2FUG: NADH-quinone oxidoreductase chain 1

Name: PDB 2FUG: Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus
Published: 2006-02-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: oxidoreductase

Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Determined by X-ray diffraction at 3.3 Å resolution. Released 14 Feb 2006.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Thermus thermophilus
Chains: 32
Atoms: 73,916
Mol. weight: 1137.72 kDa
Ligands: SF4, FMN, FES
Released: 14 Feb 2006

Explore 2FUG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2FUG contains 429 α-helices and 461 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: 23 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	29-33	5
α-helix	39-47	9
α-helix	50-58	9
β-strand	63	1	1
β-strand	71	1	1
α-helix	72-77	6
β-strand	88-93	6	2
α-helix	103-109	7
α-helix	111-124	14
β-strand	129-134	6	2
α-helix	139-154	16
β-strand	159	1	3
β-strand	169	1	3
β-strand	170-175	6	2
α-helix	180-183	4
α-helix	185-192	8
α-helix	198-200	3
β-strand	210	1	4
α-helix	211-213	3
β-strand	214	1	4
β-strand	216-220	5	2
α-helix	221-232	12
α-helix	235-239	5
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
β-strand	300-301	2	6
α-helix	304-307	4
β-strand	310	1	8
β-strand	327-332	6	6
α-helix	337-351	15
α-helix	357	1
α-helix	358-367	10
α-helix	368-374	7
β-strand	376	1	9
α-helix	381-395	15
α-helix	402-426	25
β-strand	430	1	9
α-helix	431-432	2

Chains 2 and B: 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	57-66	10
β-strand	78-83	6	24
α-helix	86-89	4
α-helix	93-104	12
β-strand	117-122	6	24
β-strand	134-135	2	24
β-strand	141	1	24
α-helix	147-158	12
α-helix	163-165	3
β-strand	176	1	6

Chain 3: 36 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	30
β-strand	10-13	4	30
β-strand	18	1	31
α-helix	19-26	8
β-strand	49-50	2	32
β-strand	51-53	3	30
β-strand	75	1	30
β-strand	80-81	2	32
α-helix	85	1
β-strand	86	1	31
α-helix	87	1
β-strand	92-94	3	30
α-helix	98-113	16
α-helix	125-127	3
α-helix	129-136	8
β-strand	159	1	33
α-helix	160-162	3
β-strand	168-169	2	34
β-strand	176-177	2	34
α-helix	186-193	8
β-strand	203	1	35
α-helix	206-208	3
β-strand	210	1	35
α-helix	225-229	5
β-strand	236	1	34
α-helix	238-240	3
β-strand	250-254	5	36
β-strand	265-270	6	36
β-strand	273-279	7	36
α-helix	292-296	5
α-helix	299-302	4
β-strand	310-312	3	37
β-strand	317-319	3	37
α-helix	322-333	12
β-strand	342-345	4	37
α-helix	351-363	13
β-strand	369-371	3	37
α-helix	379-381	3
α-helix	383	1
β-strand	384	1	38
α-helix	387-392	6
β-strand	396-399	4	38
α-helix	402-405	4
α-helix	407-416	10
α-helix	423-425	3
β-strand	426	1	39
β-strand	429	1	39
α-helix	441-444	4
α-helix	445-447	3
β-strand	448-452	5	38
α-helix	457-459	3
β-strand	464-467	4	38
α-helix	473-481	9
α-helix	488-499	12
β-strand	504-507	4	38
α-helix	510-512	3
α-helix	514-526	13
β-strand	531-534	4	38
α-helix	541-545	5
β-strand	566-568	3	37
α-helix	574-577	4
β-strand	583-585	3	37
α-helix	594-597	4
β-strand	600-601	2	37
α-helix	607-609	3
β-strand	612-615	4	40
β-strand	620	1	41
β-strand	621-624	4	40
α-helix	637-648	12
α-helix	657-666	10
β-strand	675	1	41
β-strand	692-693	2	42
β-strand	694	1	43
α-helix	701-703	3
α-helix	709-712	4
β-strand	733-738	6	44
β-strand	741-746	6	44
β-strand	751	1	43
β-strand	760-761	2	42

