2YBB: NADH-quinone oxidoreductase subunit 1

Name: PDB 2YBB: Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)
Published: 2011-10-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: oxidoreductase

Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876). Determined by electron microscopy at 19.0 Å resolution. Released 19 Oct 2011.

Method: Electron microscopy
Resolution: 19.0 Å
Organisms: THERMUS THERMOPHILUS, BOS TAURUS, ESCHERICHIA COLI
Chains: 48
Atoms: 72,626
Mol. weight: 1125.23 kDa
Ligands: SF4, FMN, NAI, MG
Released: 19 Oct 2011

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

Secondary structure: helices and β-sheets

2YBB contains 459 α-helices and 275 β-strands across 44 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, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
α-helix	18-20	3
α-helix	29-34	6
α-helix	39-46	8
α-helix	50-60	11
β-strand	63	1	2
β-strand	71	1	2
α-helix	72-76	5
β-strand	88-93	6	3
α-helix	104-109	6
α-helix	111-124	14
β-strand	129-134	6	3
α-helix	140-154	15
β-strand	159	1	4
α-helix	162-164	3
β-strand	169	1	4
β-strand	170-174	5	3
α-helix	180-183	4
α-helix	185-192	8
α-helix	211-213	3
β-strand	216-220	5	3
α-helix	221-232	12
α-helix	234-239	6
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	357-359	3
α-helix	360-367	8
α-helix	368-374	7
β-strand	376	1	9
α-helix	381-394	14
α-helix	402-426	25
β-strand	430	1	9
α-helix	431-432	2

Chain 2: 11 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	86-91	6
α-helix	93-104	12
β-strand	111	1	10
β-strand	117-122	6	10
α-helix	128-130	3
β-strand	133-135	3	10
α-helix	141	1
β-strand	142-143	2	10
α-helix	147-159	13
α-helix	163-165	3
β-strand	176	1	6

Chain 3: 40 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	11
β-strand	10-13	4	11
β-strand	18	1	12
α-helix	19-26	8
β-strand	49-50	2	13
β-strand	51-53	3	11
β-strand	75	1	11
β-strand	80-81	2	13
α-helix	82-84	3
β-strand	86	1	12
α-helix	87-88	2
β-strand	92-94	3	11
α-helix	98-112	15
α-helix	119-121	3
α-helix	129-137	9
β-strand	159	1	14
β-strand	168-169	2	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	223-225	3
α-helix	226-229	4
β-strand	235-237	3	15
α-helix	238-240	3
α-helix	246-248	3
β-strand	250-254	5	17
β-strand	265-269	5	17
β-strand	274-279	6	17
α-helix	280-281	2
α-helix	292-296	5
α-helix	299-302	4
β-strand	310-312	3	18
β-strand	317-319	3	18
α-helix	322-331	10
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	385-386	2
α-helix	389-392	4
β-strand	396-399	4	19
α-helix	402-405	4
α-helix	408-417	10
α-helix	423-425	3
β-strand	426	1	20
β-strand	429	1	20
α-helix	441-444	4
β-strand	448-451	4	19
α-helix	457-460	4
β-strand	464-466	3	19
α-helix	473-481	9
α-helix	488-499	12
β-strand	504-507	4	19
α-helix	509-512	4
α-helix	515-527	13
β-strand	532-534	3	19
α-helix	541-544	4
α-helix	545-547	3
β-strand	565-568	4	18
α-helix	574-576	3
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	651-652	2
α-helix	657-667	11
β-strand	675	1	22
β-strand	692-696	5	23
α-helix	701-703	3
β-strand	714-718	5	23
α-helix	720-724	5
β-strand	733-738	6	23
β-strand	741-749	9	23
β-strand	758-762	5	23
β-strand	770-771	2	23
β-strand	774-775	2	23

Chain 4: 23 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	24
β-strand	42-46	5	24
β-strand	54-58	5	24
α-helix	66-69	4
α-helix	70-72	3
α-helix	78-80	3
α-helix	82-84	3
α-helix	90-104	15
α-helix	111-137	27
α-helix	143-164	22
β-strand	173	1	25
β-strand	177	1	26
β-strand	178	1	25
α-helix	181-183	3
α-helix	186-192	7
α-helix	197-209	13
α-helix	214-218	5
α-helix	226-232	7
α-helix	240-242	3
α-helix	248-251	4
α-helix	257-259	3
α-helix	272-296	25
β-strand	303	1	26
α-helix	314-316	3
α-helix	321-331	11
α-helix	337-338	2
β-strand	340-348	9	27
β-strand	351-359	9	27
β-strand	367-370	4	27
α-helix	373-376	4
α-helix	381-384	4
α-helix	392-398	7
α-helix	404-408	5

Chain 5: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
β-strand	17-19	3	28
β-strand	25-27	3	28
β-strand	28	1	29
α-helix	31-44	14
β-strand	48-56	9	29
β-strand	68-75	8	29
β-strand	87-94	8	29
β-strand	100	1	30
α-helix	111-121	11
β-strand	125	1	30
α-helix	155-156	2
β-strand	157-158	2	31
β-strand	164-165	2	31
α-helix	167-170	4
α-helix	187-189	3

