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Cryo-EM structure of an Escherichia coli coupled transcription-translation complex B1 (TTC-B1) containing an mRNA with a 24 nt long spacer, transcription factors NusA and NusG, and fMet-tRNAs at P-site and E-site

Analyse Cryo-EM structure of an Escherichia coli coupled transcription-translation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X6T
Type: protein + DNA + RNA
Length: 15,056 residues
Chains: 68
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.2
Source: Escherichia coli; SYNTHETIC CONSTRUCT
Molecule: 50S ribosomal protein L21; 50S ribosomal protein L22; 50S ribosomal protein L23; 50S…
EC: 2.7.7.6
UniProt: D7ZEN7, D7Z9G0, D7X2Z9, D7Z9G6, D7XH79, D7ZA73, P0A8V4, U9XYQ6, A0A073G207, A0A4S1NBU2, P0A802, U9XV73, A0A0E2KXL3, D7ZAS2, A0A0E2L2J1, D7ZK99, D6HUW2, B7MCS9, D7Z9H7, D7Z9H2, P02358, P02359, D7Z9G9, D7ZES9, D7Z9F4, B7MCR3, D7ZAN0, D7Z9G8, D7ZEL4, B7MIU7, D7Z9G4, D7Z9F9, H4UQ02, D7ZA71, V0AEG5, P0A7L8, S0YB49, D7Z9G3, D7Z9H3, D7ZFP6, P60422, D7ZGG2, P60438, D7Z9P0, D7Z9F6, B7MGC4, D7Z9G7, D7Z814, D7Z9H0, A0A0E2L017, D7ZI15, D7ZET0, D7Z9G5, A0A037Y8L6, P0ADY7, D6I1Y5, D7Z9H1, D7ZKU3, B7MAS6
Ligands: ZN, MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 3.2 · 67 distinct chains · 32% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	50S ribosomal protein L21	protein	103	0% helix, 61% strand	D7ZEN7
1	50S ribosomal protein L22	protein	110	42% helix, 35% strand	D7Z9G0
2	50S ribosomal protein L23	protein	94	29% helix, 37% strand	D7X2Z9
3	50S ribosomal protein L24	protein	103	6% helix, 47% strand	D7Z9G6
4	50S ribosomal protein L25	protein	94	23% helix, 44% strand	D7XH79
5	Nt DNA	dna	23	—	—
6	T DNA	dna	27	—	—
7	mRNA with 24 nt long spacer	rna	33	—	—
9	50S ribosomal protein L10	protein	148	24% helix, 1% strand	D7ZA73
A, B	E-site and P-site tRNA (fMet)	rna	76	—	—
AA	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	28% helix, 21% strand	P0A8V4
AB	Transcription termination/antitermination protein NusG	protein	162	22% helix, 20% strand	U9XYQ6
AC	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	301	28% helix, 27% strand	A0A073G207
AD	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	299	25% helix, 24% strand	A0A073G207
AE	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1335	35% helix, 16% strand	A0A4S1NBU2
AF	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	82	65% helix, 0% strand	P0A802
AG	Transcription termination/antitermination protein NusA	protein	495	36% helix, 11% strand	U9XV73
C	30S ribosomal protein S18	protein	66	45% helix, 3% strand	A0A0E2KXL3
D	16S rRNA	rna	1524	—	—
E	30S ribosomal protein S20	protein	86	87% helix, 0% strand	D7ZAS2
F	30S ribosomal protein S21	protein	70	69% helix, 3% strand	A0A0E2L2J1
G	30S ribosomal protein S2	protein	225	50% helix, 14% strand	D7ZK99
H	30S ribosomal protein S1	protein	259	15% helix, 14% strand	D6HUW2
I	30S ribosomal protein S3	protein	208	36% helix, 29% strand	B7MCS9
J	30S ribosomal protein S4	protein	205	46% helix, 10% strand	D7Z9H7
K	30S ribosomal protein S5	protein	156	31% helix, 37% strand	D7Z9H2
L	30S ribosomal protein S6	protein	104	32% helix, 44% strand	P02358
M	30S ribosomal protein S7	protein	151	57% helix, 7% strand	P02359
N	30S ribosomal protein S8	protein	129	32% helix, 34% strand	D7Z9G9
O	30S ribosomal protein S9	protein	127	33% helix, 22% strand	D7ZES9
P	30S ribosomal protein S10	protein	99	27% helix, 39% strand	D7Z9F4
Q	30S ribosomal protein S11	protein	117	21% helix, 31% strand	B7MCR3
R	30S ribosomal protein S12	protein	121	11% helix, 27% strand	D7ZAN0
S	30S ribosomal protein S14	protein	100	57% helix, 2% strand	D7Z9G8
T	30S ribosomal protein S15	protein	88	76% helix, 0% strand	D7ZEL4
U	30S ribosomal protein S16	protein	82	28% helix, 33% strand	B7MIU7
V	30S ribosomal protein S17	protein	80	4% helix, 50% strand	D7Z9G4
W	30S ribosomal protein S19	protein	83	27% helix, 11% strand	D7Z9F9
X	30S ribosomal protein S13	protein	116	54% helix, 5% strand	H4UQ02
Y	50S ribosomal protein L11	protein	141	16% helix, 7% strand	D7ZA71
Z	50S ribosomal protein L7/L12	protein	30	13% helix, 0% strand	V0AEG5
a	23S rRNA	rna	2880	—	—
b	50S ribosomal protein L27	protein	76	0% helix, 41% strand	P0A7L8
c	50S ribosomal protein L28	protein	77	27% helix, 34% strand	S0YB49
d	5S rRNA	rna	120	—	—
e	50S ribosomal protein L29	protein	62	79% helix, 0% strand	D7Z9G3
f	50S ribosomal protein L30	protein	58	38% helix, 26% strand	D7Z9H3
g	50S ribosomal protein L31	protein	66	21% helix, 24% strand	D7ZFP6
h	50S ribosomal protein L2	protein	271	8% helix, 30% strand	P60422
i	50S ribosomal protein L32	protein	56	20% helix, 11% strand	D7ZGG2
j	50S ribosomal protein L3	protein	209	13% helix, 37% strand	P60438
k	50S ribosomal protein L33	protein	52	0% helix, 52% strand	D7Z9P0
l	50S ribosomal protein L4	protein	201	37% helix, 12% strand	D7Z9F6
m	50S ribosomal protein L34	protein	46	59% helix, 0% strand	B7MGC4
n	50S ribosomal protein L5	protein	177	40% helix, 19% strand	D7Z9G7
o	50S ribosomal protein L35	protein	64	36% helix, 11% strand	D7Z814
p	50S ribosomal protein L6	protein	175	22% helix, 34% strand	D7Z9H0
q	50S ribosomal protein L36	protein	38	8% helix, 47% strand	A0A0E2L017
r	50S ribosomal protein L9	protein	149	35% helix, 23% strand	D7ZI15
s	50S ribosomal protein L13	protein	142	36% helix, 19% strand	D7ZET0
t	50S ribosomal protein L14	protein	123	7% helix, 39% strand	D7Z9G5
u	50S ribosomal protein L15	protein	144	23% helix, 13% strand	A0A037Y8L6
v	50S ribosomal protein L16	protein	136	19% helix, 28% strand	P0ADY7
w	50S ribosomal protein L17	protein	119	53% helix, 17% strand	D6I1Y5
x	50S ribosomal protein L18	protein	116	48% helix, 20% strand	D7Z9H1
y	50S ribosomal protein L19	protein	114	18% helix, 44% strand	D7ZKU3
z	50S ribosomal protein L20	protein	117	79% helix, 0% strand	B7MAS6

