Het-PDB Navi2 (PDB: 4LFZ)

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Data format:

Color scheme of protein:

Ligands
Code	Name		Style	Show	Link
MG	Magnesium ion				PoSSuM
ZN	Zinc ion				PoSSuM

Non-standard Residues
Code	Name	Show
1MG	1n-methylguanosine-5'-monophosphate
PPU	Puromycin-5'-monophosphate

Glycosylation
Code	Name	Emphasize

Modification
Code	Name	Show

Download interaction data: 4LFZ

Code :

4LFZ PDBj RCSB PDB PDBe

Header :

RIBOSOME

Title :

Crystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-U in the Absence of Paromomycin

Release Data :

2014-08-06

Compound :

mol_id	molecule	chains
1	16S rRNA	QA,XA

mol_id	molecule	chains
2	30S ribosomal protein S2	QB,XB

mol_id	molecule	chains
3	30S ribosomal protein S3	QC,XC

mol_id	molecule	chains
4	30S ribosomal protein S4	QD,XD

mol_id	molecule	chains
5	30S ribosomal protein S5	QE,XE

mol_id	molecule	chains
6	30S ribosomal protein S6	QF,XF

mol_id	molecule	chains
7	30S ribosomal protein S7	QG,XG

mol_id	molecule	chains
8	30S ribosomal protein S8	QH,XH

mol_id	molecule	chains
9	30S ribosomal protein S9	QI,XI

mol_id	molecule	chains
10	30S ribosomal protein S10	QJ,XJ

mol_id	molecule	chains
11	30S ribosomal protein S11	QK,XK

mol_id	molecule	chains
12	30S ribosomal protein S12	QL,XL

mol_id	molecule	chains
13	30S ribosomal protein S13	QM,XM

mol_id	molecule	chains
14	30S ribosomal protein S14	QN,XN

mol_id	molecule	chains
15	30S ribosomal protein S15	QO,XO

mol_id	molecule	chains
16	30S ribosomal protein S16	QP,XP

mol_id	molecule	chains
17	30S ribosomal protein S17	QQ,XQ

mol_id	molecule	chains
18	30S ribosomal protein S18	QR,XR

mol_id	molecule	chains
19	30S ribosomal protein S19	QS,XS

mol_id	molecule	chains
20	30S ribosomal protein S20	QT,XT

mol_id	molecule	chains
21	30S ribosomal protein S21	QU,XU

mol_id	molecule	chains
22	P-site tRNA fMet	QV,XV

mol_id	molecule	chains
23	A-site ASL SufA6	QX,XX

mol_id	molecule	chains
24	messenger RNA	QY,XY

mol_id	molecule	chains
25	23S rRNA	RA,YA

mol_id	molecule	chains
26	5S rRNA	RB,YB

mol_id	molecule	chains
27	50S ribosomal protein L2	RD,YD

mol_id	molecule	chains
28	50S ribosomal protein L3	RE,YE

mol_id	molecule	chains
29	50S ribosomal protein L4	RF,YF

mol_id	molecule	chains
30	50S ribosomal protein L5	RG,YG

mol_id	molecule	chains
31	50S ribosomal protein L6	RH,YH

mol_id	molecule	chains
32	50S ribosomal protein L9	RI,YI

mol_id	molecule	chains
33	50S ribosomal protein L13	RN,YN

mol_id	molecule	chains
34	50S ribosomal protein L14	RO,YO

mol_id	molecule	chains
35	50S ribosomal protein L15	RP,YP

mol_id	molecule	chains
36	50S ribosomal protein L16	RQ,YQ

mol_id	molecule	chains
37	50S ribosomal protein L17	RR,YR

mol_id	molecule	chains
38	50S ribosomal protein L18	RS,YS

mol_id	molecule	chains
39	50S ribosomal protein L19	RT,YT

mol_id	molecule	chains
40	50S ribosomal protein L20	RU,YU

mol_id	molecule	chains
41	50S ribosomal protein L21	RV,YV

mol_id	molecule	chains
42	50S ribosomal protein L22	RW,YW

mol_id	molecule	chains
43	50S ribosomal protein L23	RX,YX

mol_id	molecule	chains
44	50S ribosomal protein L24	RY,YY

mol_id	molecule	chains
45	50S ribosomal protein L25	RZ,YZ

mol_id	molecule	chains
46	50S ribosomal protein L27	R0,Y0

mol_id	molecule	chains
47	50S ribosomal protein L28	R1,Y1

mol_id	molecule	chains
48	50S ribosomal protein L29	R2,Y2

mol_id	molecule	chains
49	50S ribosomal protein L30	R3,Y3

mol_id	molecule	chains
50	50S ribosomal protein L31	R4,Y4

mol_id	molecule	chains
51	50S ribosomal protein L32	R5,Y5

mol_id	molecule	chains
52	50S ribosomal protein L33	R6,Y6

mol_id	molecule	chains
53	50S ribosomal protein L34	R7,Y7

mol_id	molecule	chains
54	50S ribosomal protein L35	R8,Y8

mol_id	molecule	chains
55	50S ribosomal protein L36	R9,Y9

mol_id	molecule	chains
