6ZJL: NADH-quinone oxidoreductase subunit 1

Respiratory complex I from Thermus thermophilus, NAD+ dataset, major state. Determined by electron microscopy at 4.3 Å resolution. Released 2 Sept 2020.

Method
Electron microscopy
Resolution
4.3 Å
Organism
Thermus thermophilus
Chains
15
Atoms
36,057
Mol. weight
526.09 kDa
Ligands
SF4, FMN, FES
Released
2 Sept 2020

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

Secondary structure: helices and β-sheets

6ZJL contains 228 α-helices and 125 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, 14 β-strands

ElementResiduesLengthSheet
β-strand611
α-helix29-335
α-helix39-479
α-helix50-6011
α-helix72-776
β-strand88-9362
α-helix102-1098
α-helix111-12414
β-strand129-13462
α-helix140-15415
β-strand170-17562
α-helix180-1834
α-helix185-1939
α-helix211-2133
β-strand216-22052
α-helix221-2255
α-helix227-2337
α-helix235-2395
β-strand24111
β-strand249-25463
β-strand25814
β-strand262-26763
α-helix272-2732
α-helix274-2796
β-strand28314
β-strand287-29155
α-helix298-2992
β-strand300-30125
α-helix304-3074
α-helix317-3193
β-strand32713
β-strand329-33245
α-helix337-35014
α-helix357-3615
α-helix362-3676
α-helix368-3747
α-helix381-39010
α-helix392-3954
α-helix402-41615
α-helix418-4269
α-helix430-4345
Chain 2: 9 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix8-169
α-helix23-264
α-helix27-3812
α-helix43-5311
α-helix57-648
β-strand78-8366
α-helix86-905
α-helix93-10412
β-strand117-12266
α-helix128-1303
β-strand133-13646
β-strand139-14356
α-helix147-15812
β-strand17613
Chain 3: 33 helices, 40 β-strands
ElementResiduesLengthSheet
β-strand4-637
β-strand9-1137
α-helix19-268
β-strand4918
β-strand51-5337
β-strand8118
β-strand91-9447
α-helix98-11215
α-helix115-1162
α-helix129-1379
β-strand168-17149
β-strand174-17639
α-helix186-1938
β-strand201-202210
α-helix206-2083
β-strand211-212210
α-helix223-2253
α-helix226-2294
β-strand235-23739
α-helix238-2403
α-helix246-2483
β-strand250-255611
β-strand264-270711
β-strand273-279711
α-helix292-2954
β-strand310-312312
β-strand317-319312
α-helix322-33110
β-strand341-345512
α-helix351-36313
β-strand369-371312
β-strand384113
β-strand395-399513
α-helix402-4054
α-helix409-4179
α-helix421-4255
β-strand426114
β-strand429114
α-helix441-4433
β-strand448-452513
α-helix458-4614
β-strand464-467413
α-helix468-4692
α-helix473-4819
α-helix488-49912
β-strand503-507513
α-helix509-5124
α-helix515-52713
β-strand531-534413
α-helix541-5466
β-strand565-568412
α-helix574-5774
β-strand582-587612
β-strand600-603412
α-helix607-6093
β-strand612-615415
β-strand620116
β-strand621-624415
α-helix625-6273
α-helix637-64711
α-helix657-66711
β-strand675116
β-strand692-696517
α-helix701-7033
α-helix708-7114
β-strand714-718517
α-helix720-7256
β-strand733-738617
β-strand741-749917
α-helix7541
β-strand758-762517
β-strand770-771217
β-strand774117
Chain 4: 21 helices, 11 β-strands
ElementResiduesLengthSheet
β-strand27-30418
β-strand42-47618
β-strand52-58718
α-helix66-694
α-helix70-723
α-helix75-784
α-helix82-843
α-helix91-10515
α-helix111-13929
α-helix145-16420
β-strand173119
β-strand177120
β-strand178119
α-helix181-1833
α-helix186-20823
α-helix212-2187
α-helix226-2316
α-helix240-2423
α-helix248-2514
α-helix257-2593
α-helix272-29524
β-strand303120
α-helix311-3133
α-helix321-33212
β-strand339-342421
β-strand345-348421
β-strand351-3601021
β-strand367-371521
α-helix373-3775
α-helix381-3844
α-helix393-4008
α-helix404-4085
Chain 5: 6 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix4-129
β-strand19-20222
β-strand24-25222
β-strand28-29223
α-helix34-4310
β-strand48-56923
β-strand68-75823
β-strand88-94723
β-strand102124
α-helix111-12111
α-helix125-1262
β-strand127124
β-strand157-158225
β-strand164-165225
α-helix167-1693
α-helix187-1904
Chain 6: 10 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix22-3413
β-strand38-42526
α-helix45-528
β-strand77-81526
β-strand85127
α-helix86-883
α-helix89-979
β-strand104-108526
α-helix110-1134
β-strand123127
α-helix127-1293
β-strand135-137326
α-helix142-1432
α-helix144-15815
β-strand163128
α-helix1681
β-strand169128
α-helix170-1712
Chain 7: 5 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix5-2723
β-strand30-36733
α-helix38-414
α-helix47-482
β-strand54-60733
β-strand66-72733
β-strand82-86533
β-strand91-98833
β-strand102-105433
β-strand108-109233
α-helix1101
α-helix112-12615
Chain 9: 9 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix5-1814
α-helix301
β-strand31-32229
β-strand39-43530
β-strand45131
β-strand51131
α-helix58-625
β-strand68-74732
α-helix75-762
β-strand82131
β-strand86-94932
α-helix103-1075
β-strand113-116430
α-helix126-1294
β-strand130-132332
α-helix133-1353
α-helix144-1529
α-helix155-1584
β-strand161-162229

