8RGT: Open Complex I from murine brain

Open Complex I from murine brain. Determined by electron microscopy at 3.1 Å resolution. Released 24 Apr 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Mus musculus
Chains: 45
Atoms: 67,123
Mol. weight: 1076.67 kDa
Ligands: SF4, 3PE, PC1, FES
Released: 24 Apr 2024

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

Secondary structure: helices and β-sheets

8RGT contains 465 α-helices and 195 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 1: 26 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	33-39	7
α-helix	45-51	7
α-helix	53-63	11
α-helix	65	1
β-strand	66	1	16
α-helix	67	1
β-strand	74	1	16
α-helix	75-80	6
β-strand	92-97	6	17
α-helix	106-113	8
α-helix	115-129	15
β-strand	133-138	6	17
α-helix	143-159	17
α-helix	166-168	3
β-strand	174-179	6	17
α-helix	185-187	3
α-helix	189-197	9
α-helix	202-205	4
α-helix	209	1
α-helix	215-217	3
β-strand	220-224	5	17
α-helix	225-237	13
α-helix	239-244	6
β-strand	246-247	2	18
β-strand	250-251	2	18
β-strand	253-260	8	19
β-strand	262	1	20
β-strand	266-271	6	19
β-strand	275	1	21
α-helix	276-279	4
α-helix	280-284	5
β-strand	287	1	20
β-strand	294-298	5	19
β-strand	307-308	2	19
α-helix	309-312	4
β-strand	316	1	21
α-helix	319-324	6
β-strand	333-338	6	19
α-helix	343-357	15
α-helix	363-381	19
α-helix	387-399	13
α-helix	407-421	15
α-helix	423-437	15

Chain 2: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	25-37	13
α-helix	39	1
β-strand	40	1	14
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	15
α-helix	106-110	5
α-helix	113-124	12
β-strand	130-131	2	15
β-strand	137-142	6	15
β-strand	154-156	3	15
β-strand	159-162	4	15
α-helix	166-178	13
β-strand	185-186	2	15
α-helix	195	1
α-helix	205-206	2
α-helix	213-214	2

Chain 3: 38 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	22
β-strand	16-20	5	22
β-strand	25	1	23
α-helix	26-33	8
α-helix	36-38	3
α-helix	47-48	2
β-strand	56-57	2	24
β-strand	58-59	2	22
β-strand	66-67	2	24
α-helix	71	1
β-strand	72	1	23
α-helix	73	1
β-strand	78-80	3	22
α-helix	84-100	17
α-helix	105-107	3
α-helix	115-123	9
α-helix	133-135	3
β-strand	146-148	3	25
α-helix	150-152	3
α-helix	158-162	5
α-helix	163-167	5
β-strand	173-175	3	26
α-helix	178-180	3
β-strand	182-184	3	26
α-helix	198-202	5
β-strand	208-210	3	25
β-strand	223-228	6	27
β-strand	237-243	7	27
β-strand	246-252	7	27
β-strand	255	1	28
β-strand	260	1	28
α-helix	265-269	5
α-helix	270-275	6
β-strand	278	1	29
β-strand	283-285	3	30
β-strand	291-293	3	30
α-helix	296-309	14
α-helix	312-314	3
β-strand	315-319	5	30
α-helix	325-337	13
β-strand	343-345	3	30
β-strand	358	1	31
α-helix	359-362	4
β-strand	364	1	32
α-helix	367-373	7
β-strand	376-380	5	32
α-helix	384-387	4
α-helix	389-401	13
β-strand	405-409	5	32
β-strand	420-423	4	32
α-helix	427-434	8
α-helix	438-445	8
β-strand	449-454	6	32
α-helix	455-458	4
α-helix	463-481	19
β-strand	490-493	4	32
α-helix	497-505	9
α-helix	507	1
β-strand	508-509	2	30
α-helix	512-516	5
β-strand	521-525	5	30
β-strand	542-547	6	30
β-strand	549	1	29
β-strand	559-562	4	30
β-strand	571-574	4	33
β-strand	580-583	4	33
α-helix	584-585	2
α-helix	596-607	12
α-helix	616-626	11
β-strand	633	1	33
α-helix	642-651	10
α-helix	654-657	4
α-helix	668-671	4
α-helix	676-680	5
α-helix	682-692	11

