8CA3: NADH-ubiquinone oxidoreductase chain 3

Name: PDB 8CA3: Cryo-EM structure NDUFS4 knockout complex I from Mus musculus heart (Class 2).
Published: 2023-12-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: oxidoreductase

Cryo-EM structure NDUFS4 knockout complex I from Mus musculus heart (Class 2). Determined by electron microscopy at 3.2 Å resolution. Released 20 Dec 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Mus musculus
Chains: 43
Atoms: 63,712
Mol. weight: 1032.23 kDa
Ligands: SF4, PC1, FES, FMN
Released: 20 Dec 2023

Explore 8CA3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CA3 contains 463 α-helices and 171 β-strands across 43 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	2-5	4
α-helix	6-30	25
α-helix	35-37	3
α-helix	42-55	14

Chain A: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	2-23	22
α-helix	31-34	4
α-helix	36-37	2
α-helix	56-72	17
α-helix	75-78	4
α-helix	84-108	25
α-helix	113-114	2

Chain b: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	5-14	10
α-helix	16-34	19
α-helix	38-47	10
α-helix	54-58	5
α-helix	78-81	4

Chain B: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	36-53	18
β-strand	58	1	1
α-helix	65-73	9
α-helix	79-82	4
β-strand	87	1	1
α-helix	90-92	3
β-strand	95-99	5	2
β-strand	103	1	3
α-helix	107-116	10
α-helix	118	1
β-strand	122-126	5	2
α-helix	128-131	4
α-helix	134-136	3
β-strand	142	1	3
α-helix	146-148	3
β-strand	154-156	3	2
α-helix	161-162	2
α-helix	163-178	16
α-helix	182-188	7

Chain c: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	14-46	33

Chain C: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	16-32	17
β-strand	37-42	6	4
β-strand	48-52	5	4
α-helix	54-56	3
α-helix	57-66	10
β-strand	74-82	9	4
β-strand	90-98	9	4
β-strand	103-111	9	4
β-strand	112	1	5
β-strand	115	1	5
β-strand	117-118	2	6
α-helix	127-138	12
β-strand	142-143	2	6
β-strand	172-177	6	7
β-strand	182-187	6	7
α-helix	193-195	3
α-helix	207-209	3

Chain d: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	16-20	5
α-helix	22-25	4
α-helix	29-49	21
α-helix	58-96	39
α-helix	98-100	3
α-helix	102-104	3
β-strand	108	1	8
α-helix	114-116	3

Chain D: 25 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
α-helix	12-14	3
β-strand	18	1	9
α-helix	25-27	3
α-helix	30-32	3
α-helix	39-44	6
β-strand	47-51	5	10
β-strand	63-69	7	10
β-strand	72-79	8	10
α-helix	87-91	5
α-helix	96-106	11
α-helix	111-126	16
α-helix	132-161	30
α-helix	165-185	21
β-strand	194-195	2	11
β-strand	198-199	2	11
α-helix	202-204	3
α-helix	207-229	23
α-helix	233-239	7
α-helix	247-253	7
α-helix	258-261	4
α-helix	269-272	4
α-helix	278-280	3
β-strand	285-287	3	12
α-helix	293-317	25
β-strand	324	1	11
α-helix	332-334	3
α-helix	335-338	4
α-helix	342-353	12
β-strand	361-369	9	13
β-strand	372-380	9	13
β-strand	388-392	5	13
α-helix	394-400	7
α-helix	402-405	4
β-strand	410	1	10
α-helix	411-417	7
α-helix	425-429	5

35 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	245	Mus musculus	Q9D6J6
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial	F	protein	464	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

30 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8CA3_1 NADH-ubiquinone oxidoreductase chain 3 (chains A)
MNLYTVIFINILLSLTLILVAFWLPQMNLYSEKANPYECGFDPTSSARLPFSMKFFLVAI
TFLLFDLEIALLLPLPWAIQTIKTSTMMIMAFILVTILSLGLAYEWTQKGLEWTE

Sequence of entity 2 (B), FASTA

>8CA3_2 NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (chains B)
MAALAAPGLLSVRILGLRTAQVQLRRVHQSVATEGPSPSPSPSLSSTQSAVSKAGAGAVV
PKLSHLPRSRAEYVVTKLDDLINWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVV
FRASPRQADVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRG
CDRIVPVDIYVPGCPPTAEALLYGILQLQRKIKREQKLKIWYRR

Sequence of entity 3 (C), FASTA

>8CA3_3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (chains C)
MAAAAARVWCRGLLGAASVGRGAGRPSVLWQHVRRESAAADKRPTVRPRSDVTHKQLSAF
GEYVAEILPKYVQQVQVSCLDELEICIHPDGVIPTLTFLRDHTNAQFKSLADLTAVDVPT
RQNRFEIVYNLLSLRFNSRIRVKTYADELTPIDSIVSVHIAANWYEREVWDMFGVFFFNH
PDLRRILTDYGFEGHPFRKDFPLTGYVELRYDDEVKRVVAEPVELAQEFRKFDLNSPWEA
FPAYRQPPESLKLEAGDKKPETK