Chain 6: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	19-34	16
β-strand	41-42	2	32
α-helix	46-50	5
β-strand	78-81	4	32
β-strand	85	1	33
α-helix	89-97	9
β-strand	105-108	4	32
α-helix	109-113	5
β-strand	123	1	33
α-helix	127-129	3
β-strand	135-137	3	32
α-helix	142-143	2
α-helix	144-158	15
β-strand	163	1	34
α-helix	168	1
β-strand	169	1	34
α-helix	170-171	2

Chain 7: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-26	22
β-strand	31-36	6	35
α-helix	38-41	4
β-strand	54-60	7	35
β-strand	66-72	7	35
β-strand	78	1	14
β-strand	82-86	5	35
β-strand	91-95	5	35
β-strand	96-98	3	36
β-strand	102-105	4	36
β-strand	108-109	2	36
α-helix	112-126	15

Chain 8: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	31-32	2	38
β-strand	42-43	2	39
β-strand	45	1	40
β-strand	51	1	40
α-helix	58-62	5
β-strand	68-74	7	41
α-helix	75-76	2
β-strand	82	1	40
β-strand	86-94	9	41
α-helix	103-107	5
β-strand	113-114	2	39
β-strand	123	1	32
α-helix	126-128	3
β-strand	130-132	3	41
α-helix	133-136	4
β-strand	137	1	39
α-helix	144-149	6
β-strand	161-162	2	38

32 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 15	7	protein	129	THERMUS THERMOPHILUS	Q5SKZ7
NADH-quinone oxidoreductase subunit 9	8	protein	182	THERMUS THERMOPHILUS	Q56224
Cytochrome B-C1 complex subunit 1, mitochondrial	A, a	protein	446	BOS TAURUS	P31800
Cytochrome B-C1 complex subunit 2, mitochondrial	B, b	protein	439	BOS TAURUS	P23004
Cytochrome B	C, c	protein	379	BOS TAURUS	P00157
Cytochrome C1, heme protein, mitochondrial	D, d	protein	241	BOS TAURUS	P00125

25 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>2YBB_1 NADH-QUINONE OXIDOREDUCTASE SUBUNIT 1 (chains 1)
MTGPILSGLDPRFERTLYAHVGKEGSWTLDYYLRHGGYETAKRVLKEKTPDEVIEEVKRS
GLRGRGGAGFPTGLKWSFMPKDDGKQHYLICNADESEPGSFKDRYILEDVPHLLIEGMIL
AGYAIRATVGYIYVRGEYRRAADRLEQAIKEARARGYLGKNLFGTDFSFDLHVHRGAGAY
ICGEETALMNSLEGLRANPRLKPPFPAQSGLWGKPTTINNVETLASVVPIMERGADWFAQ
MGTEQSKGMKLYQISGPVKRPGVYELPMGTTFRELIYEWAGGPLEPIQAIIPGGSSTPPL
PFTEEVLDTPMSYEHLQAKGSMLGTGGVILIPERVSMVDAMWNLTRFYAHESCGKCTPCR
EGVAGFMVNLFAKIGTGQGEEKDVENLEALLPLIEGRSFCPLADAAVWPVKGSLRHFKDQ
YLALAREKRPVPRPSLWR

Sequence of entity 2 (2), FASTA

>2YBB_2 NADH-QUINONE OXIDOREDUCTASE SUBUNIT 2 (chains 2)
MGFFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEV
MGVASFYSYYQFVPTGKYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQ
KVECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRAGKRLEEIELPGKCGHHVHEVE
V

Sequence of entity 3 (3), FASTA

>2YBB_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

>2YBB_4 NADH-QUINONE OXIDOREDUCTASE SUBUNIT 4 (chains 4)
MREEFLEEIPLDAPPEEAKELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIG
YLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAETIRVIL
NELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKE
DLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLR
ASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLEPG
PVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSD
GGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR

Sequence of entity 5 (5), FASTA

>2YBB_5 NADH-QUINONE OXIDOREDUCTASE SUBUNIT 5 (chains 5)
MRLERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKAMGFNFLADIVGLDYLTY
PDPRPERFAVVYELVSLPGWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYD
LFGIVFEGHPDLRKILTPEDLEGHPLRKDYPLGETPTLFREGRYIIPAEFRAALTGKDPG
LTFYKGGSRKGYRSLWADLKKAREVKG

Sequence of entity 6 (6), FASTA

>2YBB_6 NADH-QUINONE OXIDOREDUCTASE SUBUNIT 6 (chains 6)
MALKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDL
ARFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFNN
YAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRGQAYNERGERLPPVAAWKRTR
G

Sequence of entity 7 (7), FASTA

>2YBB_7 NADH-QUINONE OXIDOREDUCTASE SUBUNIT 15 (chains 7)
MSASSERELYEAWVELLSWMREYAQAKGVRFEKEADFPDFIYRMERPYDLPTTIMTASLS
DGLGEPFLLADVSPRHAKLKRIGLRLPRAHIHLHAHYEPGKGLVTGKIPLTKERFFALAD
RAREALAFA

