6G2J: NADH-ubiquinone oxidoreductase chain 3

Name: PDB 6G2J: Mouse mitochondrial complex I in the active state
Published: 2018-06-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: oxidoreductase

Mouse mitochondrial complex I in the active state. Determined by electron microscopy at 3.3 Å resolution. Released 6 Jun 2018.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Mus musculus
Chains: 45
Atoms: 66,810
Mol. weight: 1065.95 kDa
Ligands: 3PE, SF4, FES, FMN
Released: 6 Jun 2018

Explore 6G2J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6G2J contains 397 α-helices and 180 β-strands across 45 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 a: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	2-5	4
α-helix	6-10	5
α-helix	12-14	3
α-helix	18-31	14
α-helix	42-51	10

Chain A: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	4-22	19
α-helix	56-72	17
α-helix	75-78	4
α-helix	86-107	22

Chain b: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	7-13	7
α-helix	18-28	11
α-helix	32-34	3
α-helix	38-40	3
α-helix	41-47	7
α-helix	54-56	3
β-strand	57	1	76

Chain B: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	37-53	17
β-strand	57	1	1
β-strand	58	1	2
α-helix	65-70	6
α-helix	80-82	3
β-strand	87	1	2
α-helix	90-92	3
β-strand	95-99	5	1
β-strand	103	1	3
α-helix	106-114	9
β-strand	122-126	5	1
α-helix	128-131	4
β-strand	142	1	3
α-helix	146-148	3
β-strand	154-156	3	1
α-helix	163-166	4
α-helix	173-176	4
α-helix	184-187	4

Chain c: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	14-42	29

Chain C: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	17-31	15
β-strand	37-42	6	4
β-strand	48-52	5	4
α-helix	54-56	3
α-helix	58-60	3
α-helix	62-65	4
β-strand	74-78	5	4
β-strand	81-82	2	5
β-strand	90-91	2	5
β-strand	93-97	5	4
β-strand	104-108	5	4
α-helix	127-137	11
β-strand	172-177	6	6
β-strand	182-187	6	6

Chain d: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	2-4	3
α-helix	31-48	18
α-helix	61-96	36
α-helix	98-100	3
α-helix	114-116	3

Chain D: 21 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	29-32	4
β-strand	50	1	7
β-strand	65	1	7
β-strand	68	1	8
β-strand	72	1	9
β-strand	73	1	8
β-strand	77	1	7
α-helix	91-93	3
α-helix	102-106	5
α-helix	112-126	15
α-helix	132-142	11
α-helix	145-154	10
α-helix	156-159	4
α-helix	165-173	9
α-helix	175-182	8
α-helix	202-204	3
α-helix	208-229	22
α-helix	234-238	5
α-helix	247-253	7
α-helix	261-263	3
β-strand	285-287	3	10
α-helix	295-316	22
α-helix	337-340	4
α-helix	343-351	9
α-helix	358-359	2
β-strand	361-362	2	11
β-strand	367-368	2	12
β-strand	373-374	2	12
β-strand	375-376	2	13
β-strand	379-380	2	11
β-strand	391-392	2	13
α-helix	399-402	4
β-strand	410	1	9
α-helix	411-417	7
α-helix	419-421	3

37 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-ubiquinone oxidoreductase chain 3	A	protein	115	Mus musculus	P03899 (AlphaFold model)
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial	B	protein	224	Mus musculus	Q9DC70 (AlphaFold model)
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial	C	protein	263	Mus musculus	Q9DCT2 (AlphaFold model)
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial	D	protein	463	Mus musculus	Q91WD5 (AlphaFold model)
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial	E	protein	248	Mus musculus	Q9D6J6
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial	F	protein	428	Mus musculus	Q91YT0
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial	G	protein	727	Mus musculus	Q91VD9
NADH-ubiquinone oxidoreductase chain 1	H	protein	318	Mus musculus	P03888
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial	I	protein	212	Mus musculus	Q8K3J1
NADH-ubiquinone oxidoreductase chain 6	J	protein	172	Mus musculus	P03925
NADH-ubiquinone oxidoreductase chain 4L	K	protein	98	Mus musculus	P03903
NADH-ubiquinone oxidoreductase chain 5	L	protein	607	Mus musculus	P03921

