8IB2: Dematin actin binding protein

Structure of mammalian spectrin-actin junctional complex of membrane skeleton, Pointed-end segment, headpiece domain of dematin optimized. Determined by electron microscopy at 3.8 Å resolution. Released 26 Apr 2023.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Sus scrofa
Chains: 6
Atoms: 15,229
Mol. weight: 256.62 kDa
Ligands: ADP
Released: 26 Apr 2023

Explore 8IB2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8IB2 contains 119 α-helices and 99 β-strands across 6 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 5: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	345-348	4
α-helix	358-359	2
α-helix	373-380	8
α-helix	384-389	6
α-helix	392-401	10

Chain B: 22 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-38	4	2
β-strand	53-54	2	2
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	2
β-strand	71-72	2	3
β-strand	75-76	2	3
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	1
α-helix	113-126	14
β-strand	131-136	6	1
α-helix	137-145	9
β-strand	149-155	7	4
β-strand	160-166	7	4
β-strand	169-170	2	4
β-strand	176-178	3	4
α-helix	182-192	11
α-helix	193-195	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	239-241	3	5
β-strand	247-249	3	5
α-helix	251-254	4
α-helix	259-262	4
α-helix	274-283	10
α-helix	290-295	6
β-strand	297-299	3	4
α-helix	303-305	3
α-helix	309-320	12
β-strand	329-330	2	4
α-helix	335-337	3
α-helix	338-346	9
α-helix	352-354	3
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain C: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	8-12	5	6
β-strand	16-21	6	6
β-strand	29-32	4	6
β-strand	35-38	4	7
β-strand	53-54	2	7
α-helix	56-60	5
β-strand	65-68	4	7
β-strand	71-72	2	8
β-strand	75-76	2	8
α-helix	80-87	8
α-helix	88-92	5
α-helix	98-100	3
β-strand	103-107	5	6
α-helix	114-125	12
β-strand	131-136	6	6
α-helix	137-145	9
β-strand	150-155	6	9
β-strand	160-166	7	9
β-strand	169-170	2	9
α-helix	172-174	3
β-strand	176-178	3	9
α-helix	182-193	12
α-helix	194-196	3
α-helix	203-215	13
α-helix	223-232	10
β-strand	239-241	3	10
β-strand	247-249	3	10
α-helix	253-259	7
α-helix	274-283	10
α-helix	290-294	5
β-strand	297-300	4	9
α-helix	303-305	3
α-helix	309-320	12
β-strand	329-330	2	9
α-helix	335-337	3
α-helix	338-346	9
α-helix	352-355	4
β-strand	357-358	2	6
α-helix	359-365	7
α-helix	366-369	4
α-helix	370-373	4

Chain D: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	11
β-strand	16-20	5	11
β-strand	29-32	4	11
β-strand	35-38	4	12
β-strand	41-42	2	4
β-strand	53-54	2	12
α-helix	56-60	5
β-strand	65-68	4	12
β-strand	71-72	2	13
β-strand	75-76	2	13
α-helix	80-91	12
α-helix	98-100	3
β-strand	103-107	5	11
α-helix	113-125	13
β-strand	131-136	6	11
α-helix	137-145	9
β-strand	150-155	6	14
β-strand	160-166	7	14
β-strand	169-170	2	14
α-helix	172-174	3
β-strand	176-178	3	14
α-helix	182-192	11
α-helix	203-205	3
α-helix	206-215	10
α-helix	223-232	10
β-strand	239-241	3	15
β-strand	247-249	3	15
α-helix	251-255	5
α-helix	258-261	4
α-helix	274-283	10
α-helix	290-294	5
β-strand	297-298	2	14
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	14
α-helix	335-337	3
α-helix	338-346	9
α-helix	350-355	6
β-strand	357-358	2	11
α-helix	359-365	7
α-helix	367-369	3
α-helix	370-373	4

