3I9V: NADH-quinone oxidoreductase subunit 1

Name: PDB 3I9V: Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 2 mol/ASU
Published: 2009-09-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: oxidoreductase

Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 2 mol/ASU. Determined by X-ray diffraction at 3.1 Å resolution. Released 15 Sept 2009.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Thermus thermophilus
Chains: 16
Atoms: 37,520
Mol. weight: 569.6 kDa
Ligands: SF4, FMN, FES, MN
Released: 15 Sept 2009

Explore 3I9V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3I9V contains 227 α-helices and 248 β-strands across 16 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.

Chains 1 and A: 26 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
α-helix	29-34	6
α-helix	39-46	8
α-helix	50-58	9
β-strand	63	1	2
β-strand	71	1	2
α-helix	72-76	5
β-strand	88-92	5	3
α-helix	103-109	7
α-helix	111-125	15
β-strand	129-134	6	3
α-helix	139-154	16
β-strand	159	1	4
α-helix	162-164	3
β-strand	169	1	4
β-strand	170-175	6	3
α-helix	180-183	4
α-helix	185-192	8
α-helix	198-201	4
α-helix	211-213	3
β-strand	216-220	5	3
α-helix	221-225	5
α-helix	227-232	6
α-helix	235-239	5
β-strand	241	1	1
β-strand	242	1	5
β-strand	247	1	5
β-strand	249-255	7	6
β-strand	258	1	7
β-strand	262-267	6	6
β-strand	271	1	8
α-helix	272-273	2
α-helix	274-279	6
β-strand	283	1	7
β-strand	287-291	5	6
α-helix	298-299	2
β-strand	300-301	2	6
α-helix	304-307	4
β-strand	310	1	8
α-helix	317-319	3
β-strand	327-332	6	6
α-helix	337-351	15
α-helix	357-367	11
α-helix	368-374	7
α-helix	381-394	14
α-helix	402-426	25
α-helix	430-432	3

Chains 2 and B: 10 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	24-26	3
α-helix	27-38	12
α-helix	43-53	11
α-helix	57-64	8
β-strand	78-83	6	9
α-helix	86-89	4
α-helix	93-104	12
β-strand	117-122	6	9
α-helix	128-130	3
β-strand	134-135	2	9
β-strand	142	1	9
α-helix	147-158	12
α-helix	163-165	3
β-strand	176	1	6

Chain 3: 33 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	10
β-strand	10-13	4	10
β-strand	18	1	11
α-helix	19-25	7
β-strand	49-50	2	12
β-strand	51-53	3	10
β-strand	75	1	10
β-strand	80-81	2	12
α-helix	85	1
β-strand	86	1	11
α-helix	87-88	2
β-strand	91-94	4	10
α-helix	98-112	15
α-helix	125-127	3
α-helix	129-137	9
α-helix	160-162	3
β-strand	168-171	4	13
β-strand	174-176	3	13
α-helix	186-193	8
β-strand	201-202	2	14
β-strand	211-212	2	14
α-helix	226-229	4
β-strand	235-237	3	13
α-helix	238-240	3
β-strand	250-255	6	15
β-strand	264-270	7	15
β-strand	272	1	16
β-strand	273-279	7	15
α-helix	292-296	5
β-strand	310-312	3	17
β-strand	317-319	3	17
α-helix	322-334	13
β-strand	341-345	5	18
α-helix	353-363	11
β-strand	369-371	3	18
α-helix	379-381	3
α-helix	383	1
β-strand	384	1	19
α-helix	387-392	6
β-strand	396-399	4	19
α-helix	402-405	4
α-helix	408-417	10
β-strand	426	1	20
β-strand	429	1	20
β-strand	448-452	5	19
α-helix	457-459	3
β-strand	464-467	4	19
α-helix	473-481	9
α-helix	488-499	12
β-strand	504-507	4	19
α-helix	510-513	4
α-helix	515-527	13
β-strand	532-534	3	19
α-helix	541-547	7
β-strand	565-568	4	18
α-helix	574-577	4
β-strand	582-585	4	18
β-strand	600-601	2	17
α-helix	607-609	3
β-strand	612-615	4	21
β-strand	620	1	22
β-strand	621-624	4	21
β-strand	629	1	16
α-helix	637-646	10
α-helix	651-652	2
α-helix	657-667	11
β-strand	675	1	22
β-strand	692-696	5	23
α-helix	701-703	3
α-helix	708-711	4
β-strand	715-718	4	23
α-helix	720-725	6
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	774-775	2	23

