9CFV: Delta-NTR myosin-1c

Cryo-EM structure of delta-NTR myosin-1c bound to F-actin. Determined by electron microscopy at 2.7 Å resolution. Released 12 Feb 2025.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Oryctolagus cuniculus, Mus musculus
Chains: 5
Atoms: 15,664
Mol. weight: 235.73 kDa
Ligands: MG, ADP
Released: 12 Feb 2025

Explore 9CFV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CFV contains 124 α-helices and 88 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 B: 28 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	24	1	2
β-strand	29-32	4	1
β-strand	35-38	4	3
β-strand	53-54	2	3
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	3
β-strand	71-72	2	4
β-strand	75-76	2	4
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	113-125	13
β-strand	131-136	6	1
α-helix	137-144	8
β-strand	150-155	6	5
β-strand	160-166	7	5
β-strand	169-170	2	5
α-helix	172-174	3
β-strand	176-178	3	5
α-helix	182-192	11
α-helix	193-195	3
α-helix	203-216	14
α-helix	223-232	10
α-helix	234-236	3
β-strand	238-241	4	6
β-strand	247-250	4	6
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-284	11
α-helix	287-294	8
β-strand	297-300	4	5
α-helix	302-304	3
α-helix	309-320	12
α-helix	326-327	2
β-strand	329-330	2	5
α-helix	335-337	3
α-helix	338-348	11
α-helix	351-354	4
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	366-369	4
α-helix	370-373	4

Chain C: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	7
β-strand	16-21	6	7
β-strand	29-32	4	7
β-strand	35-38	4	8
α-helix	41-42	2
β-strand	53-54	2	8
α-helix	56-61	6
β-strand	65-68	4	8
β-strand	71-72	2	9
β-strand	75-76	2	9
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	7
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	7
α-helix	137-145	9
β-strand	150-155	6	10
β-strand	160-166	7	10
β-strand	169-170	2	10
β-strand	176-178	3	10
α-helix	182-193	12
α-helix	194-196	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	11
β-strand	247-250	4	11
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-283	10
α-helix	289-294	6
β-strand	297-300	4	10
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	10
α-helix	333-337	5
α-helix	338-348	11
α-helix	350-352	3
β-strand	357-358	2	7
α-helix	359-364	6
α-helix	367-369	3
α-helix	370-373	4

Chain D: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	12
β-strand	16-21	6	12
β-strand	29-32	4	12
β-strand	35-38	4	13
β-strand	42	1	5
β-strand	53-54	2	13
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	13
β-strand	71-72	2	14
β-strand	75-76	2	14
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
β-strand	103-107	5	12
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	12
α-helix	137-145	9
β-strand	150-155	6	15
β-strand	160-166	7	15
β-strand	169-170	2	15
β-strand	176-178	3	15
α-helix	182-193	12
α-helix	194-196	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	16
β-strand	247-250	4	16
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-284	11
α-helix	287-294	8
β-strand	297-300	4	15
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	15
α-helix	338-348	11
α-helix	350-352	3
β-strand	357-358	2	12
α-helix	359-365	7
α-helix	369-373	5

Chain P: 38 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	17
α-helix	16-18	3
α-helix	25-37	13
β-strand	42-45	4	17
β-strand	48-52	5	17
α-helix	59-61	3
α-helix	63-69	7
α-helix	81-94	14
β-strand	99-105	7	17
α-helix	111-124	14
α-helix	129-141	13
α-helix	143-150	8
β-strand	151-152	2	18
β-strand	160-161	2	18
β-strand	164-172	9	17
β-strand	177-185	9	17
α-helix	189-192	4
β-strand	202	1	18
α-helix	203-211	9
α-helix	214-219	6
α-helix	226-228	3
α-helix	230-233	4
α-helix	245-258	14
α-helix	263-280	18
β-strand	284-286	3	19
α-helix	287	1
β-strand	291	1	20
β-strand	292-294	3	19
α-helix	297-306	10
α-helix	311-317	7
β-strand	320-325	6	21
β-strand	328-333	6	21
α-helix	334	1
β-strand	335	1	20
α-helix	336-363	28
β-strand	379-386	8	17
β-strand	396	1	22
α-helix	398-429	32
α-helix	441-449	9
α-helix	455-464	10
α-helix	471-481	11
β-strand	488-490	3	22
α-helix	498-500	3
β-strand	506-511	6	22
β-strand	514-519	6	22
α-helix	523-527	5
α-helix	533-539	7
α-helix	547-550	4
α-helix	553-557	5
β-strand	560	1	2
α-helix	561-564	4
α-helix	565-582	18
β-strand	584-591	8	17
α-helix	604-613	10
α-helix	616-624	9
β-strand	629-632	4	23
α-helix	633-640	8
α-helix	641-643	3
α-helix	645-647	3
α-helix	655-665	11
β-strand	673-675	3	23
β-strand	679-682	4	23
α-helix	685-718	34