32 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>6G2J_1 NADH-ubiquinone oxidoreductase chain 3 (chains A)
MNLYTVIFINILLSLTLILVAFWLPQMNLYSEKANPYECGFDPTSSARLPFSMKFFLVAI
TFLLFDLEIALLLPLPWAIQTIKTSTMMIMAFILVTILSLGLAYEWTQKGLEWTE

Sequence of entity 2 (B), FASTA

>6G2J_2 NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (chains B)
MAALAAPGLLSVRILGLRTAQVQLRRVHQSVATEGPSPSPSPSLSSTQSAVSKAGAGAVV
PKLSHLPRSRAEYVVTKLDDLINWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVV
FRASPRQADVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRG
CDRIVPVDIYVPGCPPTAEALLYGILQLQRKIKREQKLKIWYRR

Sequence of entity 3 (C), FASTA

>6G2J_3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (chains C)
MAAAAARVWCRGLLGAASVGRGAGRPSVLWQHVRRESAAADKRPTVRPRSDVTHKQLSAF
GEYVAEILPKYVQQVQVSCLDELEICIHPDGVIPTLTFLRDHTNAQFKSLADLTAVDVPT
RQNRFEIVYNLLSLRFNSRIRVKTYADELTPIDSIVSVHIAANWYEREVWDMFGVFFFNH
PDLRRILTDYGFEGHPFRKDFPLTGYVELRYDDEVKRVVAEPVELAQEFRKFDLNSPWEA
FPAYRQPPESLKLEAGDKKPETK

Sequence of entity 4 (D), FASTA

>6G2J_4 NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (chains D)
MAALRALRCLRGVGAPVLRPGSGIRLPSQPSRGARQWQPDIEWAEQFSGAVMYPSKETAH
WKPPPWNDVDILKEKAVTNMTLNFGPQHPAAHGVLRLVLELSGEMVRKCDPHIGLLHRGT
EKLIEYKTYLQALPYFDRLDYVSMMCNEQAYSIAVEKLLNIQPPPRAQWIRVLFGEITRI
LNHIMAVTTHALDIGAMTPFFWMFEEREKMFEFYERVSGARMHAAYIRPGGVHQDLPLGL
LDDIYEFSKNFSLRIDEVEEMLTNNRIWRNRTVDIGVVTAEDALNYGFSGVMLRGSGIQW
DLRKTQPYDVYDQVEFDVPIGSRGDCYDRYLCRVEEMRQSLRIIEQCLNKMPPGEIKVDD
AKVSPPKRAEMKTSMESLIHHFKLYTEGYQVPPGATYTAIEAPKGEFGVYLVSDGSSRPY
RCKIKAPGFAHLAGLDKMSKGHMLADVVAIIGTQDIVFGEIDR

Sequence of entity 5 (E), FASTA

>6G2J_5 NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (chains E)
MFSLALRARATGLAAQWGRHARNLHKTAVHNGAGGALFVHRDTPENNPDTPFDFTPENYK
RIEAIVKNYPEGHQAAAVLPVLDLAQRQNGWLPISAMNKVAEVLQVPPMRVYEVATFYTM
YNRKPVGKYHIQVCTTTPCMLRDSDSILETLQRKLGIKVGETTPDKLFTLIEVECLGACV
NAPMVQINDNYYEDLTPKDIEEIIDELKAGKVPKPGPRSGRFCCEPAGGLTSLTEPPKGP
GFGVQAGL