Chain 6: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	35-53	19
β-strand	55	1	1
β-strand	57-61	5	2
α-helix	64-73	10
α-helix	79-82	4
β-strand	84	1	1
β-strand	95-99	5	2
β-strand	103	1	3
α-helix	107-116	10
β-strand	122-126	5	2
α-helix	127-132	6
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	163-179	17
α-helix	182-187	6

Chain 7: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	46
α-helix	9	1
β-strand	10	1	46
α-helix	11	1
α-helix	23-25	3
α-helix	40-45	6
α-helix	48-49	2
β-strand	50-52	3	47
β-strand	56-59	4	48
α-helix	64-66	3
α-helix	68-70	3
β-strand	71-74	4	48
β-strand	82-83	2	47
β-strand	90-93	4	47

Chain 9: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	34
β-strand	3-4	2	12
α-helix	16-28	13
α-helix	30-44	15
α-helix	46-47	2
β-strand	66-69	4	35
β-strand	71	1	36
β-strand	77	1	36
α-helix	84-88	5
β-strand	94-100	7	37
β-strand	106-114	9	37
α-helix	123-127	5
β-strand	133-136	4	35
β-strand	143	1	2
α-helix	147-149	3
β-strand	150-151	2	37
α-helix	153-162	10
α-helix	164-174	11

Chain a: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	2-5	4
α-helix	6-30	25
α-helix	42-55	14
α-helix	66-68	3

Chain A: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	2-23	22
α-helix	50-52	3
α-helix	53-72	20
α-helix	75-78	4
α-helix	84-107	24

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 dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial	6	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	2	protein	248	Mus musculus	Q9D6J6 (AlphaFold model)
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial	1	protein	464	Mus musculus	Q91YT0
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial	3	protein	727	Mus musculus	Q91VD9
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial	9	protein	212	Mus musculus	Q8K3J1
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial	P	protein	377	Mus musculus	Q9DC69
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial	Q	protein	175	Mus musculus	Q9CXZ1
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial	7	protein	116	Mus musculus	P52503
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2	S	protein	99	Mus musculus	Q9CQ75
Acyl carrier protein, mitochondrial	T, U	protein	156	Mus musculus	Q9CR21

32 more molecules are not listed.

Sequence of entity 1 (6), FASTA

>8RGT_1 NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (chains 6)
MAALAAPGLLSVRILGLRTAQVQLRRVHQSVATEGPSPSPSPSLSSTQSAVSKAGAGAVV
PKLSHLPRSRAEYVVTKLDDLINWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVV
FRASPRQADVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRG
CDRIVPVDIYVPGCPPTAEALLYGILQLQRKIKREQKLKIWYRR

Sequence of entity 2 (C), FASTA

>8RGT_2 NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (chains C)
MAAAAARVWCRGLLGAASVGRGAGRPSVLWQHVRRESAAADKRPTVRPRSDVTHKQLSAF
GEYVAEILPKYVQQVQVSCLDELEICIHPDGVIPTLTFLRDHTNAQFKSLADLTAVDVPT
RQNRFEIVYNLLSLRFNSRIRVKTYADELTPIDSIVSVHIAANWYEREVWDMFGVFFFNH
PDLRRILTDYGFEGHPFRKDFPLTGYVELRYDDEVKRVVAEPVELAQEFRKFDLNSPWEA
FPAYRQPPESLKLEAGDKKPETK