Chain 4: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	24
β-strand	30	1	25
β-strand	42-43	2	25
β-strand	46	1	24
β-strand	54	1	24
β-strand	57-58	2	25
α-helix	66-69	4
α-helix	70-72	3
α-helix	77-80	4
α-helix	91-101	11
α-helix	102-106	5
α-helix	111-139	29
α-helix	144-164	21
β-strand	173	1	26
β-strand	177	1	27
β-strand	178	1	26
α-helix	181-183	3
α-helix	186-209	24
α-helix	214-218	5
β-strand	224	1	28
α-helix	226-232	7
α-helix	240-242	3
α-helix	248-251	4
α-helix	257-259	3
β-strand	270	1	28
α-helix	272-295	24
β-strand	303	1	27
α-helix	311-313	3
α-helix	314-318	5
α-helix	321-332	12
α-helix	337-338	2
β-strand	340-343	4	29
β-strand	346-348	3	30
β-strand	351-353	3	30
β-strand	354-359	6	29
β-strand	367-371	5	29
α-helix	373-376	4
α-helix	391-393	3
α-helix	395-398	4
α-helix	404-408	5

Chain 5: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
β-strand	19	1	31
β-strand	25	1	31
β-strand	26-28	3	32
α-helix	31-43	13
β-strand	49-56	8	32
β-strand	68-74	7	32
β-strand	88-94	7	32
β-strand	100	1	33
α-helix	111-120	10
β-strand	125	1	33
β-strand	157-158	2	34
β-strand	164-165	2	34
α-helix	167-169	3
α-helix	187-189	3

Chains 6 and F: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	19-32	14
β-strand	39-42	4	35
α-helix	46-50	5
β-strand	78-81	4	35
β-strand	85	1	36
α-helix	89-97	9
β-strand	105-108	4	35
α-helix	109-113	5
β-strand	123	1	36
α-helix	127-129	3
β-strand	135-137	3	35
α-helix	144-158	15
β-strand	163	1	37
α-helix	168	1
β-strand	169	1	37
α-helix	170-171	2

Chains 7 and H: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-26	22
β-strand	31-36	6	42
α-helix	38-41	4
β-strand	54-60	7	42
β-strand	66-72	7	42
β-strand	82-86	5	42
β-strand	91-95	5	42
β-strand	96-98	3	43
β-strand	102-105	4	43
β-strand	108-109	2	43
α-helix	112-126	15

Chains 9 and G: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	30	1
β-strand	31-32	2	38
β-strand	41-43	3	39
β-strand	45	1	40
β-strand	51	1	40
α-helix	58-62	5
β-strand	68-73	6	41
β-strand	87-94	8	41
α-helix	103-107	5
β-strand	113-115	3	39
β-strand	123	1	35
α-helix	126-129	4
β-strand	130-131	2	41
α-helix	133-136	4
β-strand	137	1	39
α-helix	144-149	6
β-strand	161-162	2	38
α-helix	168-170	3

3 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, A	protein	438	Thermus thermophilus	Q56222 (AlphaFold model)
NADH-quinone oxidoreductase subunit 2	2, B	protein	181	Thermus thermophilus	Q56221 (AlphaFold model)
NADH-quinone oxidoreductase subunit 3	3, C	protein	783	Thermus thermophilus	Q56223 (AlphaFold model)
NADH-quinone oxidoreductase subunit 4	4, D	protein	409	Thermus thermophilus	Q56220 (AlphaFold model)
NADH-quinone oxidoreductase subunit 5	5, E	protein	207	Thermus thermophilus	Q56219
NADH-quinone oxidoreductase subunit 6	6, F	protein	181	Thermus thermophilus	Q56218
NADH-quinone oxidoreductase subunit 9	9, G	protein	182	Thermus thermophilus	Q56224
NADH-quinone oxidoreductase subunit 15	7, H	protein	129	Thermus thermophilus	Q5SKZ7

Sequence of entity 1 (1, A), FASTA

>3I9V_1 NADH-quinone oxidoreductase subunit 1 (chains 1, A)
MTGPILSGLDPRFERTLYAHVGKEGSWTLDYYLRHGGYETAKRVLKEKTPDEVIEEVKRS
GLRGRGGAGFPTGLKWSFMPKDDGKQHYLICNADESEPGSFKDRYILEDVPHLLIEGMIL
AGYAIRATVGYIYVRGEYRRAADRLEQAIKEARARGYLGKNLFGTDFSFDLHVHRGAGAY
ICGEETALMNSLEGLRANPRLKPPFPAQSGLWGKPTTINNVETLASVVPIMERGADWFAQ
MGTEQSKGMKLYQISGPVKRPGVYELPMGTTFRELIYEWAGGPLEPIQAIIPGGSSTPPL
PFTEEVLDTPMSYEHLQAKGSMLGTGGVILIPERVSMVDAMWNLTRFYAHESCGKCTPCR
EGVAGFMVNLFAKIGTGQGEEKDVENLEALLPLIEGRSFCPLADAAVWPVKGSLRHFKDQ
YLALAREKRPVPRPSLWR