Sequence of entity 6 (F), FASTA

>6G2J_6 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (chains F)
TSFGSLKDEDRIFTNLYGRHDWRLKGALRRGDWYKTKEILLKGPDWILGEMKTSGLRGRG
GAGFPTGLKWSFMNKPSDGRPKYLVVNADEGEPGTCKDREIMRHDPHKLVEGCLVGGRAM
GARAAYIYIRGEFYNEASNLQVAIREAYEAGLIGKNACGSDYDFDVFVVRGAGAYICGEE
TALIESIEGKQGKPRLKPPFPADVGVFGCPTTVANVETVAVSPTICRRGGTWFAGFGRER
NSGTKLFNISGHVNHPCTVEEEMSVPLKELIEKHAGGVTGGWDNLLAVIPGGSSTPLIPK
SVCETVLMDFDALVQAQTGLGTAAVIVMDRSTDIVKAIARLIEFYKHESCGQCTPCREGV
DWMNKVMARFVKGDARPAEIDSLWEISKQIEGHTICALGDGAAWPVQGLIRHFRPELEDR
MQRFAQQH

Sequence of entity 7 (G), FASTA

>6G2J_7 NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial (chains G)
MLRIPIKRALIGLSNSPKGYVRTTGTAASNLIEVFVDGQSVMVEPGTTVLQACEKVGMQI
PRFCYHERLSVAGNCRMCLVEIEKAPKVVAACAMPVMKGWNILTNSEKSKKAREGVMEFL
LANHPLDCPICDQGGECDLQDQSMMFGSDRSRFLEGKRAVEDKNIGPLVKTIMTRCIQCT
RCIRFASEIAGVDDLGTTGRGNDMQVGTYIEKMFMSELSGNVIDICPVGALTSKPYAFTA
RPWETRKTESIDVMDAVGSNIVVSTRTGEVMRILPRMHEDINEEWISDKTRFAYDGLKRQ
RLTEPMVRNEKGLLTYTSWEDALSRVAGMLQNFEGNAVAAIAGGLVDAEALVALKDLLNK
VDSDNLCTEEIFPTEGAGTDLRSNYLLNTTIAGVEEADVVLLVGTNPRFEAPLFNARIRK
SWLHNDLKVALIGSPVDLTYRYDHLGDSPKILQDIASGRHSFCEVLKDAKKPMVVLGSSA
LQRDDGAAILVAVSNMVQKIRVTTGVAAEWKVMNILHRIASQVAALDLGYKPGVEAIRKN
PPKMLFLLGADGGCITRQDLPKDCFIVYQGHHGDVGAPMADVILPGAAYTEKSATYVNTE
GRAQQTKVAVTPPGLAREDWKIIRALSEIAGITLPYDTLDQVRNRLEEVSPNLVRYDDIE
ETNYFQQASELAKLVNQEVLADPLVPPQLTIKDFYMTDSISRASQTMAKCVKAVTEGAQA
VEEPSIC

Sequence of entity 8 (H), FASTA

>6G2J_8 NADH-ubiquinone oxidoreductase chain 1 (chains H)
MFFINILTLLVPILIAMAFLTLVERKILGYMQLRKGPNIVGPYGILQPFADAMKLFMKEP
MRPLTTSMSLFIIAPTLSLTLALSLWVPLPMPHPLINLNLGILFILATSSLSVYSILWSG
WASNSKYSLFGALRAVAQTISYEVTMAIILLSVLLMNGSYSLQTLITTQEHMWLLLPAWP
MAMMWFISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFALFFMAEYTNIILMNALTTI
IFLGPLYYINLPELYSTNFMMEALLLSSTFLWIRASYPRFRYDQLMHLLWKNFLPLTLAL
CMWHISLPIFTAGVPPYM

Sequence of entity 9 (I), FASTA

>6G2J_9 NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (chains I)
MYRLSSSMLPRALAQAMRTGHLNGQSLHSSAVAATYKYVNKKEQESEVDMKSATDNAARI
LMWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCE
AICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTETH
EELLYNKEKLLNNGDKWEAEIAANIQADYLYR

Sequence of entity 10 (J), FASTA

>6G2J_10 NADH-ubiquinone oxidoreductase chain 6 (chains J)
MNNYIFVLSSLFLVGCLGLALKPSPIYGGLGLIVSGFVGCLMVLGFGGSFLGLMVFLIYL
GGMLVVFGYTTAMATEEYPETWGSNWLILGFLVLGVIMEVFLICVLNYYDEVGVINLDGL
GDWLMYEVDDVGVMLEGGIGVAAMYSCATWMMVVAGWSLFAGIFIIIEITRD