56	tRNA acceptor end mimic	Z6,Z8

Source :

mol_id	organism_scientific
1	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
2	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
3	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
4	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
5	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
6	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
7	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
8	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
9	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
10	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
11	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
12	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
13	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
14	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
15	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
16	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
17	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
18	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
19	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
20	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
21	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
22	Escherichia coli (taxid:83333)
	strain: K12

mol_id	organism_scientific
23	Synthetic (taxid:32630)
	synthetic: yes other_details: RNA oligonucleotide

mol_id	organism_scientific
24	Synthetic (taxid:32630)
	synthetic: yes other_details: RNA oligonucleotide

mol_id	organism_scientific
25	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
26	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
27	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
28	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
29	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
30	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
31	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
32	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
33	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
34	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
35	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
36	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
37	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
38	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
39	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
40	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
41	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
42	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
43	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
44	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
45	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
46	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
47	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
48	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
49	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
50	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
51	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
52	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
53	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
54	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
55	Thermus thermophilus (taxid:300852)
	strain: HB8

mol_id	organism_scientific
56	Synthetic (taxid:32630)
	synthetic: yes other_details: RNA oligonucleotide

Authors :

Maehigashi, T., Dunkle, J.A., Dunham, C.M.

Keywords :

Protein biosynthesis, ribosome, RNA, tRNA, transfer RNA, 30S, 70S, 16S, 23S, ribosomal subunit

Exp. method :

X-RAY DIFFRACTION ( 3.92000059074 Å )

Citation :

Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops.

Maehigashi, T.,Dunkle, J.A.,Miles, S.J. et al.
(2014) Proc.Natl.Acad.Sci.USA 111 : 12740 - 12745

