8UU6

Cryo-EM structure of the ratcheted Listeria innocua 70S ribosome in complex with p/E-tRNA (structure II-A)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Mechanistic insights into the alternative ribosome recycling by HflXr.

Seely, S.M.Basu, R.S.Gagnon, M.G.

(2024) Nucleic Acids Res 

  • DOI: https://doi.org/10.1093/nar/gkae128
  • Primary Citation of Related Structures:  
    8UU4, 8UU5, 8UU6, 8UU7, 8UU8, 8UU9, 8UUA

  • PubMed Abstract: 

    During stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue factors such as HflXr, a homolog of the conserved housekeeping GTPase HflX that catalyzes the dissociation of translationally inactive ribosomes into individual subunits. Here we use time-resolved cryo-electron microscopy to elucidate the mechanism of ribosome recycling by Listeria monocytogenes HflXr. Within the 70S ribosome, HflXr displaces helix H69 of the 50S subunit and induces long-range movements of the platform domain of the 30S subunit, disrupting inter-subunit bridges B2b, B2c, B4, B7a and B7b. Our findings unveil a unique ribosome recycling strategy by HflXr which is distinct from that mediated by RRF and EF-G. The resemblance between HflXr and housekeeping HflX suggests that the alternative ribosome recycling mechanism reported here is universal in the prokaryotic kingdom.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2B [auth b]249Listeria innocuaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3C [auth c]218Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A0U4VSU9 (Listeria innocua)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4D [auth d]200Listeria innocuaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5E [auth e]167Listeria innocuaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6F [auth f]97Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A7X0WKH5 (Listeria innocua)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7G [auth g]156Listeria innocuaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8H [auth h]132Listeria innocuaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9I [auth i]130Listeria innocuaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10J [auth j]102Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A0U5A730 (Listeria innocua)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11K [auth k]129Listeria innocuaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12L [auth l]137Listeria innocuaMutation(s): 0 
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Find proteins for A0A660JM56 (Listeria innocua)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13M [auth m]121Listeria innocuaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14N [auth n]61Listeria innocuaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15O [auth o]89Listeria innocuaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16P [auth p]90Listeria innocuaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17Q [auth q]87Listeria innocuaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18R [auth r]79Listeria innocuaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19S [auth s]92Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A0U4VSH5 (Listeria innocua)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20T [auth t]84Listeria innocuaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2Y [auth C]277Listeria innocuaMutation(s): 0 
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Find proteins for A0A0U5A742 (Listeria innocua)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3Z [auth D]209Listeria innocuaMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4AA [auth E]207Listeria innocuaMutation(s): 0 
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Find proteins for A0A0U4VSH7 (Listeria innocua)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5BA [auth F]179Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A0U5AWX6 (Listeria innocua)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6CA [auth G]178Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A0U5ALU0 (Listeria innocua)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13DA [auth L]145Listeria innocuaMutation(s): 0 
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Find proteins for A0A0U5AGN0 (Listeria innocua)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14EA [auth M]122Listeria innocuaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15FA [auth N]146Listeria innocuaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16GA [auth O]144Listeria innocuaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17HA [auth P]135Listeria innocuaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18IA [auth Q]119Listeria innocuaMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19JA [auth R]114Listeria innocuaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20KA [auth S]119Listeria innocuaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21LA [auth T]102Listeria innocuaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22MA [auth U]118Listeria innocuaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23NA [auth V]94Listeria innocuaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24OA [auth W]103Listeria innocuaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27PA [auth Y]96Listeria innocuaMutation(s): 0 
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Find proteins for A0A660JMC7 (Listeria innocua)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28QA [auth Z]62Listeria innocuaMutation(s): 0 
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Find proteins for A0A660JJV9 (Listeria innocua)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29RA [auth 1]63Listeria innocuaMutation(s): 0 
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Find proteins for A0A0U5AGL9 (Listeria innocua)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30SA [auth 2]59Listeria innocuaMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31BTA [auth 3]81Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A0U4MT39 (Listeria innocua)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32UA [auth 4]57Listeria innocuaMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33VA [auth 5]49Listeria innocuaMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34WA [auth 6]44Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A660JKZ6 (Listeria innocua)
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UniProt GroupA0A660JKZ6
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL35XA [auth 7]66Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A660JIB9 (Listeria innocua)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL36YA [auth 8]37Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A0U5AM58 (Listeria innocua)
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UniProt GroupA0A0U5AM58
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S Ribosomal RNAA [auth a]1,550Listeria innocua
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Entity ID: 21
MoleculeChains LengthOrganismImage
p/E Hybrid State Phenylalanine tRNAU [auth x]76Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
F-Stop mRNAV [auth w]21Escherichia phage T4
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Entity ID: 23
MoleculeChains LengthOrganismImage
23S Ribosomal RNAW [auth A]2,932Listeria innocua
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Entity ID: 24
MoleculeChains LengthOrganismImage
5S Ribosomal RNAX [auth B]116Listeria innocua
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
RB [auth n],
VE [auth 4],
WE [auth 5],
XE [auth 8]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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UE [auth O]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth a]
AC [auth A]
AD [auth A]
AE [auth A]
BB [auth a]
AB [auth a],
AC [auth A],
AD [auth A],
AE [auth A],
BB [auth a],
BC [auth A],
BD [auth A],
BE [auth A],
CB [auth a],
CC [auth A],
CD [auth A],
CE [auth A],
DB [auth a],
DC [auth A],
DD [auth A],
DE [auth A],
EB [auth a],
EC [auth A],
ED [auth A],
EE [auth A],
FB [auth a],
FC [auth A],
FD [auth A],
FE [auth A],
GB [auth a],
GC [auth A],
GD [auth A],
GE [auth A],
HB [auth a],
HC [auth A],
HD [auth A],
HE [auth A],
IB [auth a],
IC [auth A],
ID [auth A],
IE [auth A],
JB [auth a],
JC [auth A],
JD [auth A],
JE [auth A],
KB [auth a],
KC [auth A],
KD [auth A],
KE [auth A],
LB [auth a],
LC [auth A],
LD [auth A],
LE [auth A],
MB [auth a],
MC [auth A],
MD [auth A],
ME [auth A],
NB [auth a],
NC [auth A],
ND [auth A],
NE [auth A],
OB [auth a],
OC [auth A],
OD [auth A],
OE [auth A],
PB [auth a],
PC [auth A],
PD [auth A],
PE [auth A],
QB [auth a],
QC [auth A],
QD [auth A],
QE [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
SB [auth q],
SC [auth A],
SD [auth A],
SE [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth D],
UB [auth A],
UC [auth A],
UD [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
ZA [auth a],
ZB [auth A],
ZC [auth A],
ZD [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2.4158
RECONSTRUCTIONcryoSPARC4.1.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUniversity of Texas Medical Branch Startup Funds
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM136936
Welch FoundationUnited StatesH-2032-20230405
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32-GM008280

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references