6N1D

X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid State


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.268 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state.

Zhou, J.Lancaster, L.Donohue, J.P.Noller, H.F.

(2019) Proc. Natl. Acad. Sci. U.S.A. 116: 7813-7818

  • DOI: 10.1073/pnas.1901310116

  • PubMed Abstract: 
  • The elongation factor G (EF-G)-catalyzed translocation of mRNA and tRNA through the ribosome is essential for vacating the ribosomal A site for the next incoming aminoacyl-tRNA, while precisely maintaining the translational reading frame. Here, the 3 ...

    The elongation factor G (EF-G)-catalyzed translocation of mRNA and tRNA through the ribosome is essential for vacating the ribosomal A site for the next incoming aminoacyl-tRNA, while precisely maintaining the translational reading frame. Here, the 3.2-Å crystal structure of a ribosome translocation intermediate complex containing mRNA and two tRNAs, formed in the absence of EF-G or GTP, provides insight into the respective roles of EF-G and the ribosome in translocation. Unexpectedly, the head domain of the 30S subunit is rotated by 21°, creating a ribosomal conformation closely resembling the two-tRNA chimeric hybrid state that was previously observed only in the presence of bound EF-G. The two tRNAs have moved spontaneously from their A/A and P/P binding states into ap/P and pe/E states, in which their anticodon loops are bound between the 30S body domain and its rotated head domain, while their acceptor ends have moved fully into the 50S P and E sites, respectively. Remarkably, the A-site tRNA translocates fully into the classical P-site position. Although the mRNA also undergoes movement, codon-anticodon interaction is disrupted in the absence of EF-G, resulting in slippage of the translational reading frame. We conclude that, although movement of both tRNAs and mRNA (along with rotation of the 30S head domain) can occur in the absence of EF-G and GTP, EF-G is essential for enforcing coupled movement of the tRNAs and their mRNA codons to maintain the reading frame.


    Organizational Affiliation

    Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064.,Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064 harry@nuvolari.ucsc.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
AL01, BL01
228Thermus thermophilusMutation(s): 0 
Gene Names: rplA
Find proteins for A0A1J1EJ43 (Thermus thermophilus)
Go to UniProtKB:  A0A1J1EJ43
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
AL02, BL02
276Thermus 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
AL03, BL03
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
AL04, BL04
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
AL05, BL05
181Thermus 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
AL06, BL06
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
AL09, BL09
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
AL13, BL13
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
AL14, BL14
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
AL15, BL15
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
AL16, BL16
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
AL17, BL17
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
AL18, BL18
111Thermus 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
AL19, BL19
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
AL20, BL20
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
AL21, BL21
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
AL22, BL22
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
AL23, BL23
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
AL24, BL24
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
AL25, BL25
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
AL27, BL27
84Thermus 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
AL28, BL28
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
AL29, BL29
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
AL30, BL30
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
AL31, BL31
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
AL32, BL32
59Thermus 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: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
AL33, BL33
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
AL34, BL34
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
AL35, BL35
64Thermus 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
AL36, BL36
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: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AS02, BS02
255Thermus 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
AS03, BS03
238Thermus 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
AS04, BS04
208Thermus 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
AS05, BS05
161Thermus 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
AS06, BS06
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
AS07, BS07
155Thermus 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
AS08, BS08
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
AS09, BS09
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
AS10, BS10
104Thermus 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
AS11, BS11
128Thermus 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
AS12, BS12
131Thermus 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
AS13, BS13
125Thermus 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
AS14, BS14
60Thermus 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
AS15, BS15
88Thermus 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
AS16, BS16
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
AS17, BS17
104Thermus 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
AS18, BS18
87Thermus 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
AS19, BS19
92Thermus 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
AS20, BS20
105Thermus 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
ATHX, BTHX
26Thermus 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 rRNAA16S,B16S1518Thermus thermophilus HB27
Entity ID: 2
MoleculeChainsLengthOrganism
23S rRNAA23S,B23S2881Thermus thermophilus HB27
Entity ID: 3
MoleculeChainsLengthOrganism
5s rRNAA5S,B5S119Thermus thermophilus HB27
Entity ID: 34
MoleculeChainsLengthOrganism
mRNAAMRN,BMRN17synthetic construct
Entity ID: 35
MoleculeChainsLengthOrganism
P-tRNAAPTN,BPTN76Escherichia coli
Entity ID: 56
MoleculeChainsLengthOrganism
A tRNABATN85Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
AS04, BS04
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A16S, A23S, A5S, AL01, AL02, AL04, AL06, AL14, AL15, AL17, AL20, AL21, AL23, AL24, AL27, AL28, AL33, AL34, AS02, AS03, AS06, AS08, B16S, B23S, B5S, BATN, BL01, BL02, BL03, BL04, BL15, BL16, BL18, BL19, BL20, BL21, BL22, BL23, BL24, BL25, BL28, BL29, BL30, BL31, BL32, BL33, BL34, BL35, BL36, BS16, BS17, BTHX
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  8 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
APTN, BATN, BPTN
RNA LINKINGC9 H13 N2 O9 PU
CM0
Query on CM0
APTN, BPTN
RNA LINKINGC11 H15 N2 O12 P

--

6MZ
Query on 6MZ
APTN, BPTN
RNA LINKINGC11 H16 N5 O7 PA
4SU
Query on 4SU
APTN, BPTN
RNA LINKINGC9 H13 N2 O8 P SU
MIA
Query on MIA
BATN
RNA LINKINGC16 H24 N5 O7 P SA
G7M
Query on G7M
APTN, BPTN
RNA LINKINGC11 H17 N5 O8 PG
QUO
Query on QUO
BATN
RNA LINKINGC17 H26 N5 O10 PG
5MU
Query on 5MU
APTN, BATN, BPTN
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.268 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 207.450α = 90.00
b = 442.870β = 90.00
c = 613.000γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACphasing
PHENIXrefinement
XSCALEdata scaling

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 Sciences (NIH/NIGMS)United StatesR35-GM118156

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Type: Data collection, Database references
  • Version 1.2: 2019-05-01
    Type: Data collection, Database references
  • Version 2.0: 2019-07-03
    Type: Data collection, Non-polymer description, Structure summary
  • Version 2.1: 2020-01-01
    Type: Author supporting evidence