Chain 4: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	47
β-strand	44-47	4	47
β-strand	55-58	4	47
α-helix	66-69	4
α-helix	70-72	3
α-helix	75-81	7
α-helix	82-84	3
α-helix	90-104	15
α-helix	111-140	30
α-helix	143-163	21
β-strand	173-174	2	48
β-strand	177-178	2	48
α-helix	181-183	3
α-helix	186-193	8
α-helix	202-208	7
β-strand	247	1	49
β-strand	249	1	49
α-helix	273-295	23
β-strand	303	1	48
α-helix	323-332	10
α-helix	337-338	2
β-strand	346	1	50
β-strand	353	1	50
β-strand	355-358	4	51
β-strand	367-370	4	51
α-helix	374-377	4
α-helix	381-384	4
α-helix	390-392	3
α-helix	395-398	4
α-helix	404-408	5

Chains 5, E, N and W: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	2-11	10
β-strand	17-19	3	54
β-strand	25-28	4	54
α-helix	34-40	7
β-strand	52-56	5	54
β-strand	68-75	8	54
β-strand	87-94	8	54
α-helix	115-124	10
α-helix	155-156	2
β-strand	157-158	2	55
β-strand	164-165	2	55
α-helix	167-170	4

Chain 6: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	19-34	16
β-strand	41-42	2	60
α-helix	45-49	5
α-helix	51-53	3
β-strand	78-81	4	60
β-strand	85	1	61
α-helix	89-97	9
β-strand	105-108	4	60
α-helix	109-113	5
β-strand	123	1	61
α-helix	127-129	3
β-strand	135-137	3	60
α-helix	144-159	16
α-helix	168-171	4

Chains 7, H, Q and Z: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-27	24
β-strand	30-36	7	68
α-helix	38-41	4
β-strand	54-60	7	68
β-strand	66-72	7	68
β-strand	78	1	33
β-strand	82-86	5	68
β-strand	91-95	5	68
β-strand	96-98	3	69
β-strand	102-104	3	69
β-strand	109	1	69
α-helix	112-126	15

Chain 9: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	31-32	2	64
β-strand	41-43	3	65
β-strand	45	1	66
β-strand	51	1	66
α-helix	58-62	5
β-strand	68-74	7	67
β-strand	82	1	66
β-strand	86-94	9	67
α-helix	103-107	5
β-strand	113-115	3	65
β-strand	123	1	60
α-helix	126-128	3
β-strand	130-131	2	67
β-strand	137	1	65
α-helix	144-153	10
β-strand	161-162	2	64

14 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 chain 1	1, A, J, S	protein	438	Thermus thermophilus	Q56222 (AlphaFold model)
NADH-quinone oxidoreductase chain 2	2, B, K, T	protein	181	Thermus thermophilus	Q56221 (AlphaFold model)
NADH-quinone oxidoreductase chain 3	3, C, L, U	protein	783	Thermus thermophilus	Q56223 (AlphaFold model)
NADH-quinone oxidoreductase chain 4	4, D, M, V	protein	409	Thermus thermophilus	Q56220 (AlphaFold model)
NADH-quinone oxidoreductase chain 5	5, E, N, W	protein	207	Thermus thermophilus	Q56219
NADH-quinone oxidoreductase chain 6	6, F, O, X	protein	181	Thermus thermophilus	Q56218
NADH-quinone oxidoreductase chain 9	9, G, P, Y	protein	182	Thermus thermophilus	Q56224
conserved hypothetical protein	7, H, Q, Z	protein	129	Thermus thermophilus	Q5SKZ7

Sequence of entity 1 (1, A, J, S), FASTA

>2FUG_1 NADH-quinone oxidoreductase chain 1 (chains 1, A, J, S)
MTGPILSGLDPRFERTLYAHVGKEGSWTLDYYLRHGGYETAKRVLKEKTPDEVIEEVKRS
GLRGRGGAGFPTGLKWSFMPKDDGKQHYLICNADESEPGSFKDRYILEDVPHLLIEGMIL
AGYAIRATVGYIYVRGEYRRAADRLEQAIKEARARGYLGKNLFGTDFSFDLHVHRGAGAY
ICGEETALMNSLEGLRANPRLKPPFPAQSGLWGKPTTINNVETLASVVPIMERGADWFAQ
MGTEQSKGMKLYQISGPVKRPGVYELPMGTTFRELIYEWAGGPLEPIQAIIPGGSSTPPL
PFTEEVLDTPMSYEHLQAKGSMLGTGGVILIPERVSMVDAMWNLTRFYAHESCGKCTPCR
EGVAGFMVNLFAKIGTGQGEEKDVENLEALLPLIEGRSFCPLADAAVWPVKGSLRHFKDQ
YLALAREKRPVPRPSLWR

