-helix	720-725	6
β-strand	734-738	5	21
β-strand	741-749	9	21
α-helix	754	1
β-strand	758-762	5	21
β-strand	770-771	2	21
β-strand	774	1	21

Chain 4: 21 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	22
β-strand	42-48	7	22
β-strand	51-58	8	22
α-helix	66-69	4
α-helix	70-72	3
α-helix	77-80	4
α-helix	82-84	3
α-helix	90-105	16
α-helix	111-139	29
α-helix	145-164	20
β-strand	174	1	23
β-strand	177	1	23
α-helix	186-208	23
α-helix	212-218	7
β-strand	224	1	24
α-helix	226-231	6
α-helix	239-242	4
α-helix	248-251	4
α-helix	257-259	3
β-strand	270	1	24
α-helix	272-295	24
α-helix	311-313	3
α-helix	321-332	12
α-helix	337-338	2
β-strand	340-342	3	25
β-strand	346-348	3	26
β-strand	351-353	3	26
β-strand	354-359	6	25
β-strand	367-371	5	25
α-helix	373-377	5
α-helix	381-384	4
β-strand	389	1	22
α-helix	390-400	11
α-helix	404-408	5

Chain 5: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	4-13	10
β-strand	19	1	27
β-strand	25	1	27
β-strand	28	1	28
α-helix	34-43	10
β-strand	48-56	9	28
β-strand	68-75	8	28
β-strand	78	1	29
β-strand	80	1	29
β-strand	88-94	7	28
β-strand	102	1	30
α-helix	111-121	11
α-helix	125-126	2
β-strand	127	1	30
β-strand	157-158	2	31
β-strand	164-165	2	31
α-helix	167-170	4
α-helix	187-190	4

Chain 6: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	22-34	13
β-strand	38-42	5	32
α-helix	47-52	6
α-helix	72-74	3
β-strand	77-81	5	32
β-strand	85	1	33
α-helix	86-88	3
α-helix	89-97	9
β-strand	104-108	5	32
α-helix	110-113	4
β-strand	123	1	33
α-helix	127-129	3
α-helix	132-133	2
β-strand	135-137	3	32
α-helix	142-143	2
α-helix	144-158	15
β-strand	163	1	34
β-strand	169	1	34

Chain 7: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-27	23
β-strand	30-36	7	40
α-helix	38-41	4
β-strand	54-60	7	40
β-strand	66-72	7	40
β-strand	82-85	4	40
β-strand	93-95	3	40
β-strand	96-98	3	41
β-strand	102-105	4	41
β-strand	108-109	2	41
α-helix	110	1
α-helix	112-126	15

Chain 9: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-18	15
β-strand	31-32	2	35
β-strand	39-43	5	36
β-strand	45	1	37
β-strand	51	1	37
α-helix	58-62	5
β-strand	68-74	7	38
α-helix	75-76	2
β-strand	82	1	37
β-strand	86-94	9	38
α-helix	103-107	5
β-strand	113-116	4	36
β-strand	123	1	32
α-helix	126-129	4
β-strand	130-132	3	38
α-helix	133-135	3
β-strand	137	1	36
α-helix	144-152	9
α-helix	155-157	3
β-strand	161-162	2	35
β-strand	163	1	39
β-strand	177	1	39

7 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	protein	438	Thermus thermophilus	Q56222 (AlphaFold model)
NADH-quinone oxidoreductase subunit 2	2	protein	181	Thermus thermophilus	Q56221 (AlphaFold model)
NADH-quinone oxidoreductase subunit 3	3	protein	783	Thermus thermophilus	Q56223 (AlphaFold model)
NADH-quinone oxidoreductase subunit 4	4	protein	409	Thermus thermophilus	Q56220 (AlphaFold model)
NADH-quinone oxidoreductase subunit 5	5	protein	207	Thermus thermophilus	Q56219
NADH-quinone oxidoreductase subunit 6	6	protein	181	Thermus thermophilus	Q56218
NADH-quinone oxidoreductase subunit 9	9	protein	182	Thermus thermophilus	Q56224
NADH-quinone oxidoreductase subunit 15	7	protein	129	Thermus thermophilus	Q5SKZ7
NADH-quinone oxidoreductase subunit 7	A	protein	119	Thermus thermophilus	Q56217
NADH-quinone oxidoreductase subunit 10	J	protein	176	Thermus thermophilus	Q56225
NADH-quinone oxidoreductase subunit 11	K	protein	95	Thermus thermophilus	Q56226
NADH-quinone oxidoreductase subunit 12	L	protein	606	Thermus thermophilus	Q56227