Chain R: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-21	15
β-strand	27-29	3	24
α-helix	33-39	7
α-helix	46-56	11
β-strand	63-65	3	24
α-helix	66-76	11
α-helix	80-82	3
α-helix	83-93	11
β-strand	100-102	3	25
α-helix	103-111	9
α-helix	119-129	11
β-strand	136-138	3	25
α-helix	139-146	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	B, C, D	protein	375	Oryctolagus cuniculus	P68135 (AlphaFold model)
Unconventional myosin-Ic	P	protein	793	Mus musculus	Q9WTI7 (AlphaFold model)
Calmodulin-1	R	protein	148	Mus musculus	P0DP26 (AlphaFold model)

Sequence of entity 1 (B, C, D), FASTA

>9CFV_1 Actin, alpha skeletal muscle (chains B, C, D)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Sequence of entity 2 (P), FASTA

>9CFV_2 Unconventional myosin-Ic (chains P)
MESALTARDRVGVQDFVLLENFTSEAAFIENLRRRFRENLIYTYIGPVLVSVNPYRDLQI
YSRQHMERYRGVSFYEVPPHLFAVADTVYRALRTERRDQAVMISGESGAGKTEATKRLLQ
FYAETCPAPERGGAVRDRLLQSNPVLEAFGNAKTLRNDNSSRFGKYMDVQFDFKGAPVGG
HILSYLLEKSRVVHQNHGERNFHVFYQLLEGGEEETLRRLGLERNPQSYLYLVKGQCAKV
SSINDKSDWKVMRKALSVIDFTEDEVEDLLSIVASVLHLGNIHFAADEDSNAQVTTENQL
KYLTRLLGVEGTTLREALTHRKIIAKGEELLSPLNLEQAAYARDALAKAVYSRTFTWLVR
KINRSLASKDAESPSWRSTTVLGLLDIYGFEVFQHNSFEQFCINYCNEKLQQLFIELTLK
SEQEEYEAEGIAWEPVQYFNNKIICDLVEEKFKGIISILDEECLRPGEATDLTFLEKLED
TVKPHPHFLTHKLADQKTRKSLDRGEFRLLHYAGEVTYSVTGFLDKNNDLLFRNLKETMC
SSMNPIMAQCFDKSELSDKKRPETVATQFKMSLLQLVEILRSKEPAYIRCIKPNDAKQPG
RFDEVLIRHQVKYLGLMENLRVRRAGFAYRRKYEAFLQRYKSLCPETWPMWAGRPQDGVA
VLVRHLGYKPEEYKMGRTKIFIRFPKTLFATEDSLEVRRQSLATKIQAAWRGFHWRQKFL
RVKRSAICIQSWWRGTLGRRKAAKRKWAAQTIRRLIRGFILRHSPRCGGLNDIFEAQKIE
WHEAADYKDDDDK

Sequence of entity 3 (R), FASTA

>9CFV_3 Calmodulin-1 (chains R)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3

Primary citation

High-resolution structures of Myosin-IC reveal a unique actin-binding orientation, ADP release pathway, and power stroke trajectory. Chavali, S.S., Carman, P.J., Shuman, H. et al. Proc Natl Acad Sci U S A (2025) 122:e2415457122-e2415457122. DOI 10.1073/pnas.2415457122 · PubMed

Other PDB entries of the same protein (UniProt P68135 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4B1Y 1.29 Å, Structure of the Phactr1 RPEL-3 bound to G-actin
2FXU 1.35 Å, X-ray Structure of Bistramide A- Actin Complex at 1.35 A resolution.
4K41 1.4 Å, Crystal structure of actin in complex with marine macrolide kabiramide C
1QZ5 1.45 Å, Structure of rabbit actin in complex with kabiramide C
1WUA 1.45 Å, The structure of Aplyronine A-actin complex
2Q0U 1.45 Å, Structure of Pectenotoxin-2 and Latrunculin B Bound to Actin
2V52 1.45 Å, Structure of MAL-RPEL2 complexed to G-actin
3MN5 1.5 Å, Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation
2PBD 1.5 Å, Ternary complex of profilin-actin with the poly-PRO-GAB domain of VASP*
5ZZA 1.53 Å, OdinProfilin/Rabbit Actin Complex
1J6Z 1.54 Å, Uncomplexed actin
1QZ6 1.6 Å, Structure of rabbit actin in complex with jaspisamide A

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