6GSL

Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAArg in the A-site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Tautomeric G•U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria.

Rozov, A.Wolff, P.Grosjean, H.Yusupov, M.Yusupova, G.Westhof, E.

(2018) Nucleic Acids Res. 46: 7425-7435

  • DOI: 10.1093/nar/gky547
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report new crystallographic structures of Thermus thermophilus ribosomes complexed with long mRNAs and native Escherichia coli tRNAs. They complete the full set of combinations of Watson-Crick G•C and miscoding G•U pairs at the first two positions ...

    We report new crystallographic structures of Thermus thermophilus ribosomes complexed with long mRNAs and native Escherichia coli tRNAs. They complete the full set of combinations of Watson-Crick G•C and miscoding G•U pairs at the first two positions of the codon-anticodon duplex in ribosome functional complexes. Within the tight decoding center, miscoding G•U pairs occur, in all combinations, with a non-wobble geometry structurally indistinguishable from classical coding Watson-Crick pairs at the same first two positions. The contacts with the ribosomal grip surrounding the decoding center are all quasi-identical, except in the crowded environment of the amino group of a guanosine at the second position; in which case a G in the codons may be preferred. In vivo experimental data show that the translational errors due to miscoding by G•U pairs at the first two positions are the most frequently encountered ones, especially at the second position and with a G on the codon. Such preferred miscodings involve a switch from an A-U to a G•U pair in the tRNA/mRNA complex and very rarely from a G = C to a G•U pair. It is concluded that the frequencies of such occurrences are only weakly affected by the codon/anticodon structures but depend mainly on the stability and lifetime of the complex, the modifications present in the anticodon loop, especially those at positions 34 and 37, in addition to the relative concentration of cognate/near-cognate tRNA species present in the cellular tRNA pool.


    Organizational Affiliation

    Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964, CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, 67404 Illkirch, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
1E, 12
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
2E, 22
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
3E, 32
209Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
4E, 42
162Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
5E, 52
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
6E, 62
156Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
7E, 72
138Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
8E, 82
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
1I, 1A
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
2I, 2A
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
3I, 3A
132Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
4I, 4A
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
5I, 5A
61Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsZ (rpsN)
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY6
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
6I, 6A
89Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
7I, 7A
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
8I, 8A
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY7
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
9I, 9A
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AI, AA
93Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
BI, BA
106Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
1F, 1B
27Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
71, 79
229Thermus thermophilusMutation(s): 0 
Gene Names: rplA (rpl1)
Find proteins for P27150 (Thermus thermophilus)
Go to UniProtKB:  P27150
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
11, 19
276Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60405
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
21, 29
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN8
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
31, 39
210Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN9
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
41, 49
182Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ0
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
51, 59
180Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY8
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7/L12
18, 28
125Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplL
Find proteins for Q8VVE2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8VVE2
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
61, 69
148Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplI
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ1
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
38
173Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplJ
Find proteins for Q8VVE3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8VVE3
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
48
147Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplK
Find proteins for Q5SLP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP6
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
58, 15
140Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplM
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60488
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
68, 25
122Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP8
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
78, 35
150Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplO
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ7
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
88, 45
141Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplP
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60489
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
98, 55
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplQ (rpl17)
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q9Z9H5
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
A8, 65
112Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ4
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
B8, 75
146Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplS
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60490
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
C8, 85
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplT
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60491
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
D8, 95
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplU
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60492
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
E8, A5
113Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
F8, B5
96Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP0
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
G8, C5
110Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP9
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
H8, D5
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplY (rpl25, rptL5)
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHZ1
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
I8, E5
85Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60493
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
J8, F5
98Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60494
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
K8, G5
72Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP6
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
L8, H5
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmD
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ6
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
M8
71Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmE
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJE1
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
N8, J5
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmF (rpl32)
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80339
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
O8
54Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmG (rpl33)
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P35871
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
P8, L5
49Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
Q8, M5
65Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKU1
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNA13,1G1522Thermus thermophilus HB8
Entity ID: 22
MoleculeChainsLengthOrganism
tRNAArg1K,1L77Escherichia coli K-12
Entity ID: 23
MoleculeChainsLengthOrganism
tRNAfMet2K,2L77Escherichia coli K-12
Entity ID: 24
MoleculeChainsLengthOrganism
tRNAArg3K,3L77Escherichia coli K-12
Entity ID: 25
MoleculeChainsLengthOrganism
mRNA4K,4L27Escherichia coli K-12
Entity ID: 26
MoleculeChainsLengthOrganism
23S ribosomal RNA1H,142917Thermus thermophilus HB8
Entity ID: 27
MoleculeChainsLengthOrganism
5S ribosomal RNA16,1J122Thermus thermophilus HB8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
32, 3E
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
5A, 5I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
11, 13, 14, 16, 1G, 1H, 1J, 1K, 1L, 21, 25, 29, 2A, 2K, 2L, 31, 32, 35, 39, 3E, 41, 45, 4K, 4L, 52, 55, 5E, 6I, 75, 78, 88, 98, C5, E5, F5, I8, M5, N8, P8, Q8
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  9 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
1K, 1L, 2K, 2L
RNA LINKINGC9 H13 N2 O9 PU
RSP
Query on RSP
1K, 1L
RNA LINKINGC9 H14 N3 O7 P S

--

OMC
Query on OMC
2K, 2L
RNA LINKINGC10 H16 N3 O8 PC
30U
Query on 30U
1K, 1L
NON-POLYMERC15 H14 N4 O4 S

--

4SU
Query on 4SU
1K, 1L, 2K, 2L
RNA LINKINGC9 H13 N2 O8 P SU
7MG
Query on 7MG
1K, 1L, 2K, 2L
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
1K, 1L, 2K, 2L
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
1K, 1L
RNA LINKINGC11 H16 N5 O7 PA
H2U
Query on H2U
1K, 1L
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 210.050α = 90.00
b = 449.390β = 90.00
c = 618.660γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-15-CE11-0021-01
FranceDBF20160635745
French National Research AgencyFranceANR-10-LABX-0036_NETRNA
European Research Council294312
Russian FederationRussian Government Program of Competitive Growth of Kazan Federal University

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-09-05
    Type: Data collection, Database references