6ORE

Release complex 70S


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy.

Fu, Z.Indrisiunaite, G.Kaledhonkar, S.Shah, B.Sun, M.Chen, B.Grassucci, R.A.Ehrenberg, M.Frank, J.

(2019) Nat Commun 10: 2579-2579

  • DOI: 10.1038/s41467-019-10608-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of ...

    When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away. Surprisingly, free RF2 is compact, with only 20 Å between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden.,Department of Biological Sciences, Columbia University, New York, NY, 10027, USA. jf2192@cumc.columbia.edu.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA. jf2192@cumc.columbia.edu.,Department of Biological Sciences, Barnard College, New York, NY, 10027, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
FME-PHE-PHE
A
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
B
271Escherichia coli 2-005-03_S4_C2Mutation(s): 0 
Gene Names: rplB
Find proteins for A0A029IK04 (Escherichia coli 2-005-03_S4_C2)
Go to UniProtKB:  A0A029IK04
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
C
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
D
201Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplD
Find proteins for D7Z9F6 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9F6
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
E
177Escherichia coli 909945-2Mutation(s): 0 
Gene Names: rplE
Find proteins for V0AXZ0 (Escherichia coli 909945-2)
Go to UniProtKB:  V0AXZ0
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
F
175Escherichia coli H386Mutation(s): 0 
Gene Names: rplF
Find proteins for A0A1X3JB47 (Escherichia coli H386)
Go to UniProtKB:  A0A1X3JB47
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
G
149Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplI
Find proteins for D7ZI15 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZI15
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplM
Find proteins for D7ZET0 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZET0
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
123Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplN
Find proteins for D7Z9G5 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G5
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
144Escherichia coliMutation(s): 0 
Gene Names: rplO
Find proteins for A0A037Y8L6 (Escherichia coli)
Go to UniProtKB:  A0A037Y8L6
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
119Escherichia coliMutation(s): 0 
Gene Names: rplQ
Find proteins for A0A2T1LEK9 (Escherichia coli)
Go to UniProtKB:  A0A2T1LEK9
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
116Escherichia coli Xuzhou21Mutation(s): 0 
Gene Names: rplR
Find proteins for A0A0F6C9R0 (Escherichia coli Xuzhou21)
Go to UniProtKB:  A0A0F6C9R0
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
114Escherichia coli B185Mutation(s): 0 
Gene Names: rplS
Find proteins for D6IC61 (Escherichia coli B185)
Go to UniProtKB:  D6IC61
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
117Escherichia coli KTE73Mutation(s): 0 
Gene Names: rplT
Find proteins for S1EK76 (Escherichia coli KTE73)
Go to UniProtKB:  S1EK76
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplU
Find proteins for D7ZEN7 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZEN7
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplV
Find proteins for D7Z9G0 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G0
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
94Escherichia coli 2-005-03_S4_C2Mutation(s): 0 
Gene Names: rplW
Find proteins for A0A029IKB7 (Escherichia coli 2-005-03_S4_C2)
Go to UniProtKB:  A0A029IKB7
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
103Escherichia coli PCN033Mutation(s): 0 
Gene Names: rplX
Find proteins for A0A0G3K7Z5 (Escherichia coli PCN033)
Go to UniProtKB:  A0A0G3K7Z5
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coli MS 84-1Mutation(s): 0 
Gene Names: rplY
Find proteins for D7XH79 (Escherichia coli MS 84-1)
Go to UniProtKB:  D7XH79
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
76Escherichia coli 113290Mutation(s): 0 
Gene Names: rpmA
Find proteins for U9XYH0 (Escherichia coli 113290)
Go to UniProtKB:  U9XYH0
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
77Escherichia coli ATCC BAA-2209Mutation(s): 0 
Gene Names: rpmB
Find proteins for V8F9Y0 (Escherichia coli ATCC BAA-2209)
Go to UniProtKB:  V8F9Y0
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
62Escherichia coli H386Mutation(s): 0 
Gene Names: rpmC
Find proteins for A0A1X3JBH6 (Escherichia coli H386)
Go to UniProtKB:  A0A1X3JBH6
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
58Escherichia coli chi7122Mutation(s): 0 
Gene Names: rpmD
Find proteins for J7R6H0 (Escherichia coli chi7122)
Go to UniProtKB:  J7R6H0
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
a
66Escherichia coli 1-392-07_S4_C3Mutation(s): 0 
Gene Names: rpmE
Find proteins for A0A080FR68 (Escherichia coli 1-392-07_S4_C3)
Go to UniProtKB:  A0A080FR68
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
56Escherichia coli PCN033Mutation(s): 0 
Gene Names: rpmF
Find proteins for A0A0G3K5Y7 (Escherichia coli PCN033)
Go to UniProtKB:  A0A0G3K5Y7
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
c
52Escherichia coli DEC2EMutation(s): 0 
Gene Names: rpmG
Find proteins for H4LIZ0 (Escherichia coli DEC2E)
Go to UniProtKB:  H4LIZ0
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
d
46Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmH
Find proteins for B7MGC4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MGC4
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
e
64Escherichia coli 1.2741Mutation(s): 0 
Gene Names: rpmI
Find proteins for I2RJ64 (Escherichia coli 1.2741)
Go to UniProtKB:  I2RJ64
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
f