PubMed: 25128388
DOI: 10.1073/pnas.1409436111

Chain :	QB, XB
UniProt :	P80371 (RS2_THET8)
Reaction :	-

Chain :	QC, XC
UniProt :	P80372 (RS3_THET8)
Reaction :	-

Chain :	QD, XD
UniProt :	P80373 (RS4_THET8)
Reaction :	-

Chain :	QE, XE
UniProt :	Q5SHQ5 (RS5_THET8)
Reaction :	-

Chain :	QF, XF
UniProt :	Q5SLP8 (RS6_THET8)
Reaction :	-

Chain :	QG, XG
UniProt :	P17291 (RS7_THET8)
Reaction :	-

Chain :	QH, XH
UniProt :	Q5SHQ2 (RS8_THET8)
Reaction :	-

Chain :	QI, XI
UniProt :	P80374 (RS9_THET8)
Reaction :	-

Chain :	QJ, XJ
UniProt :	Q5SHN7 (RS10_THET8)
Reaction :	-

Chain :	QK, XK
UniProt :	P80376 (RS11_THET8)
Reaction :	-

Chain :	QL, XL
UniProt :	Q5SHN3 (RS12_THET8)
Reaction :	-

Chain :	QM, XM
UniProt :	P80377 (RS13_THET8)
Reaction :	-

Chain :	QN, XN
UniProt :	Q5SHQ1 (RS14Z_THET8)
Reaction :	-

Chain :	QO, XO
UniProt :	Q5SJ76 (RS15_THET8)
Reaction :	-

Chain :	QP, XP
UniProt :	Q5SJH3 (RS16_THET8)
Reaction :	-

Chain :	QQ, XQ
UniProt :	Q5SHP7 (RS17_THET8)
Reaction :	-

Chain :	QR, XR
UniProt :	Q5SLQ0 (RS18_THET8)
Reaction :	-

Chain :	QS, XS
UniProt :	Q5SHP2 (RS19_THET8)
Reaction :	-

Chain :	QT, XT
UniProt :	P80380 (RS20_THET8)
Reaction :	-

Chain :	QU, XU
UniProt :	Q5SIH3 (RSHX_THET8)
Reaction :	-

Chain :	RD, YD
UniProt :	P60405 (RL2_THET8)
Reaction :	-

Chain :	RE, YE
UniProt :	Q5SHN8 (RL3_THET8)
Reaction :	-

Chain :	RF, YF
UniProt :	Q5SHN9 (RL4_THET8)
Reaction :	-

Chain :	RG, YG
UniProt :	Q5SHQ0 (RL5_THET8)
Reaction :	-

Chain :	RH, YH
UniProt :	Q5SHQ3 (RL6_THET8)
Reaction :	-

Chain :	RI, YI
UniProt :	Q5SLQ1 (RL9_THET8)
Reaction :	-

Chain :	RN, YN
UniProt :	P60488 (RL13_THET8)
Reaction :	-

Chain :	RO, YO
UniProt :	Q5SHP8 (RL14_THET8)
Reaction :	-

Chain :	RP, YP
UniProt :	Q5SHQ7 (RL15_THET8)
Reaction :	-

Chain :	RQ, YQ
UniProt :	P60489 (RL16_THET8)
Reaction :	-

Chain :	RR, YR
UniProt :	Q9Z9H5 (RL17_THET8)
Reaction :	-

Chain :	RS, YS
UniProt :	Q5SHQ4 (RL18_THET8)
Reaction :	-

Chain :	RT, YT
UniProt :	P60490 (RL19_THET8)
Reaction :	-

Chain :	RU, YU
UniProt :	P60491 (RL20_THET8)
Reaction :	-

Chain :	RV, YV
UniProt :	P60492 (RL21_THET8)
Reaction :	-

Chain :	RW, YW
UniProt :	Q5SHP3 (RL22_THET8)
Reaction :	-

Chain :	RX, YX
UniProt :	Q5SHP0 (RL23_THET8)
Reaction :	-

Chain :	RY, YY
UniProt :	Q5SHP9 (RL24_THET8)
Reaction :	-

Chain :	RZ, YZ
UniProt :	Q5SHZ1 (RL25_THET8)
Reaction :	-

Chain :	R0, Y0
UniProt :	P60493 (RL27_THET8)
Reaction :	-

Chain :	R1, Y1
UniProt :	P60494 (RL28_THET8)
Reaction :	-

Chain :	R2, Y2
UniProt :	Q5SHP6 (RL29_THET8)
Reaction :	-

Chain :	R3, Y3
UniProt :	Q5SHQ6 (RL30_THET8)
Reaction :	-

Chain :	R4, Y4
UniProt :	Q5SJE1 (RL31_THET8)
Reaction :	-

Chain :	R5, Y5
UniProt :	P80339 (RL32_THET8)
Reaction :	-

Chain :	R6, Y6
UniProt :	P35871 (RL33_THET8)
Reaction :	-

Chain :	R7, Y7
UniProt :	P80340 (RL34_THET8)
Reaction :	-

Chain :	R8, Y8
UniProt :	Q5SKU1 (RL35_THET8)
Reaction :	-

Chain :	R9, Y9
UniProt :	P80256 (RL36_THETH)
Reaction :	-

PDB ID: 4LFZ

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Structure summary

Reaction