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Cryo-EM structure of the type III-B cmr-beta bound to cognate target RNA and amppnp, state 2, in the presence of ssdna

Analyse Cryo-EM structure of the type III-B cmr-beta bound to cognate target RNA and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SH8
Type: protein + RNA
Length: 8,261 residues
Chains: 39
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CRISPR-associated protein, CMR5 family; CRISPR-associated ramp protein, CMR4 family…
UniProt: F0NDX5, F0NDX6, F0NDX1, F0NDX3, F0NDX4, F0NDX2, F0NDX7
Ligands: ANP, MN, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 12 distinct chains · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CRISPR-associated protein, CMR5 family	protein	153	76% helix, 0% strand	F0NDX5
B	CRISPR-associated protein, CMR5 family	protein	151	61% helix, 0% strand	F0NDX5
C	CRISPR-associated protein, CMR5 family	protein	154	73% helix, 0% strand	F0NDX5
D, E, F	CRISPR-associated ramp protein, CMR4 family	protein	285	25% helix, 31% strand	F0NDX6
G	CRISPR-associated ramp protein, CMR4 family	protein	283	25% helix, 29% strand	F0NDX6
H	CRISPR-associated protein, CMR3 family	protein	312	22% helix, 31% strand	F0NDX1
I	CRISPR-associated ramp protein, CMR6 family	protein	284	40% helix, 19% strand	F0NDX3
J	CMR1,CRISPR-associated ramp protein, CMR1 family	protein	467	34% helix, 19% strand	F0NDX4
K	CRISPR-associated protein, CMR2 family	protein	1024	43% helix, 10% strand	F0NDX2
L, M, N, O, P, Q, R, S, T, W, X, l, m, n, o, p, q, r, s, t, w, x, Z, z, Y, y	CRISPR-associated protein cmrx	protein	173	12% helix, 24% strand	F0NDX7
U	Cognate target RNA	rna	32	—	—
V	Crrna	rna	48	—	—

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains K
MN · Manganese (II) ion · metal · 3 copies · chains K
ZN · Zinc ion · metal · chains K

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	1084	0.89	0.91	143	empty
2	879	0.88	0.91	105	empty
3	628	0.86	0.90	78	empty
4	559	0.84	0.90	54	empty
5	887	0.84	0.86	89	empty

Interfaces

105 interfaces between chains.

H–K · 2891 Å² buried · 39 hydrogen bonds · protein-protein
I–J · 2038 Å² buried · 24 hydrogen bonds · protein-protein
F–G · 1721 Å² buried · 17 hydrogen bonds · protein-protein
D–I · 1717 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1602 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 disulfide (disulfide).

Compared structures

6SH8 · Cryo-EM structure of the Type III-B Cmr-beta bound to cognate target RNA and AMPPnP… · the same entry in another collection · chain B against B, 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 F0NDX5
Every structure of UniProt F0NDX6
Every structure of UniProt F0NDX1
Every structure of UniProt F0NDX3
Every structure of UniProt F0NDX4
Every structure of UniProt F0NDX2
Every structure of UniProt F0NDX7
Elsewhere: RCSB PDB 6SH8 · PDBe 6SH8 · UniProt F0NDX5 · UniProt F0NDX6 · UniProt F0NDX1 · UniProt F0NDX3 · UniProt F0NDX4 · UniProt F0NDX2 · UniProt F0NDX7

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