Sequence of entity 8 (8), FASTA

>2YBB_8 NADH-QUINONE OXIDOREDUCTASE SUBUNIT 9 (chains 8)
MTLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCA
AACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFE
MADYEYSDLVYGKEDMLVDVVGTKPQRREAKRTGKPVKVGYVVPYVRPELEGFKAPTEGG
KR

Sequence of entity 9 (A, a), FASTA

>2YBB_9 CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL (chains A, a)
TATYAQALQSVPETQVSQLDNGLRVASEQSSQPTCTVGVWIDAGSRYESEKNNGAGYFVE
HLAFKGTKNRPGNALEKEVESMGAHLNAYSTREHTAYYIKALSKDLPKAVELLADIVQNC
SLEDSQIEKERDVILQELQENDTSMRDVVFNYLHATAFQGTPLAQSVEGPSENVRKLSRA
DLTEYLSRHYKAPRMVLAAAGGLEHRQLLDLAQKHFSGLSGTYDEDAVPTLSPCRFTGSQ
ICHREDGLPLAHVAIAVEGPGWAHPDNVALQVANAIIGHYDCTYGGGAHLSSPLASIAAT
NKLCQSFQTFNICYADTGLLGAHFVCDHMSIDDMMFVLQGQWMRLCTSATESEVLRGKNL
LRNALVSHLDGTTPVCEDIGRSLLTYGRRIPLAEWESRIAEVDARVVREVCSKYFYDQCP
AVAGFGPIEQLPDYNRIRSGMFWLRF

Sequence of entity 10 (B, b), FASTA

>2YBB_10 CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL (chains B, b)
SLKVAPKVKATEAPAGVPPHPQDLEFTRLPNGLVIASLENYAPASRIGLFIKAGSRYENS
NNLGTSHLLRLASSLTTKGASSFKITRGIEAVGGKLSVTSTRENMAYTVECLRDDVDILM
EFLLNVTTAPEFRRWEVAALQPQLRIDKAVALQNPQAHVIENLHAAAYRNALANSLYCPD
YRIGKVTPVELHDYVQNHFTSARMALIGLGVSHPVLKQVAEQFLNIRGGLGLSGAKAKYH
GGEIREQNGDSLVHAALVAESAAIGSAEANAFSVLQHVLGAGPHVKRGSNATSSLYQAVA
KGVHQPFDVSAFNASYSDSGLFGFYTISQAASAGDVIKAAYNQVKTIAQGNLSNPDVQAA
KNKLKAGYLMSVESSEGFLDEVGSQALAAGSYTPPSTVLQQIDAVADADVINAAKKFVSG
RKSMAASGNLGHTPFIDEL

Sequence of entity 11 (C, c), FASTA

>2YBB_11 CYTOCHROME B (chains C, c)
MTNIRKSHPLMKIVNNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTT
TAFSSVTHICRDVNYGWIIRYMHANGASMFFICLYMHVGRGLYYGSYTFLETWNIGVILL
LTVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFA
FHFILPFIIMAIAMVHLLFLHETGSNNPTGISSDVDKIPFHPYYTIKDILGALLLILALM
LLVLFAPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALAFSILI
LALIPLLHTSKQRSMMFRPLSQCLFWALVADLLTLTWIGGQPVEHPYITIGQLASVLYFL
LILVLMPTAGTIENKLLKW

Sequence of entity 12 (D, d), FASTA

>2YBB_12 CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL (chains D, d)
SDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQVCSSCHSMDYVAYRHLVGVCYTEDE
AKALAEEVEVQDGPNEDGEMFMRPGKLSDYFPKPYPNPEAARAANNGALPPDLSYIVRAR
HGGEDYVFSLLTGYCEPPTGVSLREGLYFNPYFPGQAIGMAPPIYNEVLEFDDGTPATMS
QVAKDVCTFLRWAAEPEHDHRKRMGLKMLLMMGLLLPLVYAMKRHKWSVLKSRKLAYRPP
K

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	7
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	1
NAI	1,4-dihydronicotinamide adenine dinucleotide	C21 H29 N7 O14 P2	1
MG	Magnesium ion	Mg	7
FES	FE2/S2 (inorganic) cluster	Fe2 S2	4
CA	Calcium ion	Ca	1
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	5
SMA	Stigmatellin a	C30 H42 O7	2
UQ1	Ubiquinone-1	C14 H18 O4	2
HEC	Heme C	C34 H36 Fe N4 O4	2
CDL	Cardiolipin	C81 H156 O17 P2	4
HEA	Heme-a	C49 H56 Fe N4 O6	2
CU	Copper (II) ion	Cu	3
ZN	Zinc ion	Zn	1

Primary citation

Arrangement of Electron Transport Chain Components in Bovine Mitochondrial Supercomplex I(1)III(2)Iv(1). Althoff, T., Mills, D.J., Popot, J.-L. et al. EMBO J (2011) 30:4652. DOI 10.1038/EMBOJ.2011.324 · 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
6ZIY 4.25 Å, Respiratory complex I from Thermus thermophilus, NADH dataset, major state

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