38Escherichia coli (strain UMEA 3162-1)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for A0A0E2L017 (Escherichia coli (strain UMEA 3162-1))
Go to UniProtKB:  A0A0E2L017
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
g
225Escherichia coliMutation(s): 0 
Gene Names: rpsB
Find proteins for C3TPN2 (Escherichia coli)
Go to UniProtKB:  C3TPN2
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
h
208Escherichia coliMutation(s): 0 
Gene Names: rpsC
Find proteins for A0A376HTV6 (Escherichia coli)
Go to UniProtKB:  A0A376HTV6
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
i
205Escherichia coli KTE75Mutation(s): 0 
Gene Names: rpsD
Find proteins for L3PZ69 (Escherichia coli KTE75)
Go to UniProtKB:  L3PZ69
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
j
156Escherichia coli 2-427-07_S4_C3Mutation(s): 0 
Gene Names: rpsE
Find proteins for A0A073FR78 (Escherichia coli 2-427-07_S4_C3)
Go to UniProtKB:  A0A073FR78
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
k
104Escherichia coliMutation(s): 0 
Gene Names: rpsF
Find proteins for A0A376ZL25 (Escherichia coli)
Go to UniProtKB:  A0A376ZL25
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
l
151Escherichia coli KTE64Mutation(s): 0 
Gene Names: rpsG
Find proteins for S1D5F0 (Escherichia coli KTE64)
Go to UniProtKB:  S1D5F0
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
m
129Escherichia coli (strain MS 21-1)Mutation(s): 0 
Gene Names: rpsH
Find proteins for D8A1L7 (Escherichia coli (strain MS 21-1))
Go to UniProtKB:  D8A1L7
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
n
127Escherichia coli UMEA 3718-1Mutation(s): 0 
Gene Names: rpsI
Find proteins for T9TH92 (Escherichia coli UMEA 3718-1)
Go to UniProtKB:  T9TH92
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
o
99Escherichia coli chi7122Mutation(s): 0 
Gene Names: rpsJ
Find proteins for J7RLQ6 (Escherichia coli chi7122)
Go to UniProtKB:  J7RLQ6
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
p
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
q
123Escherichia coli KTE112Mutation(s): 0 
Gene Names: rpsL
Find proteins for L4V1L2 (Escherichia coli KTE112)
Go to UniProtKB:  L4V1L2
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
r
116Escherichia coli HVH 87Mutation(s): 0 
Gene Names: rpsM
Find proteins for T6LFY5 (Escherichia coli HVH 87)
Go to UniProtKB:  T6LFY5
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
s
100Escherichia coli chi7122Mutation(s): 0 
Gene Names: rpsN
Find proteins for J7R6H7 (Escherichia coli chi7122)
Go to UniProtKB:  J7R6H7
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
t
88Escherichia coli MS 84-1Mutation(s): 0 
Gene Names: rpsO
Find proteins for D7XN21 (Escherichia coli MS 84-1)
Go to UniProtKB:  D7XN21
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
u
82Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpsP
Find proteins for B7MIU7 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIU7
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
v
80Escherichia coli 1-250-04_S3_C2Mutation(s): 0 
Gene Names: rpsQ
Find proteins for A0A080IK26 (Escherichia coli 1-250-04_S3_C2)
Go to UniProtKB:  A0A080IK26
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
w
66Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rpsR
Find proteins for D7ZI16 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZI16
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
x
83Escherichia coli O26:H11Mutation(s): 0 
Gene Names: rpsS
Find proteins for A0A0A8UF41 (Escherichia coli O26:H11)
Go to UniProtKB:  A0A0A8UF41
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
y
86Escherichia coli 541-15Mutation(s): 0 
Gene Names: rpsT
Find proteins for I4T5W9 (Escherichia coli 541-15)
Go to UniProtKB:  I4T5W9
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
z
70Escherichia coli KTE193Mutation(s): 0 
Gene Names: rpsU
Find proteins for L3C5D9 (Escherichia coli KTE193)
Go to UniProtKB:  L3C5D9
Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNA12903Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
16S ribosomal RNA21534Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNA3120Escherichia coli
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*UP*CP*UP*UP*CP*UP*AP*A)-3')49Escherichia coli
Entity ID: 5
MoleculeChainsLengthOrganism
P-tRNA576Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
a, f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
1, 2, 3, 5, B, b, C, f, i, Q, r
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  19 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
1, 2, 5
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
1, 2
RNA LINKINGC10 H16 N3 O8 PC
6MZ
Query on 6MZ
1
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
1
RNA LINKINGC10 H15 N2 O9 PU
1MG
Query on 1MG
1
RNA LINKINGC11 H16 N5 O8 PG
FME
Query on FME
A
L-PEPTIDE LINKINGC6 H11 N O3 SMET
OMC
Query on OMC
1
RNA LINKINGC10 H16 N3 O8 PC
MA6
Query on MA6
2
RNA LINKINGC12 H18 N5 O7 PA
4SU
Query on 4SU
5
RNA LINKINGC9 H13 N2 O8 P SU
2MG
Query on 2MG
1, 2
RNA LINKINGC11 H16 N5 O8 PG
G7M
Query on G7M
1, 2
RNA LINKINGC11 H17 N5 O8 PG
UR3
Query on UR3
2
RNA LINKINGC10 H15 N2 O9 PU
OMG
Query on OMG
1
RNA LINKINGC11 H16 N5 O8 PG
5MU
Query on 5MU
1, 5
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
1
RNA LINKINGC11 H16 N5 O7 PA
0TD
Query on 0TD
q
L-PEPTIDE LINKINGC5 H9 N O4 SASP
4OC
Query on 4OC
2, 5
RNA LINKINGC11 H18 N3 O8 PC
3TD
Query on 3TD
1
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
5
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-04-30 
  • Released Date: 2019-06-19 
  • Deposition Author(s): Fu, Z.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM55440
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM29169
Swedish Research CouncilSweden--

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Type: Data collection, Database references