3 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>6ZIY_1 NADH-quinone oxidoreductase subunit 1 (chains 1)
MTGPILSGLDPRFERTLYAHVGKEGSWTLDYYLRHGGYETAKRVLKEKTPDEVIEEVKRS
GLRGRGGAGFPTGLKWSFMPKDDGKQHYLICNADESEPGSFKDRYILEDVPHLLIEGMIL
AGYAIRATVGYIYVRGEYRRAADRLEQAIKEARARGYLGKNLFGTDFSFDLHVHRGAGAY
ICGEETALMNSLEGLRANPRLKPPFPAQSGLWGKPTTINNVETLASVVPIMERGADWFAQ
MGTEQSKGMKLYQISGPVKRPGVYELPMGTTFRELIYEWAGGPLEPIQAIIPGGSSTPPL
PFTEEVLDTPMSYEHLQAKGSMLGTGGVILIPERVSMVDAMWNLTRFYAHESCGKCTPCR
EGVAGFMVNLFAKIGTGQGEEKDVENLEALLPLIEGRSFCPLADAAVWPVKGSLRHFKDQ
YLALAREKRPVPRPSLWR

Sequence of entity 2 (2), FASTA

>6ZIY_2 NADH-quinone oxidoreductase subunit 2 (chains 2)
MGFFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEV
MGVASFYSYYQFVPTGKYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQ
KVECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRAGKRLEEIELPGKCGHHVHEVE
V

Sequence of entity 3 (3), FASTA

>6ZIY_3 NADH-quinone oxidoreductase subunit 3 (chains 3)
MVRVKVNDRIVEVPPGTSVMDAVFHAGYDVPLFCSEKHLSPIGACRMCLVRIGLPKKGPD
GKPLLNEKGEPEIQWQPKLAASCVTAVADGMVVDTLSDVVREAQAGMVEFTLLNHPLDCP
TCDKGGACELQDRTVEYGLYEKYYQKGPLELPVYTRFEFTRRHVDKHHPLSPFVILDRER
CIHCKRCVRYFEEVPGDEVLDFIERGVHTFIGTMDFGLPSGFSGNITDICPVGALLDLTA
RFRARNWEMEETPTTCALCPVGCGITADTRSGELLRIRAREVPEVNEIWICDAGRFGHEW
ADQNRLKTPLVRKEGRLVEATWEEAFLALKEGLKEARGEEVGLYLAHDATLEEGLLASEL
AKALKTPHLDFQGRTAAPASLFPPASLEDLLQADFALVLGDPTEEAPILHLRLSEFVRDL
KPPHRYNHGTPFADLQIKERMPRRTDKMALFAPYRAPLMKWAAIHEVHRPGEEREILLAL
LGDKEGSEMVAKAKEAWEKAKNPVLILGAGVLQDTVAAERARLLAERKGAKVLAMTPAAN
ARGLEAMGVLPGAKGASWDEPGALYAYYGFVPPEEALKGKRFVVMHLSHLHPLAERYAHV
VLPAPTFYEKRGHLVNLEGRVLPLSPAPIENGEAEGALQVLALLAEALGVRPPFRLHLEA
QKALKARKVPEAMGRLSFRLKELRPKERKGAFYLRPTMWKAHQAVGKAQEAARAELWAHP
ETARAEALPEGAQVAVETPFGRVEARVVHREDVPKGHLYLSALGPAAGLRVEGRVLVPAG
GEA

Sequence of entity 4 (4), FASTA

>6ZIY_4 NADH-quinone oxidoreductase subunit 4 (chains 4)
MREEFLEEIPLDAPPEEAKELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIG
YLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAETIRVIL
NELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKE
DLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLR
ASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLEPG
PVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSD
GGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR

Sequence of entity 5 (5), FASTA

>6ZIY_5 NADH-quinone oxidoreductase subunit 5 (chains 5)
MRLERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKAMGFNFLADIVGLDYLTY
PDPRPERFAVVYELVSLPGWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYD
LFGIVFEGHPDLRKILTPEDLEGHPLRKDYPLGETPTLFREGRYIIPAEFRAALTGKDPG
LTFYKGGSRKGYRSLWADLKKAREVKG

