Research workbench

Cryo-EM structure of two dynein tail domains bound to dynactin and HOOK3

Analyse Cryo-EM structure of two dynein tail domains bound to dynactin and HOOK3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6F38
Type: protein
Length: 13,846 residues
Chains: 45
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ARP1 actin related protein 1 homolog a; Actin, cytoplasmic 1; Actin related protein 10…
UniProt: F2Z5G5, Q6QAQ1, I3LHK5, A0PFK5, A9XFX6, D0G6S1, A0A286ZK88, F1SKF9, F1SL58, Q14204, Q13409, O43237, Q9NP97
Ligands: ADP, ATP
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 29 distinct chains · 50% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, I	ARP1 actin related protein 1 homolog a	protein	370	37% helix, 18% strand	F2Z5G5
H	Actin, cytoplasmic 1	protein	370	42% helix, 15% strand	Q6QAQ1
J	Actin related protein 10 homolog	protein	369	39% helix, 9% strand	I3LHK5
K	Capping protein (actin filament) muscle Z-line, alpha 1	protein	278	39% helix, 27% strand	A0PFK5
L	F-actin capping protein beta subunit	protein	269	39% helix, 26% strand	A9XFX6
M	Dynactin subunit 2	protein	587	90% helix, 0% strand	—
N	Dynactin subunit 2	protein	616	86% helix, 0% strand	—
O, P	Dynactin subunit 3	protein	65	38% helix, 6% strand	—
Q, R	Dynactin subunit 2	protein	87	82% helix, 0% strand	—
U	Dynactin 6	protein	171	13% helix, 14% strand	D0G6S1
V	Dynactin subunit 5	protein	165	11% helix, 18% strand	A0A286ZK88
X	HOOK3	protein	223	98% helix, 0% strand	—
Y	Dynactin subunit 4	protein	264	10% helix, 6% strand	—
Z	Dynactin subunit 1	protein	52	65% helix, 0% strand	—
a	Dynactin subunit 2	protein	52	23% helix, 2% strand	F1SKF9
b	Dynactin subunit 2	protein	75	9% helix, 4% strand	F1SKF9
c	Dynactin subunit 2	protein	37	16% helix, 16% strand	F1SL58
d	Dynactin subunit 2	protein	24	17% helix, 0% strand	F1SL58
e, m	Cytoplasmic dynein 1 heavy chain 1	protein	926	61% helix, 2% strand	Q14204
f	Cytoplasmic dynein 1 heavy chain 1	protein	929	64% helix, 2% strand	Q14204
g, o	Cytoplasmic dynein 1 intermediate chain 2	protein	397	8% helix, 17% strand	Q13409
h	Cytoplasmic dynein 1 intermediate chain 2	protein	400	7% helix, 26% strand	Q13409
i, q, r	Cytoplasmic dynein 1 light intermediate chain 2	protein	268	41% helix, 11% strand	O43237
j	Cytoplasmic dynein 1 light intermediate chain 2	protein	275	37% helix, 9% strand	O43237
k, l, s, t	Dynein light chain roadblock-type 1	protein	93	37% helix, 17% strand	Q9NP97
n	Cytoplasmic dynein 1 heavy chain 1	protein	928	65% helix, 3% strand	Q14204
p	Cytoplasmic dynein 1 intermediate chain 2	protein	401	8% helix, 20% strand	Q13409
x	HOOK3	protein	222	99% helix, 0% strand	—
z	Dynactin subunit 1	protein	53	72% helix, 0% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 9 copies · chains A, B, C, D, E, F, G, I, J
ATP · Adenosine-5'-triphosphate · ligand · chains H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1273	0.85	0.86	125	empty
2	609	0.84	0.89	89	empty
3	783	0.83	0.86	79	empty
4	1363	0.82	0.84	155	empty
5	1428	0.82	0.83	186	empty

Interfaces

94 interfaces between chains.

X–x · 3003 Å² buried · 3 hydrogen bonds · protein-protein
m–n · 1428 Å² buried · 10 hydrogen bonds · protein-protein
e–f · 1393 Å² buried · 6 hydrogen bonds · protein-protein
e–g · 1266 Å² buried · 3 hydrogen bonds · protein-protein
n–p · 1183 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6F38 · Cryo-EM structure of two dynein tail domains bound to dynactin and HOOK3 · the same entry in another collection · chain I against I, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt F2Z5G5
Every structure of UniProt Q6QAQ1
Every structure of UniProt I3LHK5
Every structure of UniProt A0PFK5
Every structure of UniProt A9XFX6
Every structure of UniProt D0G6S1
Every structure of UniProt A0A286ZK88
Every structure of UniProt F1SKF9
Every structure of UniProt F1SL58
Every structure of UniProt Q14204
Every structure of UniProt Q13409
Every structure of UniProt O43237
Every structure of UniProt Q9NP97
Elsewhere: RCSB PDB 6F38 · PDBe 6F38 · UniProt F2Z5G5 · UniProt Q6QAQ1 · UniProt I3LHK5 · UniProt A0PFK5 · UniProt A9XFX6 · UniProt D0G6S1 · UniProt A0A286ZK88 · UniProt F1SKF9 · UniProt F1SL58 · UniProt Q14204 · UniProt Q13409 · UniProt O43237 · UniProt Q9NP97

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