Research workbench

Cryo-EM structure of the dynactin complex

Analyse Cryo-EM structure of the dynactin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZNL
Type: protein
Length: 7,001 residues
Chains: 23
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ARP1 actin related protein 1 homolog a; Actin, cytoplasmic 1; ARP11; Capping protein…
UniProt: F2Z5G5, Q6QAQ1, I3LHK5, A0PFK5, A9XFX6, A0A5G2QD80, F1SEC0, D0G6S1, A0A286ZK88, A0A4X1TB62
Ligands: ADP, ATP, ZN
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 17 distinct chains · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F, G, I	ARP1 actin related protein 1 homolog a	protein	370	39% helix, 20% strand	F2Z5G5
C	ARP1 actin related protein 1 homolog a	protein	375	38% helix, 20% strand	F2Z5G5
H	Actin, cytoplasmic 1	protein	370	41% helix, 19% strand	Q6QAQ1
J	ARP11	protein	379	41% helix, 17% strand	I3LHK5
K	Capping protein (actin filament) muscle Z-line, alpha 1	protein	278	38% helix, 30% strand	A0PFK5
L	F-actin capping protein beta subunit	protein	269	39% helix, 28% strand	A9XFX6
M	Dynactin subunit 2	protein	340	65% helix, 3% strand	A0A5G2QD80
N	Dynactin subunit 2	protein	280	75% helix, 3% strand	A0A5G2QD80
O	Dynactin subunit 3	protein	179	80% helix, 0% strand	F1SEC0
U	Dynactin 6	protein	167	8% helix, 19% strand	D0G6S1
V	Dynactin subunit 5	protein	179	8% helix, 30% strand	A0A286ZK88
Y	Dynactin subunit 4	protein	410	14% helix, 21% strand	A0A4X1TB62
Z	Dynactin subunit 1	protein	192	57% helix, 5% strand	—
m	Dynactin subunit 2	protein	325	68% helix, 3% strand	A0A5G2QD80
n	Dynactin subunit 2	protein	343	61% helix, 3% strand	A0A5G2QD80
o	Dynactin subunit 3	protein	170	79% helix, 0% strand	F1SEC0
z	Dynactin subunit 1	protein	155	68% helix, 4% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 9 copies · chains A, B, C, n, D, E, F, G, I, J, Y
ATP · Adenosine-5'-triphosphate · ligand · chains H
ZN · Zinc ion · metal · 3 copies · chains Y

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	1033	0.84	0.85	104	empty
2	938	0.84	0.85	97	empty
3	730	0.83	0.87	76	empty
4	1028	0.83	0.84	105	empty
5	952	0.82	0.83	72	empty

Interfaces

72 interfaces between chains.

K–L · 3986 Å² buried · 56 hydrogen bonds · protein-protein
m–n · 3796 Å² buried · 14 hydrogen bonds · protein-protein
J–Y · 3116 Å² buried · 19 hydrogen bonds · protein-protein
M–N · 2939 Å² buried · 9 hydrogen bonds · protein-protein
Z–m · 2732 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

Q6QAQ1 · AlphaFold monomer V2.0 prediction for actin, cytoplasmic 1 (Q6QAQ1) · a predicted model of the same protein · chain H against A, TM-score 0.96

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 A0A5G2QD80
Every structure of UniProt F1SEC0
Every structure of UniProt D0G6S1
Every structure of UniProt A0A286ZK88
Every structure of UniProt A0A4X1TB62
Elsewhere: RCSB PDB 6ZNL · PDBe 6ZNL · UniProt F2Z5G5 · UniProt Q6QAQ1 · UniProt I3LHK5 · UniProt A0PFK5 · UniProt A9XFX6 · UniProt A0A5G2QD80 · UniProt F1SEC0 · UniProt D0G6S1 · UniProt A0A286ZK88 · UniProt A0A4X1TB62

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