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains AE
MG · Magnesium ion · metal · chains 7, AE

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	1178	0.89	0.91	132	empty
2	1160	0.87	0.89	116	empty
3	861	0.87	0.90	93	empty
4	619	0.85	0.91	65	empty
5	958	0.85	0.87	77	empty

Interfaces

171 interfaces between chains.

AA–AE · 8351 Å² buried · 88 hydrogen bonds · protein-protein
a–h · 7146 Å² buried · 203 hydrogen bonds · protein-nucleic
a–j · 4984 Å² buried · 116 hydrogen bonds · protein-nucleic
a–u · 4487 Å² buried · 121 hydrogen bonds · protein-nucleic
a–l · 4107 Å² buried · 91 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

B7MCR3 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S11 (B7MCR3) · a predicted model of the same protein · chain Q against A, TM-score 0.99
B7MCS9 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S3 (B7MCS9) · a predicted model of the same protein · chain I against A, TM-score 0.98
P0A8V4 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V4) · a predicted model of the same protein · chain AA against A, TM-score 0.98
B7MIU7 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S16 (B7MIU7) · a predicted model of the same protein · chain U against A, TM-score 0.97
B7MAS6 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L20 (B7MAS6) · a predicted model of the same protein · chain z against A, TM-score 0.97
P0A802 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (P0A802) · a predicted model of the same protein · chain AF against A, TM-score 0.95
B7MGC4 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L34 (B7MGC4) · a predicted model of the same protein · chain m against A, TM-score 0.92

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