6Y11: Respiratory complex I from Thermus thermophilus

Respiratory complex I from Thermus thermophilus. Determined by X-ray diffraction at 3.11 Å resolution. Released 2 Sept 2020.

Method: X-ray diffraction
Resolution: 3.11 Å
Organism: Thermus thermophilus
Chains: 32
Atoms: 74,086
Mol. weight: 1080.58 kDa
Ligands: FES, FMN, SF4
Released: 2 Sept 2020

Explore 6Y11 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y11 contains 481 α-helices and 310 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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
α-helix	29-34	6
α-helix	39-47	9
α-helix	50-60	11
α-helix	62	1
β-strand	63	1	2
α-helix	64	1
β-strand	71	1	2
α-helix	72-76	5
β-strand	87-93	7	3
α-helix	102-109	8
α-helix	111-124	14
β-strand	127-134	8	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	236-239	4
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	272-274	3
α-helix	275-279	5
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	368-375	8
β-strand	376	1	8
α-helix	381-395	15
α-helix	402-427	26
β-strand	430	1	8
α-helix	431-432	2

Chain 2: 10 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	10
α-helix	86-90	5
α-helix	93-104	12
β-strand	111	1	10
β-strand	117-122	6	10
β-strand	134-136	3	10
α-helix	140-141	2
β-strand	142	1	10
α-helix	147-158	12
α-helix	163-165	3
β-strand	176	1	5

Chain 3: 38 helices, 45 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
α-helix	85	1
β-strand	86	1	13
α-helix	87	1
β-strand	91-94	4	11
α-helix	98-112	15
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
α-helix	206-208	3
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	264-270	7	17
β-strand	273-279	7	17
α-helix	292-296	5
β-strand	310-312	3	18
β-strand	317-319	3	18
α-helix	322-334	13
β-strand	341-345	5	18
α-helix	351-363	13
β-strand	369-371	3	18
α-helix	379-381	3
β-strand	384	1	19
α-helix	387-392	6
β-strand	395-399	5	19
α-helix	402-405	4
α-helix	409-417	9
α-helix	422-424	3
β-strand	426	1	20
β-strand	429	1	20
β-strand	434	1	12
β-strand	448-452	5	19
α-helix	457-461	5
β-strand	464-467	4	19
α-helix	473-481	9
α-helix	488-499	12
β-strand	503-507	5	19
α-helix	509-512	4
α-helix	515-527	13
β-strand	531-534	4	19
α-helix	541-546	6
β-strand	565-568	4	18
α-helix	574-577	4
β-strand	582-587	6	18
α-helix	594-597	4
β-strand	600-603	4	18
α-helix	607-609	3
β-strand	612-615	4	21
β-strand	620	1	22
β-strand	621-624	4	21
α-helix	625-627	3
α-helix	637-646	10
α-helix	650-652	3
α-helix	657-666	10
α-helix	669-671	3
α-helix	674	1
β-strand	675	1	22
α-helix	676-677	2
β-strand	692-696	5	23
α-helix	701-703	3
α-helix	706-708	3
β-strand	714-718	5	23
α-helix	720-726	7
β-strand	733-738	6	23
β-strand	741-749	9	23
α-helix	754	1
β-strand	758-762	5	23
β-strand	770-771	2	23
β-strand	774-776	3	23

Chain 4: 23 helices, 13 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	75-78	4
α-helix	90-105	16
α-helix	111-139	29
α-helix	146-164	19
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
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
β-strand	303	1	29
α-helix	311-313	3
α-helix	316-318	3
α-helix	321-332	12
α-helix	337-338	2
β-strand	340-342	3	31
β-strand	345-348	4	31
β-strand	351-359	9	31
β-strand	367-371	5	31
α-helix	373-376	4
α-helix	377-380	4
α-helix	381-384	4
α-helix	390-399	10
α-helix	404-407	4

Chain 5: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
β-strand	17-19	3	36
β-strand	25-28	4	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
α-helix	124	1
β-strand	125-127	3	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, 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	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

Chains 7 and I: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-27	23
β-strand	30-36	7	51
α-helix	38-41	4
β-strand	54-60	7	51
β-strand	66-72	7	51
β-strand	82-86	5	51
β-strand	91-98	8	51
β-strand	102-105	4	51
β-strand	108-109	2	51
α-helix	112-126	15

Chain 9: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	4-18	15
α-helix	30	1
β-strand	31-32	2	46
β-strand	39-43	5	47
β-strand	45	1	48
β-strand	51	1	48
α-helix	58-61	4
β-strand	68-74	7	49
β-strand	86-94	9	49
α-helix	103-107	5
β-strand	113-116	4	47
β-strand	123	1	43
α-helix	126-128	3
β-strand	130-131	2	49
α-helix	133-135	3
β-strand	137	1	47
α-helix	144-153	10
β-strand	161-162	2	46
β-strand	163	1	50
α-helix	168-170	3
β-strand	177	1	50

21 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	Q56222 (AlphaFold model)
NADH-quinone oxidoreductase subunit 2	2, C	protein	181	Thermus thermophilus	Q56221 (AlphaFold model)
NADH-quinone oxidoreductase subunit 3	3, D	protein	783	Thermus thermophilus	Q56223 (AlphaFold model)
NADH-quinone oxidoreductase subunit 4	4, E	protein	409	Thermus thermophilus	Q56220 (AlphaFold model)
NADH-quinone oxidoreductase subunit 5	5, F	protein	207	Thermus thermophilus	Q56219
NADH-quinone oxidoreductase subunit 6	6, G	protein	181	Thermus thermophilus	Q56218
NADH-quinone oxidoreductase subunit 9	9, O	protein	182	Thermus thermophilus	Q56224
NADH-quinone oxidoreductase subunit 15	7, I	protein	129	Thermus thermophilus	Q5SKZ7
DUF3197 domain-containing protein	W, X	protein	131	Thermus thermophilus	Q5SI52
NADH-quinone oxidoreductase subunit 7	A, P	protein	119	Thermus thermophilus	Q56217
NADH-quinone oxidoreductase subunit 10	J, R	protein	176	Thermus thermophilus	Q56225
NADH-quinone oxidoreductase subunit 11	K, S	protein	95	Thermus thermophilus	Q56226

4 more molecules are not listed.