Sequence of entity 2 (2, B), FASTA

>3I9V_2 NADH-quinone oxidoreductase subunit 2 (chains 2, B)
MGFFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEV
MGVASFYSYYQFVPTGKYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQ
KVECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRAGKRLEEIELPGKCGHHVHEVE
V

Sequence of entity 3 (3, C), FASTA

>3I9V_3 NADH-quinone oxidoreductase subunit 3 (chains 3, C)
MVRVKVNDRIVEVPPGTSVMDAVFHAGYDVPLFCSEKHLSPIGACRMCLVRIGLPKKGPD
GKPLLNEKGEPEIQWQPKLAASCVTAVADGMVVDTLSDVVREAQAGMVEFTLLNHPLDCP
TCDKGGACELQDRTVEYGLYEKYYQKGPLELPVYTRFEFTRRHVDKHHPLSPFVILDRER
CIHCKRCVRYFEEVPGDEVLDFIERGVHTFIGTMDFGLPSGFSGNITDICPVGALLDLTA
RFRARNWEMEETPTTCALCPVGCGITADTRSGELLRIRAREVPEVNEIWICDAGRFGHEW
ADQNRLKTPLVRKEGRLVEATWEEAFLALKEGLKEARGEEVGLYLAHDATLEEGLLASEL
AKALKTPHLDFQGRTAAPASLFPPASLEDLLQADFALVLGDPTEEAPILHLRLSEFVRDL
KPPHRYNHGTPFADLQIKERMPRRTDKMALFAPYRAPLMKWAAIHEVHRPGEEREILLAL
LGDKEGSEMVAKAKEAWEKAKNPVLILGAGVLQDTVAAERARLLAERKGAKVLAMTPAAN
ARGLEAMGVLPGAKGASWDEPGALYAYYGFVPPEEALKGKRFVVMHLSHLHPLAERYAHV
VLPAPTFYEKRGHLVNLEGRVLPLSPAPIENGEAEGALQVLALLAEALGVRPPFRLHLEA
QKALKARKVPEAMGRLSFRLKELRPKERKGAFYLRPTMWKAHQAVGKAQEAARAELWAHP
ETARAEALPEGAQVAVETPFGRVEARVVHREDVPKGHLYLSALGPAAGLRVEGRVLVPAG
GEA

Sequence of entity 4 (4, D), FASTA

>3I9V_4 NADH-quinone oxidoreductase subunit 4 (chains 4, D)
MREEFLEEIPLDAPPEEAKELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIG
YLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAETIRVIL
NELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKE
DLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLR
ASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLEPG
PVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSD
GGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR

Sequence of entity 5 (5, E), FASTA

>3I9V_5 NADH-quinone oxidoreductase subunit 5 (chains 5, E)
MRLERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKAMGFNFLADIVGLDYLTY
PDPRPERFAVVYELVSLPGWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYD
LFGIVFEGHPDLRKILTPEDLEGHPLRKDYPLGETPTLFREGRYIIPAEFRAALTGKDPG
LTFYKGGSRKGYRSLWADLKKAREVKG

Sequence of entity 6 (6, F), FASTA

>3I9V_6 NADH-quinone oxidoreductase subunit 6 (chains 6, F)
MALKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDL
ARFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFNN
YAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAYNERGERLPPVAAWKRTR
G

Sequence of entity 7 (9, G), FASTA

>3I9V_7 NADH-quinone oxidoreductase subunit 9 (chains 9, G)
MTLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCA
AACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFE
MADYEYSDLVYGKEDMLVDVVGTKPQRREAKRTGKPVKVGYVVPYVRPELEGFKAPTEGG
KR

Sequence of entity 8 (7, H), FASTA

>3I9V_8 NADH-quinone oxidoreductase subunit 15 (chains 7, H)
MSASSERELYEAWVELLSWMREYAQAKGVRFEKEADFPDFIYRMERPYDLPTTIMTASLS
DGLGEPFLLADVSPRHAKLKRIGLRLPRAHIHLHAHYEPGKGLVTGKIPLTKERFFALAD
RAREALAFA

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	14
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	2
FES	FE2/S2 (inorganic) cluster	Fe2 S2	4
MN	Manganese (II) ion	Mn	12
CA	Calcium ion	Ca	2

Primary citation

Structural basis for the mechanism of respiratory complex I. Berrisford, J.M., Sazanov, L.A. J Biol Chem (2009) 284:29773-29783. DOI 10.1074/jbc.M109.032144 · PubMed

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

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
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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