Sequence of entity 6 (6), FASTA

>6ZIY_6 NADH-quinone oxidoreductase subunit 6 (chains 6)
MALKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDL
ARFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFNN
YAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAYNERGERLPPVAAWKRTR
G

Sequence of entity 7 (9), FASTA

>6ZIY_7 NADH-quinone oxidoreductase subunit 9 (chains 9)
MTLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCA
AACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFE
MADYEYSDLVYGKEDMLVDVVGTKPQRREAKRTGKPVKVGYVVPYVRPELEGFKAPTEGG
KR

Sequence of entity 8 (7), FASTA

>6ZIY_8 NADH-quinone oxidoreductase subunit 15 (chains 7)
MSASSERELYEAWVELLSWMREYAQAKGVRFEKEADFPDFIYRMERPYDLPTTIMTASLS
DGLGEPFLLADVSPRHAKLKRIGLRLPRAHIHLHAHYEPGKGLVTGKIPLTKERFFALAD
RAREALAFA

Sequence of entity 9 (A), FASTA

>6ZIY_9 NADH-quinone oxidoreductase subunit 7 (chains A)
MAPIQEYVGTLIYVGVALFIGVAALLVGALLGPKKPGRAKLMPYESGNDPAGEVKRFPVH
FYVVAMLFILFDVEVAFLWPYAVSAGGLGLYGFLGVLAFTLLLFVGFLYEWWKGVMRWH

Sequence of entity 10 (J), FASTA

>6ZIY_10 NADH-quinone oxidoreductase subunit 10 (chains J)
MSLLEGLALFLLLLSGVLVVTLRNAIHAALALILNFLVLAGVYVALDARFLGFIQVIVYA
GAIVVLFLFVIMLLFAAQGEIGFDPLVRSRPLAALLALGVAGILAAGLWGLDLAFTQDLK
GGLPQALGPLLYGDWLFVLLAVGFLLMAATVVAVALVEPGKASRAKEAEKREEVAR

Sequence of entity 11 (K), FASTA

>6ZIY_11 NADH-quinone oxidoreductase subunit 11 (chains K)
MSYLLTSALLFALGVYGVLTRRTAILVFLSIELMLNAANLSLVGFARAYGLDGQVAALMV
IAVAAAEVAVGLGLIVAIFRHRESTAVDDLSELRG

Sequence of entity 12 (L), FASTA

>6ZIY_12 NADH-quinone oxidoreductase subunit 12 (chains L)
MALLGTILLPLLGFALLGLFGKRMREPLPGVLASGLVLASFLLGAGLLLSGGARFQAEWL
PGIPFSLLLDNLSGFMLLIVTGVGFLIHVYAIGYMGGDPGYSRFFAYFNLFIAMMLTLVL
ADSYPVMFIGWEGVGLASFLLIGFWYKNPQYADSARKAFIVNRIGDLGFMLGMAILWALY
GTLSISELKEAMEGPLKNPDLLALAGLLLFLGAVGKSAQIPLMVWLPDAMAGPTPVSALI
HAATMVTAGVYLIARSSFLYSVLPDVSYAIAVVGLLTAAYGALSAFGQTDIKKIVAYSTI
SQLGYMFLAAGVGAYWVALFHVFTHAFFKALLFLASGSVIHALGGEQDVRKMGGLWKHLP
QTRWHALIGALALGGLPLLSGFWSKDAILAATLTYPFGGVGFYVGALLVAVLTAMYAMRW
FVLVFLGEERGHHHPHEAPPVMLWPNHLLALGSVLAGYLALPHPLPNVLEPFLKPALAEV
EAHHLSLGAEWGLIALSAAVALLGLWAGFVFFQRKVFPAWYLAFEAASREAFYVDRAYNA
LIVNPLKALAEALFYGDRGLLSGYFGLGGAARSLGQGLARLQTGYLRVYALLFVLGALLL
LGVMRW

Ligands and cofactors

ID	Name	Formula	Copies
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2
NAI	1,4-dihydronicotinamide adenine dinucleotide	C21 H29 N7 O14 P2	1
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	1
SF4	Iron/sulfur cluster	Fe4 S4	7

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.
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
6ZJL 4.3 Å, Respiratory complex I from Thermus thermophilus, NAD+ dataset, major state

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