Sequence of entity 1 (1, B), FASTA

>6Y11_1 NADH-quinone oxidoreductase subunit 1 (chains 1, B)
MTGPILSGLDPRFERTLYAHVGKEGSWTLDYYLRHGGYETAKRVLKEKTPDEVIEEVKRS
GLRGRGGAGFPTGLKWSFMPKDDGKQHYLICNADESEPGSFKDRYILEDVPHLLIEGMIL
AGYAIRATVGYIYVRGEYRRAADRLEQAIKEARARGYLGKNLFGTDFSFDLHVHRGAGAY
ICGEETALMNSLEGLRANPRLKPPFPAQSGLWGKPTTINNVETLASVVPIMERGADWFAQ
MGTEQSKGMKLYQISGPVKRPGVYELPMGTTFRELIYEWAGGPLEPIQAIIPGGSSTPPL
PFTEEVLDTPMSYEHLQAKGSMLGTGGVILIPERVSMVDAMWNLTRFYAHESCGKCTPCR
EGVAGFMVNLFAKIGTGQGEEKDVENLEALLPLIEGRSFCPLADAAVWPVKGSLRHFKDQ
YLALAREKRPVPRPSLWR

Sequence of entity 2 (2, C), FASTA

>6Y11_2 NADH-quinone oxidoreductase subunit 2 (chains 2, C)
MGFFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEV
MGVASFYSYYQFVPTGKYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQ
KVECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRAGKRLEEIELPGKCGHHVHEVE
V

Sequence of entity 3 (3, D), FASTA

>6Y11_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

>6Y11_4 NADH-quinone oxidoreductase subunit 4 (chains 4, E)
MREEFLEEIPLDAPPEEAKELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIG
YLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAETIRVIL
NELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKE
DLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLR
ASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLEPG
PVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSD
GGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR

Sequence of entity 5 (5, F), FASTA

>6Y11_5 NADH-quinone oxidoreductase subunit 5 (chains 5, F)
MRLERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKAMGFNFLADIVGLDYLTY
PDPRPERFAVVYELVSLPGWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYD
LFGIVFEGHPDLRKILTPEDLEGHPLRKDYPLGETPTLFREGRYIIPAEFRAALTGKDPG
LTFYKGGSRKGYRSLWADLKKAREVKG

Sequence of entity 6 (6, G), FASTA

>6Y11_6 NADH-quinone oxidoreductase subunit 6 (chains 6, G)
MALKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDL
ARFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFNN
YAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAYNERGERLPPVAAWKRTR
G

Sequence of entity 7 (9, O), FASTA

>6Y11_7 NADH-quinone oxidoreductase subunit 9 (chains 9, O)
MTLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCA
AACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFE
MADYEYSDLVYGKEDMLVDVVGTKPQRREAKRTGKPVKVGYVVPYVRPELEGFKAPTEGG
KR

Sequence of entity 8 (7, I), FASTA

>6Y11_8 NADH-quinone oxidoreductase subunit 15 (chains 7, I)
MSASSERELYEAWVELLSWMREYAQAKGVRFEKEADFPDFIYRMERPYDLPTTIMTASLS
DGLGEPFLLADVSPRHAKLKRIGLRLPRAHIHLHAHYEPGKGLVTGKIPLTKERFFALAD
RAREALAFA

Sequence of entity 9 (W, X), FASTA

>6Y11_9 DUF3197 domain-containing protein (chains W, X)
MVRVGMRAAPRVSLEALKAALGGLKLSEAKVYLITDWQDKRDQARYALLLHTGKKDLLVP
DAFGPAFPGGEEALSELVGLLLAQGARRFYEAVVSPGEMTALLDLPPEELLKRVMAIANP
TDPGIYLKRAA

Sequence of entity 10 (A, P), FASTA

>6Y11_10 NADH-quinone oxidoreductase subunit 7 (chains A, P)
MAPIQEYVGTLIYVGVALFIGVAALLVGALLGPKKPGRAKLMPYESGNDPAGEVKRFPVH
FYVVAMLFILFDVEVAFLWPYAVSAGGLGLYGFLGVLAFTLLLFVGFLYEWWKGVMRWH

Sequence of entity 11 (J, R), FASTA

>6Y11_11 NADH-quinone oxidoreductase subunit 10 (chains J, R)
MSLLEGLALFLLLLSGVLVVTLRNAIHAALALILNFLVLAGVYVALDARFLGFIQVIVYA
GAIVVLFLFVIMLLFAAQGEIGFDPLVRSRPLAALLALGVAGILAAGLWGLDLAFTQDLK
GGLPQALGPLLYGDWLFVLLAVGFLLMAATVVAVALVEPGKASRAKEAEKREEVAR

Sequence of entity 12 (K, S), FASTA

>6Y11_12 NADH-quinone oxidoreductase subunit 11 (chains K, S)
MSYLLTSALLFALGVYGVLTRRTAILVFLSIELMLNAANLSLVGFARAYGLDGQVAALMV
IAVAAAEVAVGLGLIVAIFRHRESTAVDDLSELRG

Ligands and cofactors

ID	Name	Formula	Copies
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…
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
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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