Sequence of entity 3 (D), FASTA

>8RGT_3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (chains D)
MAALRALRCLRGVGAPVLRPGSGIRLPSQPSRGARQWQPDIEWAEQFSGAVMYPSKETAH
WKPPPWNDVDILKEKAVTNMTLNFGPQHPAAHGVLRLVLELSGEMVRKCDPHIGLLHRGT
EKLIEYKTYLQALPYFDRLDYVSMMCNEQAYSIAVEKLLNIQPPPRAQWIRVLFGEITRI
LNHIMAVTTHALDIGAMTPFFWMFEEREKMFEFYERVSGARMHAAYIRPGGVHQDLPLGL
LDDIYEFSKNFSLRIDEVEEMLTNNRIWRNRTVDIGVVTAEDALNYGFSGVMLRGSGIQW
DLRKTQPYDVYDQVEFDVPIGSRGDCYDRYLCRVEEMRQSLRIIEQCLNKMPPGEIKVDD
AKVSPPKRAEMKTSMESLIHHFKLYTEGYQVPPGATYTAIEAPKGEFGVYLVSDGSSRPY
RCKIKAPGFAHLAGLDKMSKGHMLADVVAIIGTQDIVFGEIDR

Sequence of entity 4 (2), FASTA

>8RGT_4 NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (chains 2)
MFSLALRARATGLAAQWGRHARNLHKTAVHNGAGGALFVHRDTPENNPDTPFDFTPENYK
RIEAIVKNYPEGHQAAAVLPVLDLAQRQNGWLPISAMNKVAEVLQVPPMRVYEVATFYTM
YNRKPVGKYHIQVCTTTPCMLRDSDSILETLQRKLGIKVGETTPDKLFTLIEVECLGACV
NAPMVQINDNYYEDLTPKDIEEIIDELKAGKVPKPGPRSGRFCCEPAGGLTSLTEPPKGP
GFGVQAGL

Sequence of entity 5 (1), FASTA

>8RGT_5 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (chains 1)
MLAARHFLGGLVPVRVSVRFSSGTTAPKKTSFGSLKDEDRIFTNLYGRHDWRLKGALRRG
DWYKTKEILLKGPDWILGEMKTSGLRGRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEG
EPGTCKDREIMRHDPHKLVEGCLVGGRAMGARAAYIYIRGEFYNEASNLQVAIREAYEAG
LIGKNACGSDYDFDVFVVRGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPT
TVANVETVAVSPTICRRGGTWFAGFGRERNSGTKLFNISGHVNHPCTVEEEMSVPLKELI
EKHAGGVTGGWDNLLAVIPGGSSTPLIPKSVCETVLMDFDALVQAQTGLGTAAVIVMDRS
TDIVKAIARLIEFYKHESCGQCTPCREGVDWMNKVMARFVKGDARPAEIDSLWEISKQIE
GHTICALGDGAAWPVQGLIRHFRPELEDRMQRFAQQHRAWQAAS

Sequence of entity 6 (3), FASTA

>8RGT_6 NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial (chains 3)
MLRIPIKRALIGLSNSPKGYVRTTGTAASNLIEVFVDGQSVMVEPGTTVLQACEKVGMQI
PRFCYHERLSVAGNCRMCLVEIEKAPKVVAACAMPVMKGWNILTNSEKSKKAREGVMEFL
LANHPLDCPICDQGGECDLQDQSMMFGSDRSRFLEGKRAVEDKNIGPLVKTIMTRCIQCT
RCIRFASEIAGVDDLGTTGRGNDMQVGTYIEKMFMSELSGNVIDICPVGALTSKPYAFTA
RPWETRKTESIDVMDAVGSNIVVSTRTGEVMRILPRMHEDINEEWISDKTRFAYDGLKRQ
RLTEPMVRNEKGLLTYTSWEDALSRVAGMLQNFEGNAVAAIAGGLVDAEALVALKDLLNK
VDSDNLCTEEIFPTEGAGTDLRSNYLLNTTIAGVEEADVVLLVGTNPRFEAPLFNARIRK
SWLHNDLKVALIGSPVDLTYRYDHLGDSPKILQDIASGRHSFCEVLKDAKKPMVVLGSSA
LQRDDGAAILVAVSNMVQKIRVTTGVAAEWKVMNILHRIASQVAALDLGYKPGVEAIRKN
PPKMLFLLGADGGCITRQDLPKDCFIVYQGHHGDVGAPMADVILPGAAYTEKSATYVNTE
GRAQQTKVAVTPPGLAREDWKIIRALSEIAGITLPYDTLDQVRNRLEEVSPNLVRYDDIE
ETNYFQQASELAKLVNQEVLADPLVPPQLTIKDFYMTDSISRASQTMAKCVKAVTEGAQA
VEEPSIC