Sequence of entity 4 (D), FASTA

>8CA3_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

>8CA3_5 NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (chains E)
MFSLALRARATGLAAQWGRHARNLHKTAVHNGAGGALFVHRDTPENNPDTPFDFTPENYK
RIEAIVKNYPEGHQAAAVLPVLDLAQRQNGWLPISAMNKVAEVLQVPPMRVYEVATFYTM
YNRKPVGKYHIQVCTTTPCMLRDSDSILETLQRKLGIKVGETTPDKLFTLIEVECLGACV
NAPMVQINDNYYEDLTPKDIEEIIDELKAGKVPKPGPRSGRFCCEPAGGLTSLTEPPKGP
GFGVQ

Sequence of entity 6 (F), FASTA

>8CA3_6 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (chains F)
MLAARHFLGGLVPVRVSVRFSSGTTAPKKTSFGSLKDEDRIFTNLYGRHDWRLKGALRRG
DWYKTKEILLKGPDWILGEMKTSGLRGRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEG
EPGTCKDREIMRHDPHKLVEGCLVGGRAMGARAAYIYIRGEFYNEASNLQVAIREAYEAG
LIGKNACGSDYDFDVFVVRGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPT
TVANVETVAVSPTICRRGGTWFAGFGRERNSGTKLFNISGHVNHPCTVEEEMSVPLKELI
EKHAGGVTGGWDNLLAVIPGGSSTPLIPKSVCETVLMDFDALVQAQTGLGTAAVIVMDRS
TDIVKAIARLIEFYKHESCGQCTPCREGVDWMNKVMARFVKGDARPAEIDSLWEISKQIE
GHTICALGDGAAWPVQGLIRHFRPELEDRMQRFAQQHRAWQAAS

Sequence of entity 7 (G), FASTA

>8CA3_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

>8CA3_8 NADH-ubiquinone oxidoreductase chain 1 (chains H)
MFFINILTLLVPILIAMAFLTLVERKILGYMQLRKGPNIVGPYGILQPFADAMKLFMKEP
MRPLTTSMSLFIIAPTLSLTLALSLWVPLPMPHPLINLNLGILFILATSSLSVYSILWSG
WASNSKYSLFGALRAVAQTISYEVTMAIILLSVLLMNGSYSLQTLITTQEHMWLLLPAWP
MAMMWFISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFALFFMAEYTNIILMNALTTI
IFLGPLYYINLPELYSTNFMMEALLLSSTFLWIRASYPRFRYDQLMHLLWKNFLPLTLAL
CMWHISLPIFTAGVPPYM

Sequence of entity 9 (I), FASTA

>8CA3_9 NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (chains I)
MYRLSSSMLPRALAQAMRTGHLNGQSLHSSAVAATYKYVNKKEQESEVDMKSATDNAARI
LMWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCE
AICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTETH
EELLYNKEKLLNNGDKWEAEIAANIQADYLYR

Sequence of entity 10 (J), FASTA

>8CA3_10 NADH-ubiquinone oxidoreductase chain 6 (chains J)
MNNYIFVLSSLFLVGCLGLALKPSPIYGGLGLIVSGFVGCLMVLGFGGSFLGLMVFLIYL
GGMLVVFGYTTAMATEEYPETWGSNWLILGFLVLGVIMEVFLICVLNYYDEVGVINLDGL
GDWLMYEVDDVGVMLEGGIGVAAMYSCATWMMVVAGWSLFAGIFIIIEITRD

Sequence of entity 11 (K), FASTA

>8CA3_11 NADH-ubiquinone oxidoreductase chain 4L (chains K)
MPSTFFNLTMAFSLSLLGTLMFRSHLMSTLLCLEGMVLSLFIMTSVTSLNSNSMSSMPIP
ITILVFAACEAAVGLALLVKVSNTYGTDYVQNLNLLQC

Sequence of entity 12 (L), FASTA

>8CA3_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
SF4	Iron/sulfur cluster	Fe4 S4	6
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	2
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	1
UQ9	Ubiquinone-9	C54 H82 O4	1
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	C41 H82 N O8 P	7
CDL	Cardiolipin	C81 H156 O17 P2	6
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	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

Structural insights into respiratory complex I deficiency and assembly from the mitochondrial disease-related ndufs4 -/- mouse. Yin, Z., Agip, A.A., Bridges, H.R. et al. EMBO J (2024) 43:225-249. DOI 10.1038/s44318-023-00001-4 · 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…
8IAP 3.2 Å, Respiratory complex Peripheral Arm of CI, focus-refined map of type I, Wild type mouse…

Browse structure collections

About this viewer

MolViewer shows 8CA3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.