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

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: 6S91
Type: protein + RNA
Length: 7,572 residues
Chains: 35
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 · 38% 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	60% helix, 0% strand	F0NDX5
C	CRISPR-associated protein, CMR5 family	protein	154	74% helix, 0% strand	F0NDX5
D, E, F	CRISPR-associated ramp protein, CMR4 family	protein	285	27% helix, 31% strand	F0NDX6
G	CRISPR-associated ramp protein, CMR4 family	protein	283	24% helix, 31% strand	F0NDX6
H	CRISPR-associated protein, CMR3 family	protein	312	21% helix, 32% strand	F0NDX1
I	CRISPR-associated ramp protein, CMR6 family	protein	284	40% helix, 18% strand	F0NDX3
J	CMR1,CRISPR-associated ramp protein, CMR1 family	protein	467	33% helix, 20% strand	F0NDX4
K	CRISPR-associated protein, CMR2 family	protein	1023	43% helix, 10% strand	F0NDX2
U	Cognate target RNA	rna	36	—	—
V	Crrna (48-mer)	rna	48	—	—
L, M, N, O, P, Q, S, T, W, X, l, m, n, o, p, q, r, s, t, w, x, R	CRISPR-associated protein cmrx	protein	173	11% helix, 27% strand	F0NDX7

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	1048	0.89	0.91	121	empty
2	758	0.88	0.91	92	empty
3	1098	0.88	0.89	93	empty
4	1182	0.87	0.88	130	empty
5	846	0.85	0.87	68	ANP, MN

Interfaces

99 interfaces between chains.

H–K · 3110 Å² buried · 39 hydrogen bonds · protein-protein
I–J · 2093 Å² buried · 21 hydrogen bonds · protein-protein
D–I · 1769 Å² buried · 16 hydrogen bonds · protein-protein
F–G · 1716 Å² buried · 22 hydrogen bonds · protein-protein
H–V · 1632 Å² buried · 34 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 15 disulfide (disulfide).

Compared structures

6S91 · Cryo-EM structure of the Type III-B Cmr-beta bound to cognate target RNA and AMPPnP… · the same entry in another collection · chain T against T, 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 6S91 · PDBe 6S91 · UniProt F0NDX5 · UniProt F0NDX6 · UniProt F0NDX1 · UniProt F0NDX3 · UniProt F0NDX4 · UniProt F0NDX2 · UniProt F0NDX7

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