Sequence of entity 2 (2, B, K, T), FASTA

>2FUG_2 NADH-quinone oxidoreductase chain 2 (chains 2, B, K, T)
MGFFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEV
MGVASFYSYYQFVPTGKYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQ
KVECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRAGKRLEEIELPGKCGHHVHEVE
V

Sequence of entity 3 (3, C, L, U), FASTA

>2FUG_3 NADH-quinone oxidoreductase chain 3 (chains 3, C, L, U)
MVRVKVNDRIVEVPPGTSVMDAVFHAGYDVPLFCSEKHLSPIGACRMCLVRIGLPKKGPD
GKPLLNEKGEPEIQWQPKLAASCVTAVADGMVVDTLSDVVREAQAGMVEFTLLNHPLDCP
TCDKGGACELQDRTVEYGLYEKYYQKGPLELPVYTRFEFTRRHVDKHHPLSPFVILDRER
CIHCKRCVRYFEEVPGDEVLDFIERGVHTFIGTMDFGLPSGFSGNITDICPVGALLDLTA
RFRARNWEMEETPTTCALCPVGCGITADTRSGELLRIRAREVPEVNEIWICDAGRFGHEW
ADQNRLKTPLVRKEGRLVEATWEEAFLALKEGLKEARGEEVGLYLAHDATLEEGLLASEL
AKALKTPHLDFQGRTAAPASLFPPASLEDLLQADFALVLGDPTEEAPILHLRLSEFVRDL
KPPHRYNHGTPFADLQIKERMPRRTDKMALFAPYRAPLMKWAAIHEVHRPGEEREILLAL
LGDKEGSEMVAKAKEAWEKAKNPVLILGAGVLQDTVAAERARLLAERKGAKVLAMTPAAN
ARGLEAMGVLPGAKGASWDEPGALYAYYGFVPPEEALKGKRFVVMHLSHLHPLAERYAHV
VLPAPTFYEKRGHLVNLEGRVLPLSPAPIENGEAEGALQVLALLAEALGVRPPFRLHLEA
QKALKARKVPEAMGRLSFRLKELRPKERKGAFYLRPTMWKAHQAVGKAQEAARAELWAHP
ETARAEALPEGAQVAVETPFGRVEARVVHREDVPKGHLYLSALGPAAGLRVEGRVLVPAG
GEA

Sequence of entity 4 (4, D, M, V), FASTA

>2FUG_4 NADH-quinone oxidoreductase chain 4 (chains 4, D, M, V)
MREEFLEEIPLDAPPEEAKELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIG
YLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAETIRVIL
NELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKE
DLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLR
ASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLEPG
PVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSD
GGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR

Sequence of entity 5 (5, E, N, W), FASTA

>2FUG_5 NADH-quinone oxidoreductase chain 5 (chains 5, E, N, W)
MRLERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKAMGFNFLADIVGLDYLTY
PDPRPERFAVVYELVSLPGWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYD
LFGIVFEGHPDLRKILTPEDLEGHPLRKDYPLGETPTLFREGRYIIPAEFRAALTGKDPG
LTFYKGGSRKGYRSLWADLKKAREVKG

Sequence of entity 6 (6, F, O, X), FASTA

>2FUG_6 NADH-quinone oxidoreductase chain 6 (chains 6, F, O, X)
MALKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDL
ARFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFNN
YAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAYNERGERLPPVAAWKRTR
G

Sequence of entity 7 (9, G, P, Y), FASTA

>2FUG_7 NADH-quinone oxidoreductase chain 9 (chains 9, G, P, Y)
MTLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCA
AACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFE
MADYEYSDLVYGKEDMLVDVVGTKPQRREAKRTGKPVKVGYVVPYVRPELEGFKAPTEGG
KR

Sequence of entity 8 (7, H, Q, Z), FASTA

>2FUG_8 conserved hypothetical protein (chains 7, H, Q, Z)
MSASSERELYEAWVELLSWMREYAQAKGVRFEKEADFPDFIYRMERPYDLPTTIMTASLS
DGLGEPFLLADVSPRHAKLKRIGLRLPRAHIHLHAHYEPGKGLVTGKIPLTKERFFALAD
RAREALAFA

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	28
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	4
FES	FE2/S2 (inorganic) cluster	Fe2 S2	8

Primary citation

Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Sazanov, L.A., Hinchliffe, P. Science (2006) 311:1430-1436. DOI 10.1126/science.1123809 · 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
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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