8CA4: PDB entry 8CA4

Cryo-EM structure NDUFS4 knockout complex I from Mus musculus heart (Class 2 N-domain). Determined by electron microscopy at 3.25 Å resolution. Released 20 Dec 2023.

Method: Electron microscopy
Resolution: 3.25 Å
Organism: Mus musculus
Chains: 5
Atoms: 11,113
Mol. weight: 182.72 kDa
Ligands: FMN, SF4, FES
Released: 20 Dec 2023

Explore 8CA4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CA4 contains 78 α-helices and 64 β-strands across 5 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 E: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	25-35	11
α-helix	43-46	4
α-helix	47-58	12
α-helix	63-73	11
α-helix	77-86	10
β-strand	98-103	6	1
α-helix	106-109	4
α-helix	113-124	12
β-strand	131	1	1
β-strand	137-142	6	1
β-strand	153-156	4	1
β-strand	159-162	4	1
α-helix	166-178	13
β-strand	185-186	2	1
α-helix	205-207	3

Chain F: 26 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	33-39	7
α-helix	45-50	6
α-helix	53-63	11
β-strand	66	1	2
β-strand	74	1	2
α-helix	75-80	6
α-helix	85-86	2
β-strand	92-97	6	3
α-helix	106-113	8
α-helix	115-129	15
β-strand	133-138	6	3
α-helix	143-159	17
β-strand	163	1	4
α-helix	166-168	3
β-strand	173	1	4
β-strand	174-179	6	3
α-helix	184-187	4
α-helix	189-197	9
α-helix	203-205	3
α-helix	209	1
α-helix	215-217	3
β-strand	220-224	5	3
α-helix	225-237	13
α-helix	239-243	5
β-strand	246	1	5
β-strand	251	1	5
β-strand	253-258	6	6
β-strand	259-260	2	7
β-strand	262	1	8
β-strand	266-271	6	6
β-strand	275	1	9
α-helix	276-278	3
α-helix	279-283	5
β-strand	287	1	8
β-strand	296-298	3	7
α-helix	305-306	2
β-strand	307-308	2	7
α-helix	309-312	4
β-strand	316	1	9
α-helix	319-324	6
β-strand	335-337	3	7
α-helix	343-357	15
α-helix	363-381	19
α-helix	388-400	13
α-helix	407-421	15
α-helix	423-434	12

Chain G: 36 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	10
β-strand	16-20	5	10
β-strand	25	1	11
α-helix	26-33	8
β-strand	56-57	2	12
β-strand	58-59	2	10
β-strand	66-67	2	12
α-helix	71	1
β-strand	72	1	11
α-helix	73	1
β-strand	78-80	3	10
α-helix	84-99	16
α-helix	105-107	3
α-helix	115-123	9
α-helix	133-135	3
α-helix	137-139	3
β-strand	146-148	3	13
α-helix	150-152	3
α-helix	158-161	4
α-helix	162-166	5
β-strand	173-175	3	14
α-helix	178-180	3
β-strand	182-184	3	14
α-helix	198-202	5
β-strand	208-210	3	13
β-strand	223-228	6	15
β-strand	237-242	6	15
β-strand	247-252	6	15
α-helix	265-269	5
α-helix	270-275	6
β-strand	278	1	16
β-strand	283-284	2	17
β-strand	292-293	2	17
α-helix	296-309	14
α-helix	312-314	3
β-strand	315-319	5	17
α-helix	325-337	13
β-strand	344-345	2	17
α-helix	355-357	3
β-strand	358	1	18
α-helix	359-361	3
α-helix	371-373	3
β-strand	376-380	5	19
α-helix	389-400	12
β-strand	405-409	5	19
β-strand	420-421	2	19
α-helix	428-434	7
α-helix	439-445	7
β-strand	449-454	6	19
α-helix	455-458	4
α-helix	463-481	19
β-strand	490-493	4	19
α-helix	499-505	7
α-helix	507	1
β-strand	508	1	17
α-helix	512-516	5
β-strand	521-525	5	17
β-strand	544-547	4	17
β-strand	549	1	16
β-strand	559-562	4	17
β-strand	572-574	3	20
β-strand	580-582	3	20
α-helix	596-606	11
α-helix	616-626	11
α-helix	628-631	4
β-strand	633	1	20
α-helix	642-650	9
α-helix	668-670	3
α-helix	676-680	5
α-helix	682-692	11

