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Cryoem structure of E. COLI rho-dependent transcription pre- termination complex bound with nusg

Analyse Cryoem structure of E. COLI rho-dependent transcription pre- termination… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XAV
Type: protein + DNA + RNA
Length: 5,869 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription TERMINATION/ANTITERMINATION protein nusg; DNA (29-mer); RNA (18-mer)…
EC: 2.7.7.6, 3.6.4.-
UniProt: P0AFG0, P0A800, P0A7Z4, P0A8V2, P0A8T7, P0AFF6, P0AG30
Ligands: ZN, MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 15 distinct chains · 34% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Transcription TERMINATION/ANTITERMINATION protein nusg	protein	95	37% helix, 19% strand	P0AFG0
N	DNA (29-mer)	dna	27	—	—
T	DNA (29-mer)	dna	29	—	—
R	RNA (18-mer)	rna	10	—	—
W	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	55	51% helix, 0% strand	P0A800
K	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	279	24% helix, 27% strand	P0A7Z4
H	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	218	17% helix, 35% strand	P0A7Z4
I	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1304	28% helix, 22% strand	P0A8V2
J	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1338	36% helix, 15% strand	P0A8T7
G	Transcription TERMINATION/ANTITERMINATION protein nusa	protein	166	28% helix, 27% strand	P0AFF6
C	Transcription termination factor rho (EC 3.6.4.-)	protein	413	41% helix, 20% strand	P0AG30
A	Transcription termination factor rho (EC 3.6.4.-)	protein	353	40% helix, 22% strand	P0AG30
B	Transcription termination factor rho (EC 3.6.4.-)	protein	407	42% helix, 21% strand	P0AG30
D, E	Transcription termination factor rho (EC 3.6.4.-)	protein	415	41% helix, 19% strand	P0AG30
F	Transcription termination factor rho (EC 3.6.4.-)	protein	345	37% helix, 22% strand	P0AG30

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains J
MG · Magnesium ion · metal · chains R, J

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	1042	0.86	0.87	98	empty
2	984	0.85	0.86	86	empty
3	737	0.84	0.88	84	empty
4	863	0.81	0.83	74	empty
5	1035	0.81	0.82	84	empty

Interfaces

38 interfaces between chains.

I–J · 8695 Å² buried · 101 hydrogen bonds · protein-protein
K–H · 1952 Å² buried · 11 hydrogen bonds · protein-protein
K–I · 1883 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1500 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1433 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6XAV · CryoEM Structure of E. coli Rho-dependent Transcription Pre-termination Complex bound… · the same entry in another collection · chain F against F, 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 P0AFG0
Every structure of UniProt P0A800
Every structure of UniProt P0A7Z4
Every structure of UniProt P0A8V2
Every structure of UniProt P0A8T7
Every structure of UniProt P0AFF6
Every structure of UniProt P0AG30
Elsewhere: RCSB PDB 6XAV · PDBe 6XAV · UniProt P0AFG0 · UniProt P0A800 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0AFF6 · UniProt P0AG30

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