5J4D

E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated stop codon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural Basis for Translation Termination on a Pseudouridylated Stop Codon.

Svidritskiy, E.Madireddy, R.Korostelev, A.A.

(2016) J.Mol.Biol. 428: 2228-2236

  • DOI: 10.1016/j.jmb.2016.04.018

  • PubMed Abstract: 
  • Pseudouridylation of messenger RNA emerges as an abundant modification involved in gene expression regulation. Pseudouridylation of stop codons in eukaryotic and bacterial cells results in stop-codon read through. The structural mechanism of this phe ...

    Pseudouridylation of messenger RNA emerges as an abundant modification involved in gene expression regulation. Pseudouridylation of stop codons in eukaryotic and bacterial cells results in stop-codon read through. The structural mechanism of this phenomenon is not known. Here we present a 3.1-Å crystal structure of Escherichia coli release factor 1 (RF1) bound to the 70S ribosome in response to the ΨAA codon. The structure reveals that recognition of a modified stop codon does not differ from that of a canonical stop codon. Our in vitro biochemical results support this finding by yielding nearly identical rates for peptide release from E. coli ribosomes programmed with pseudouridylated and canonical stop codons. The crystal structure also brings insight into E. coli RF1-specific interactions and suggests involvement of L27 in bacterial translation termination. Our results are consistent with a mechanism in which read through of a pseudouridylated stop codon in bacteria results from increased decoding by near-cognate tRNAs (miscoding) rather than from decreased efficiency of termination.


    Organizational Affiliation

    RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation St., Worcester, MA 01605, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
E, JB
275Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplB
Find proteins for Q72I07 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I07
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
F, KB
206Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q72I04 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I04
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
G, LB
205Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q72I05 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I05
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
H, MB
182Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q72I16 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I16
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
I, NB
180Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplF
Find proteins for Q72I19 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I19
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
J, OB
148Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplI
Find proteins for Q72GV5 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GV5
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
K, PB
140Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplM
Find proteins for Q72IN1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IN1
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
L, QB
122Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q72I14 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I14
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
M, RB
150Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplO
Find proteins for Q72I23 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I23
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
N, SB
141Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplP
Find proteins for Q72I11 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I11
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
O, TB
118Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplQ
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I33
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
P, UB
112Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q72I20 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I20
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
Q, VB
146Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplS
Find proteins for Q72JU9 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JU9
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
R, WB
118Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplT
Find proteins for Q72L76 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L76
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
S, XB
101Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplU
Find proteins for Q72HR2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HR2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
T, YB
113Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q72I09 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I09
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
U, ZB
96Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q72I06 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I06
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
V, AC
110Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q72I15 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I15
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
W, BC
206Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IA7
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
X, CC
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: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
Y, DC
98Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmB
Find proteins for Q72G84 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72G84
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Z, EC
72Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I12
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
AA, FC
60Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmD
Find proteins for Q72I22 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I22
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
BA, GC
71Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmE
Find proteins for Q72JR0 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JR0
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
CA, HC
60Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmF (rpl32)
Find proteins for P62652 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62652
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
DA, IC
54Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmG
Find proteins for Q72GW3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GW3
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
EA, JC
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: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
FA, KC
65Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q72L77 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L77
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
GA, LC
37Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for Q72I28 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I28
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 1
JA, OC
368Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: prfA (sueB, uar)
Find proteins for P0A7I0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7I0
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
KA, PC
256Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62662
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
LA, QC
239Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62663
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
MA, RC
209Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62664
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
NA, SC
162Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsE (rps5)
Find proteins for P62665 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62665
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
OA, TC
101Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsF (rps6)
Find proteins for P62666 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62666
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
PA, UC
156Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62667
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
QA, VC
138Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsH (rps8)
Find proteins for P62668 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62668
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
RA, WC
128Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P62669 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62669
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
SA, XC
105Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsJ (rps10)
Find proteins for P62653 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62653
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
TA, YC
129Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62654
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
UA, ZC
132Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsL (rps12)
Find proteins for P61941 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P61941
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
VA, AD
126Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
WA, BD
61Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsZ (rps14, rpsN)
Find proteins for P62656 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62656
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
XA, CD
89Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsO (rps15)
Find proteins for P62657 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62657
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
YA, DD
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsP (rps16)
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62238
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
ZA, ED
105Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsQ (rps17)
Find proteins for P62658 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62658
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AB, FD
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsR (rps18)
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62659
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
BB, GD
93Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsS (rps19)
Find proteins for P62660 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62660
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
CB, HD
106Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsT (rps20)
Find proteins for P62661 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62661
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
DB, ID
27Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P62613 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62613
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA,FB1507Thermus thermophilus HB27
Entity ID: 2
MoleculeChainsLengthOrganism
25S ribosomal RNAB,GB2880Thermus thermophilus HB27
Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNAC,HB120Thermus thermophilus HB27
Entity ID: 4
MoleculeChainsLengthOrganism
tRNAD,IA,IB,NC77Escherichia coli K-12
Entity ID: 34
MoleculeChainsLengthOrganism
mRNAHA,MC27synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
AC, BA, CA, DA, GA, GC, HC, IC, LC, V
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, AA, AD, B, BA, BB, BC, C, CA, CB, CC, CD, D, DA, DB, DC, DD, E, EA, EC, ED, F, FA, FB, FC, G, GA, GB, GC, GD, H, HA, HB, HC, HD, I, IA, IB, J, JA, JB, K, KA, KB, KC, L, LA, LB, M, MA, MB, MC, N, NA, NB, NC, O, OA, OB, OC, P, PA, PB, PC, Q, QA, QB, QC, R, RA, RB, RC, S, SA, SB, SC, T, TA, TB, TC, U, UA, UB, UC, VA, VB, VC, W, WA, WB, WC, X, XA, XB, XC, Y, YA, YB, YC, Z, ZA, ZB, ZC
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  14 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
A, B, D, FB, GB, HA, IA, IB, MC, NC
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
A, B, D, FB, GB, IA, IB, NC
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
A, FB
RNA LINKINGC12 H18 N5 O8 PG
MA6
Query on MA6
A, FB
RNA LINKINGC12 H18 N5 O7 PA
4SU
Query on 4SU
D, IA, IB, NC
RNA LINKINGC9 H13 N2 O8 P SU
2MG
Query on 2MG
A, FB
RNA LINKINGC11 H16 N5 O8 PG
UR3
Query on UR3
A, FB
RNA LINKINGC10 H15 N2 O9 PU
OMG
Query on OMG
B, GB
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
A, FB
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
B, D, GB, IA, IB, NC
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
B, GB
RNA LINKINGC11 H16 N5 O7 PA
2MU
Query on 2MU
B, GB
RNA LINKINGC11 H17 N2 O9 PU
0TD
Query on 0TD
UA, ZC
L-PEPTIDE LINKINGC5 H9 N O4 SASP
4OC
Query on 4OC
A, B, FB, GB
RNA LINKINGC11 H18 N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 211.541α = 90.00
b = 454.397β = 90.00
c = 619.473γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHENIXphasing
XSCALEdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM107465

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 2.0: 2018-07-11
    Type: Data collection, Polymer sequence