Chain E: 23 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	16
β-strand	16-21	6	16
β-strand	29-32	4	16
β-strand	35-38	4	17
β-strand	41-42	2	9
β-strand	45	1	18
β-strand	47	1	18
α-helix	48-49	2
β-strand	53-54	2	17
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	17
β-strand	71-72	2	19
β-strand	75-76	2	19
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	16
α-helix	114-125	12
β-strand	131-136	6	16
α-helix	137-145	9
β-strand	150-155	6	20
β-strand	160-166	7	20
β-strand	169-170	2	20
α-helix	172-174	3
β-strand	176-178	3	20
α-helix	182-193	12
α-helix	203-215	13
α-helix	223-232	10
β-strand	239-241	3	21
β-strand	247-249	3	21
α-helix	253-256	4
α-helix	258-260	3
α-helix	274-283	10
α-helix	290-294	5
β-strand	297-300	4	20
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	20
α-helix	338-346	9
α-helix	351-354	4
β-strand	357-358	2	16
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain F: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	22
β-strand	16-21	6	22
β-strand	29-32	4	22
β-strand	35-38	4	23
β-strand	53-54	2	23
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	23
β-strand	71-72	2	24
β-strand	75-76	2	24
α-helix	80-87	8
α-helix	88-92	5
α-helix	98-100	3
β-strand	103-107	5	22
α-helix	113-125	13
β-strand	131-136	6	22
α-helix	137-145	9
β-strand	150-155	6	25
β-strand	160-166	7	25
β-strand	169-170	2	25
α-helix	172-174	3
β-strand	176-178	3	25
α-helix	182-192	11
α-helix	203-215	13
α-helix	223-232	10
β-strand	239-241	3	26
β-strand	247-249	3	26
α-helix	251-255	5
α-helix	258-261	4
α-helix	264-266	3
α-helix	274-283	10
α-helix	290-295	6
β-strand	297-300	4	25
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	25
α-helix	335-337	3
α-helix	338-348	11
α-helix	352-354	3
β-strand	357-358	2	22
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Dematin actin binding protein	5	protein	405	Sus scrofa	F1RMC1 (AlphaFold model)
Actin, cytoplasmic 1	B, C, D, E, F	protein	375	Sus scrofa	Q6QAQ1 (AlphaFold model)

Sequence of entity 1 (5), FASTA

>8IB2_1 Dematin actin binding protein (chains 5)
MERLQKQPLTSPGSVSSSRGSSVPGSPSSIVAKMDNQVLGYKDLAAIPKDKAILDIERPD
LMIYEPHFTYSLLEHVELPRSRERSLSPKSTSPPPSPEVWAESRSPGTFPQASAPRTTGT
PRTSLPHFHHPETTRPDSNIYKKPPIYKQREPTGGSPQSKHLIEDLIIESSKFPAAQPPD
PNQPAKIETDYWPCPPSLAVVETEWRKRKASRRGAEEEEEEEDDDSGEEMKALRERQREE
LSKVTSNLGKMILKEEMEKSLPIRRKTRSLPDRTPFHTSLQAGTSKSSSLPAYGRTTLSR
LQSTDFSPSGSETESPGLQNGEGQRGRMDRGTSLPCVLEQKIYPYEMLVVTNKGRTKLPP
GVDRMRLERHLSAEDFSRVFSMSPEEFGKLALWKRNELKKKASLF

Sequence of entity 2 (B, C, D, E, F), FASTA

>8IB2_2 Actin, cytoplasmic 1 (chains B, C, D, E, F)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	5

Primary citation

Structural basis of membrane skeleton organization in red blood cells. Li, N., Chen, S., Xu, K. et al. Cell (2023) 186:1912-1929.e18. DOI 10.1016/j.cell.2023.03.017 · PubMed

Other PDB entries of the same protein (UniProt F1RMC1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8IAI 3.5 Å, Structure of mammalian spectrin-actin junctional complex of membrane skeleton, State II,…
8IAH 3.6 Å, Structure of mammalian spectrin-actin junctional complex of membrane skeleton, State I,…

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