Chain s: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	36-38	3
α-helix	44-52	9
α-helix	57-59	3

Chain S: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	17-22	6	18
α-helix	27-29	3
α-helix	30-44	15
β-strand	52-56	5	18
α-helix	60-62	3
β-strand	63-67	5	18
β-strand	73-75	3	18
α-helix	83-94	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial	E	protein	248	Mus musculus	Q9D6J6 (AlphaFold model)
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial	F	protein	464	Mus musculus	Q91YT0 (AlphaFold model)
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial	G	protein	727	Mus musculus	Q91VD9 (AlphaFold model)
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2	S	protein	99	Mus musculus	Q9CQ75 (AlphaFold model)
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial	s	protein	104	Mus musculus	Q8BK30

Sequence of entity 1 (E), FASTA

>8CA4_1 NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (chains E)
MFSLALRARATGLAAQWGRHARNLHKTAVHNGAGGALFVHRDTPENNPDTPFDFTPENYK
RIEAIVKNYPEGHQAAAVLPVLDLAQRQNGWLPISAMNKVAEVLQVPPMRVYEVATFYTM
YNRKPVGKYHIQVCTTTPCMLRDSDSILETLQRKLGIKVGETTPDKLFTLIEVECLGACV
NAPMVQINDNYYEDLTPKDIEEIIDELKAGKVPKPGPRSGRFCCEPAGGLTSLTEPPKGP
GFGVQAGL

Sequence of entity 2 (F), FASTA

>8CA4_2 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (chains F)
MLAARHFLGGLVPVRVSVRFSSGTTAPKKTSFGSLKDEDRIFTNLYGRHDWRLKGALRRG
DWYKTKEILLKGPDWILGEMKTSGLRGRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEG
EPGTCKDREIMRHDPHKLVEGCLVGGRAMGARAAYIYIRGEFYNEASNLQVAIREAYEAG
LIGKNACGSDYDFDVFVVRGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPT
TVANVETVAVSPTICRRGGTWFAGFGRERNSGTKLFNISGHVNHPCTVEEEMSVPLKELI
EKHAGGVTGGWDNLLAVIPGGSSTPLIPKSVCETVLMDFDALVQAQTGLGTAAVIVMDRS
TDIVKAIARLIEFYKHESCGQCTPCREGVDWMNKVMARFVKGDARPAEIDSLWEISKQIE
GHTICALGDGAAWPVQGLIRHFRPELEDRMQRFAQQHRAWQAAS

Sequence of entity 3 (G), FASTA

>8CA4_3 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 4 (S), FASTA

>8CA4_4 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (chains S)
MAAAAASRAVGAKLGLREIRVHLCQRSPGSQGVRDFIVQRYVELKKAHPNLPILIRECSE
VQPKLWARYAFGQEKTVSLNNLSADEVTRAMQNVLSGKA

Sequence of entity 5 (s), FASTA

>8CA4_5 NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial (chains s)
MAVSLLLRGGRIRALKAVLLEARVFPGELVSVVRLSTESEKSAKEKELHPKTQSVLKEPE
PTDTTTYKNLQHHDYNTYTFLDLNLDLSKFRLPQPSSGRESPRH

Ligands and cofactors

ID	Name	Formula	Copies
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	1
SF4	Iron/sulfur cluster	Fe4 S4	3
FES	FE2/S2 (inorganic) cluster	Fe2 S2	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 Q9D6J6 (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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