Sequence of entity 11 (K), FASTA

>6G2J_11 NADH-ubiquinone oxidoreductase chain 4L (chains K)
MPSTFFNLTMAFSLSLLGTLMFRSHLMSTLLCLEGMVLSLFIMTSVTSLNSNSMSSMPIP
ITILVFAACEAAVGLALLVKVSNTYGTDYVQNLNLLQC

Sequence of entity 12 (L), FASTA

>6G2J_12 NADH-ubiquinone oxidoreductase chain 5 (chains L)
MNIFTTSILLIFILLLSPILISMSNLIKHINFPLYTTTSIKFSFIISLLPLLMFFHNNME
YMITTWHWVTMNSMELKMSFKTDFFSILFTSVALFVTWSIMQFSSWYMHSDPNINRFIKY
LTLFLITMLILTSANNMFQLFIGWEGVGIMSFLLIGWWYGRTDANTAALQAILYNRIGDI
GFILAMVWFSLNMNSWELQQIMFSNNNDNLIPLMGLLIAATGKSAQFGLHPWLPSAMEGP
TPVSALLHSSTMVVAGIFLLVRFHPLTTNNNFILTTMLCLGALTTLFTAICALTQNDIKK
IIAFSTSSQLGLMMVTLGMNQPHLAFLHICTHAFFKAMLFMCSGSIIHSLADEQDIRKMG
NITKIMPFTSSCLVIGSLALTGMPFLTGFYSKDLIIEAINTCNTNAWALLITLIATSMTA
MYSMRIIYFVTMTKPRFPPLISINENDPDLMNPIKRLAFGSIFAGFVISYNIPPTSIPVL
TMPWFLKTTALIISVLGFLIALELNNLTMKLSMNKANPYSSFSTLLGFFPSIIHRITPMK
SLNLSLKTSLTLLDLIWLEKTIPKSTSTLHTNMTTLTTNQKGLIKLYFMSFLINIILIII
LYSINLE

Ligands and cofactors

ID	Name	Formula	Copies
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	C41 H82 N O8 P	12
SF4	Iron/sulfur cluster	Fe4 S4	6
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	1
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	4
CDL	Cardiolipin	C81 H156 O17 P2	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
NDP	NADPH dihydro-nicotinamide-adenine-dinucleotide phosphate	C21 H30 N7 O17 P3	1
ZN	Zinc ion	Zn	1
EHZ	~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]prop…	C25 H49 N2 O9 P S	2

Primary citation

Cryo-EM structures of complex I from mouse heart mitochondria in two biochemically defined states. Agip, A.A., Blaza, J.N., Bridges, H.R. et al. Nat Struct Mol Biol (2018) 25:548-556. DOI 10.1038/s41594-018-0073-1 · PubMed

Other PDB entries of the same protein (UniProt P03899 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8OM1 2.39 Å, Mitochondrial complex I from Mus musculus in the active state
8OLT 2.84 Å, Mitochondrial complex I from Mus musculus in the active state bound with piericidin A
8RGR 2.9 Å, Closed Complex I from murine liver
6ZTQ 3.0 Å, Cryo-EM structure of respiratory complex I from Mus musculus inhibited by piericidin A…
8RGP 3.0 Å, Closed Complex I from murine brain
8RGQ 3.0 Å, Open Complex I from murine liver
7B93 3.04 Å, Cryo-EM structure of mitochondrial complex I from Mus musculus inhibited by IACS-2858 at…
6ZR2 3.1 Å, Cryo-EM structure of respiratory complex I in the active state from Mus musculus at 3.1 A
8RGT 3.1 Å, Open Complex I from murine brain
8XNL 3.1 Å, Respiratory complex Peripheral Arm of CI, close form A, focus-refined map of type I,…
7AK5 3.17 Å, Cryo-EM structure of respiratory complex I in the deactive state from Mus musculus at…
8CA3 3.2 Å, Cryo-EM structure NDUFS4 knockout complex I from Mus musculus heart (Class 2).

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