Sequence of entity 7 (9), FASTA

>8RGT_7 NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (chains 9)
MYRLSSSMLPRALAQAMRTGHLNGQSLHSSAVAATYKYVNKKEQESEVDMKSATDNAARI
LMWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCE
AICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTETH
EELLYNKEKLLNNGDKWEAEIAANIQADYLYR

Sequence of entity 8 (P), FASTA

>8RGT_8 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial (chains P)
MAAAVRFRVVRALPMSRPAITAAATSVFCGSSHRQLHHAVIPHGKGGRSSVSGVVATVFG
ATGFLGRYVVNHLGRMGSQVIIPYRCDVYDIMHLRLMGDLGQLTFLEWDARDKDSIRKAV
QHSNVVINLIGREWETRNFDFEDVFVNIPRAIAQASKEAGVERFIHVSHLNASMKSSSKS
LRSKAVGEKEVRSVFPEAIIIRPSDIFGREDRFLNHFANYRWFLAVPLVSLGFKTVKQPV
YVADVSKGIVNATKDPDAVGKTFAFTGPNRYLLFHLVKYIFGMTHRTFIPYPLPLFVYSW
IGKLFGLSPFEPWTTKDKVERIHISDVMPTDLPGLEDLGVQPTPLELKSIEVLRRHRTYR
WLSSEIEETKPAKTVNY

Sequence of entity 9 (Q), FASTA

>8RGT_9 NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial (chains Q)
MAAVSISVSLRQAMLGRRAMATAAVSVCRVPSRLLSTSTWKLADNQTRDTQLITVDEKLD
ITTLTGVPEEHIKTRKVRIFVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWASTADP
LSNMVLTFSAKEDAIAFAEKNGWSYDVEEKKVPKPKSKSYGANFSWNKRTRVSTK

Sequence of entity 10 (7), FASTA

>8RGT_10 NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial (chains 7)
MAAVLTFRRLLTLPRAARGFGVQVSPSGEKITHTGQVYDEKDYRRVRFVDRQKEVNENFA
IDLIAQQPVNEVEHRIIACDGGGGALGHPKVYINLDKETKTGTCGYCGLQFKQHHH

Sequence of entity 11 (S), FASTA

>8RGT_11 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (chains S)
MAAAAASRAVGAKLGLREIRVHLCQRSPGSQGVRDFIVQRYVELKKAHPNLPILIRECSE
VQPKLWARYAFGQEKTVSLNNLSADEVTRAMQNVLSGKA

Sequence of entity 12 (T, U), FASTA

>8RGT_12 Acyl carrier protein, mitochondrial (chains T, U)
MASRVLCACVRRLPAAFAPLPRLPTLALARPLSTTLCPEGIRRRPGALQSALALAQVPGT
VTHLCRQYSDAPPLTLDGIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIM
AMEDEFGFEIPDIDAEKLMCPQEIVDYIADKKDVYE

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	6
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	C41 H82 N O8 P	17
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	4
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	1
NDP	NADPH dihydro-nicotinamide-adenine-dinucleotide phosphate	C21 H30 N7 O17 P3	1
ZN	Zinc ion	Zn	1
ZMP	S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}ami…	C25 H49 N2 O8 P S	2
CDL	Cardiolipin	C81 H156 O17 P2	6
DGT	2'-deoxyguanosine-5'-triphosphate	C10 H16 N5 O13 P3	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (K) are not listed.

Primary citation

SCAF1 drives the compositional diversity of mammalian respirasomes. Vercellino, I., Sazanov, L.A. Nat Struct Mol Biol (2024) 31:1061-1071. DOI 10.1038/s41594-024-01255-0 · PubMed

Other PDB entries of the same protein (UniProt Q9DC70 (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
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).
8IAP 3.2 Å, Respiratory complex Peripheral Arm of CI, focus-refined map of type I, Wild type mouse…

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