7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
NADH-quinone oxidoreductase subunit 11protein438Thermus thermophilusQ56222 (AlphaFold model)
NADH-quinone oxidoreductase subunit 22protein181Thermus thermophilusQ56221 (AlphaFold model)
NADH-quinone oxidoreductase subunit 33protein783Thermus thermophilusQ56223 (AlphaFold model)
NADH-quinone oxidoreductase subunit 44protein409Thermus thermophilusQ56220 (AlphaFold model)
NADH-quinone oxidoreductase subunit 55protein207Thermus thermophilusQ56219
NADH-quinone oxidoreductase subunit 66protein181Thermus thermophilusQ56218
NADH-quinone oxidoreductase subunit 99protein182Thermus thermophilusQ56224
NADH-quinone oxidoreductase subunit 157protein129Thermus thermophilusQ5SKZ7
NADH-quinone oxidoreductase subunit 7Aprotein119Thermus thermophilusQ56217
NADH-quinone oxidoreductase subunit 10Jprotein176Thermus thermophilusQ56225
NADH-quinone oxidoreductase subunit 11Kprotein95Thermus thermophilusQ56226
NADH-quinone oxidoreductase subunit 12Lprotein606Thermus thermophilusQ56227

3 more molecules are not listed.

Sequence of entity 1 (1), FASTA
>6ZJL_1 NADH-quinone oxidoreductase subunit 1 (chains 1)
MTGPILSGLDPRFERTLYAHVGKEGSWTLDYYLRHGGYETAKRVLKEKTPDEVIEEVKRS
GLRGRGGAGFPTGLKWSFMPKDDGKQHYLICNADESEPGSFKDRYILEDVPHLLIEGMIL
AGYAIRATVGYIYVRGEYRRAADRLEQAIKEARARGYLGKNLFGTDFSFDLHVHRGAGAY
ICGEETALMNSLEGLRANPRLKPPFPAQSGLWGKPTTINNVETLASVVPIMERGADWFAQ
MGTEQSKGMKLYQISGPVKRPGVYELPMGTTFRELIYEWAGGPLEPIQAIIPGGSSTPPL
PFTEEVLDTPMSYEHLQAKGSMLGTGGVILIPERVSMVDAMWNLTRFYAHESCGKCTPCR
EGVAGFMVNLFAKIGTGQGEEKDVENLEALLPLIEGRSFCPLADAAVWPVKGSLRHFKDQ
YLALAREKRPVPRPSLWR
Sequence of entity 2 (2), FASTA
>6ZJL_2 NADH-quinone oxidoreductase subunit 2 (chains 2)
MGFFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEV
MGVASFYSYYQFVPTGKYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQ
KVECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRAGKRLEEIELPGKCGHHVHEVE
V
Sequence of entity 3 (3), FASTA
>6ZJL_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
>6ZJL_4 NADH-quinone oxidoreductase subunit 4 (chains 4)
MREEFLEEIPLDAPPEEAKELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIG
YLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAETIRVIL
NELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKE
DLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLR
ASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLEPG
PVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSD
GGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR
Sequence of entity 5 (5), FASTA
>6ZJL_5 NADH-quinone oxidoreductase subunit 5 (chains 5)
MRLERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKAMGFNFLADIVGLDYLTY
PDPRPERFAVVYELVSLPGWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYD
LFGIVFEGHPDLRKILTPEDLEGHPLRKDYPLGETPTLFREGRYIIPAEFRAALTGKDPG
LTFYKGGSRKGYRSLWADLKKAREVKG
Sequence of entity 6 (6), FASTA
>6ZJL_6 NADH-quinone oxidoreductase subunit 6 (chains 6)
MALKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDL
ARFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFNN
YAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAYNERGERLPPVAAWKRTR
G
Sequence of entity 7 (9), FASTA
>6ZJL_7 NADH-quinone oxidoreductase subunit 9 (chains 9)
MTLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCA
AACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFE
MADYEYSDLVYGKEDMLVDVVGTKPQRREAKRTGKPVKVGYVVPYVRPELEGFKAPTEGG
KR
Sequence of entity 8 (7), FASTA
>6ZJL_8 NADH-quinone oxidoreductase subunit 15 (chains 7)
MSASSERELYEAWVELLSWMREYAQAKGVRFEKEADFPDFIYRMERPYDLPTTIMTASLS
DGLGEPFLLADVSPRHAKLKRIGLRLPRAHIHLHAHYEPGKGLVTGKIPLTKERFFALAD
RAREALAFA
Sequence of entity 9 (A), FASTA
>6ZJL_9 NADH-quinone oxidoreductase subunit 7 (chains A)
MAPIQEYVGTLIYVGVALFIGVAALLVGALLGPKKPGRAKLMPYESGNDPAGEVKRFPVH
FYVVAMLFILFDVEVAFLWPYAVSAGGLGLYGFLGVLAFTLLLFVGFLYEWWKGVMRWH
Sequence of entity 10 (J), FASTA
>6ZJL_10 NADH-quinone oxidoreductase subunit 10 (chains J)
MSLLEGLALFLLLLSGVLVVTLRNAIHAALALILNFLVLAGVYVALDARFLGFIQVIVYA
GAIVVLFLFVIMLLFAAQGEIGFDPLVRSRPLAALLALGVAGILAAGLWGLDLAFTQDLK
GGLPQALGPLLYGDWLFVLLAVGFLLMAATVVAVALVEPGKASRAKEAEKREEVAR
Sequence of entity 11 (K), FASTA
>6ZJL_11 NADH-quinone oxidoreductase subunit 11 (chains K)
MSYLLTSALLFALGVYGVLTRRTAILVFLSIELMLNAANLSLVGFARAYGLDGQVAALMV
IAVAAAEVAVGLGLIVAIFRHRESTAVDDLSELRG
Sequence of entity 12 (L), FASTA
>6ZJL_12 NADH-quinone oxidoreductase subunit 12 (chains L)
MALLGTILLPLLGFALLGLFGKRMREPLPGVLASGLVLASFLLGAGLLLSGGARFQAEWL
PGIPFSLLLDNLSGFMLLIVTGVGFLIHVYAIGYMGGDPGYSRFFAYFNLFIAMMLTLVL
ADSYPVMFIGWEGVGLASFLLIGFWYKNPQYADSARKAFIVNRIGDLGFMLGMAILWALY
GTLSISELKEAMEGPLKNPDLLALAGLLLFLGAVGKSAQIPLMVWLPDAMAGPTPVSALI
HAATMVTAGVYLIARSSFLYSVLPDVSYAIAVVGLLTAAYGALSAFGQTDIKKIVAYSTI
SQLGYMFLAAGVGAYWVALFHVFTHAFFKALLFLASGSVIHALGGEQDVRKMGGLWKHLP
QTRWHALIGALALGGLPLLSGFWSKDAILAATLTYPFGGVGFYVGALLVAVLTAMYAMRW
FVLVFLGEERGHHHPHEAPPVMLWPNHLLALGSVLAGYLALPHPLPNVLEPFLKPALAEV
EAHHLSLGAEWGLIALSAAVALLGLWAGFVFFQRKVFPAWYLAFEAASREAFYVDRAYNA
LIVNPLKALAEALFYGDRGLLSGYFGLGGAARSLGQGLARLQTGYLRVYALLFVLGALLL
LGVMRW

Ligands and cofactors

IDNameFormulaCopies
SF4Iron/sulfur clusterFe4 S47
FMNFlavin mononucleotideC17 H21 N4 O9 P1
FESFE2/S2 (inorganic) clusterFe2 S22

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:

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