1MDU: Chicken actin trimer

Crystal structure of the chicken actin trimer complexed with human gelsolin segment 1 (GS-1). Determined by X-ray diffraction at 2.2 Å resolution. Released 7 Jan 2003.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Homo sapiens, Gallus gallus
Chains: 4
Atoms: 8,159
Mol. weight: 113.78 kDa
Ligands: ATP, CA
Released: 7 Jan 2003

Explore 1MDU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1MDU contains 60 α-helices and 56 β-strands across 4 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: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
β-strand	16-23	8	1
β-strand	26-29	4	1
α-helix	30-31	2
α-helix	32-34	3
β-strand	37-39	3	2
β-strand	43-51	9	1
β-strand	57-65	9	1
α-helix	71-87	17
β-strand	93-98	6	1
α-helix	104-108	5
β-strand	115-117	3	2
α-helix	121-123	3

Chain B: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	10-14	5	3
β-strand	18-23	6	3
β-strand	24	1	4
β-strand	26	1	4
β-strand	31-34	4	3
β-strand	37-40	4	5
β-strand	55-56	2	5
α-helix	57-62	6
α-helix	64-66	3
β-strand	67-70	4	5
β-strand	73-74	2	6
β-strand	77-78	2	6
α-helix	81-89	9
α-helix	90-96	7
α-helix	100-102	3
β-strand	105-109	5	3
α-helix	115-127	13
β-strand	133-138	6	3
α-helix	139-146	8
β-strand	152-157	6	7
β-strand	162-168	7	7
β-strand	171-172	2	7
α-helix	174-176	3
β-strand	178-180	3	7
α-helix	184-197	14
α-helix	208-218	11
α-helix	225-234	10
β-strand	240-243	4	8
β-strand	249-252	4	8
α-helix	255-261	7
α-helix	266-269	4
α-helix	274-275	2
α-helix	276-284	9
α-helix	289-291	3
α-helix	292-296	5
β-strand	299-302	4	7
α-helix	304-306	3
α-helix	311-322	12
β-strand	331-332	2	7
α-helix	340-350	11
α-helix	352-357	6
β-strand	359-360	2	3
α-helix	361-367	7
α-helix	369-372	4

Chain D: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
β-strand	16-22	7	9
β-strand	27-29	3	9
α-helix	30-31	2
α-helix	32-34	3
β-strand	37-39	3	10
β-strand	43-51	9	9
β-strand	57-65	9	9
α-helix	71-87	17
β-strand	93-98	6	9
α-helix	104-108	5
β-strand	115-117	3	10
α-helix	121-123	3

Chain E: 25 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	8-9	2
β-strand	10-14	5	11
β-strand	18-23	6	11
β-strand	24	1	12
β-strand	26	1	12
β-strand	31-34	4	11
β-strand	37-39	3	13
β-strand	55-56	2	13
α-helix	58-61	4
β-strand	68-70	3	13
β-strand	73-74	2	14
β-strand	77-78	2	14
α-helix	81-90	10
α-helix	91-96	6
α-helix	100-102	3
β-strand	105-109	5	11
α-helix	115-123	9
α-helix	124-128	5
β-strand	133-138	6	11
α-helix	139-146	8
β-strand	152-157	6	15
β-strand	162-168	7	15
β-strand	171-172	2	15
α-helix	174-176	3
β-strand	178-180	3	15
α-helix	184-197	14
α-helix	207-218	12
α-helix	225-234	10
β-strand	240-243	4	16
α-helix	248	1
β-strand	249-252	4	16
α-helix	255-261	7
α-helix	266-269	4
α-helix	274-275	2
α-helix	276-284	9
α-helix	289-291	3
α-helix	292-296	5
β-strand	299-302	4	15
α-helix	304-306	3
α-helix	311-322	12
β-strand	331-332	2	15
α-helix	340-350	11
α-helix	352-356	5
β-strand	359-360	2	11
α-helix	361-367	7
α-helix	369-372	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
gelsolin precursor	A, D	protein	125	Homo sapiens	P06396 (AlphaFold model)
a-actin	B, E	protein	377	Gallus gallus	P68139 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>1MDU_1 gelsolin precursor (chains A, D)
MVVEHPEFLKAGKEPGLQIWRVEKFDLVPVPTNLYGDFFTGDAYVILKTVQLRNGNLQYD
LHYWLGNECSQDESGAAAIFTVQLDDYLNGRAVQHREVQGFESATFLGYFKSGLKYKKGG
VASGF

Sequence of entity 2 (B, E), FASTA

>1MDU_2 a-actin (chains B, E)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
CA	Calcium ion	Ca	7

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

Primary citation

Structure of an F-actin trimer disrupted by gelsolin and implications for the mechanism of severing. Dawson, J.F., Sablin, E.P., Spudich, J.A. et al. J Biol Chem (2003) 278:1229-1238. DOI 10.1074/jbc.M209160200 · PubMed

Other PDB entries of the same protein (UniProt P06396 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5FAF 1.05 Å, N184K pathological variant of gelsolin domain 2 (orthorhombic form)
6QW3 1.3 Å, Calcium-bound gelsolin domain 2
6LJE 1.4 Å, Crystal structure of gelsolin G3 domain (calcium and magnesium condition)
6LJF 1.5 Å, Crystal structure of gelsolin G3 domain (calcium condition)
2FH1 1.55 Å, C-terminal half of gelsolin soaked in low calcium at pH 4.5
3CIP 1.6 Å, Complex of Dictyostelium Discoideum Actin with Gelsolin
1KCQ 1.65 Å, Human Gelsolin Domain 2 with a Cd2+ bound
3CI5 1.7 Å, Complex of Phosphorylated Dictyostelium Discoideum Actin with Gelsolin
5FAE 1.7 Å, N184K pathological variant of gelsolin domain 2 (trigonal form)
5O2Z 1.7 Å, Domain swap dimer of the G167R variant of gelsolin second domain
1D4X 1.75 Å, Crystal Structure of Caenorhabditis Elegans Mg-ATP Actin Complexed with Human Gelsolin…
1NLV 1.8 Å, Crystal Structure Of Dictyostelium Discoideum Actin Complexed With Ca ATP And Human…

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