8UU4

Cryo-EM structure of the Listeria innocua 70S ribosome in complex with HPF (structure I-A)

  • Classification: RIBOSOME
  • Organism(s): Listeria innocua
  • Mutation(s): No 

  • Deposited: 2023-10-31 Released: 2024-02-28 
  • Deposition Author(s): Seely, S.M., Basu, R.S., Gagnon, M.G.
  • Funding Organization(s): Other government, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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
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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
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7G [auth g]156Listeria innocuaMutation(s): 0 
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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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Find proteins for A0A0U5A6U3 (Listeria innocua)
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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
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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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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13M [auth m]121Listeria innocuaMutation(s): 0 
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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 
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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: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome hibernation promoting factorU [auth w]187Listeria innocuaMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2X [auth C]277Listeria innocuaMutation(s): 0 
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Find proteins for A0A0U5A742 (Listeria innocua)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3Y [auth D]209Listeria innocuaMutation(s): 0 
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Find proteins for A0A0U5ADD0 (Listeria innocua)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4Z [auth E]207Listeria innocuaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5AA [auth F]179Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A0U5AWX6 (Listeria innocua)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6BA [auth G]178Listeria innocuaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13CA [auth L]145Listeria innocuaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14DA [auth M]122Listeria innocuaMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15EA [auth N]146Listeria innocuaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16FA [auth O]144Listeria innocuaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17GA [auth P]135Listeria innocuaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18HA [auth Q]119Listeria innocuaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19IA [auth R]114Listeria innocuaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20JA [auth S]119Listeria innocuaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21KA [auth T]102Listeria innocuaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22LA [auth U]118Listeria innocuaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23MA [auth V]94Listeria innocuaMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24NA [auth W]103Listeria innocuaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27OA [auth Y]96Listeria innocuaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28PA [auth Z]62Listeria innocuaMutation(s): 0 
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Find proteins for A0A660JJV9 (Listeria innocua)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29QA [auth 1]63Listeria innocuaMutation(s): 0 
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Find proteins for A0A0U5AGL9 (Listeria innocua)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30RA [auth 2]59Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A0U4VSJ1 (Listeria innocua)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31BSA [auth 3]81Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A0U4MT39 (Listeria innocua)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32TA [auth 4]57Listeria innocuaMutation(s): 0 
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UniProt GroupA0A660JNN0
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33UA [auth 5]49Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A660JRA4 (Listeria innocua)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34VA [auth 6]44Listeria innocuaMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL35WA [auth 7]66Listeria innocuaMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL36XA [auth 8]37Listeria innocuaMutation(s): 0 
UniProt
Find proteins for A0A0U5AM58 (Listeria innocua)
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S Ribosomal RNAA [auth a]1,550Listeria innocua
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Entity ID: 22
MoleculeChains LengthOrganismImage
23S Ribosomal RNAV [auth A]2,932Listeria innocua
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Entity ID: 23
MoleculeChains LengthOrganismImage
5S Ribosomal RNAW [auth B]116Listeria innocua
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
GS [auth 4],
HS [auth 5],
IS [auth 8],
JH [auth n]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AB [auth a]
AC [auth a]
AD [auth a]
AE [auth a]
AF [auth a]
AB [auth a],
AC [auth a],
AD [auth a],
AE [auth a],
AF [auth a],
AG [auth a],
AH [auth a],
AI [auth A],
AJ [auth A],
AK [auth A],
AL [auth A],
AM [auth A],
AN [auth A],
AO [auth A],
AP [auth A],
AQ [auth A],
AR [auth A],
AS [auth A],
BB [auth a],
BC [auth a],
BD [auth a],
BE [auth a],
BF [auth a],
BG [auth a],
BH [auth a],
BI [auth A],
BJ [auth A],
BK [auth A],
BL [auth A],
BM [auth A],
BN [auth A],
BO [auth A],
BP [auth A],
BQ [auth A],
BR [auth A],
BS [auth A],
CB [auth a],
CC [auth a],
CD [auth a],
CE [auth a],
CF [auth a],
CG [auth a],
CH [auth a],
CI [auth A],
CJ [auth A],
CK [auth A],
CL [auth A],
CM [auth A],
CN [auth A],
CO [auth A],
CP [auth A],
CQ [auth A],
CR [auth A],
CS [auth A],
DB [auth a],
DC [auth a],
DD [auth a],
DE [auth a],
DF [auth a],
DG [auth a],
DH [auth a],
DI [auth A],
DJ [auth A],
DK [auth A],
DL [auth A],
DM [auth A],
DN [auth A],
DO [auth A],
DP [auth A],
DQ [auth A],
DR [auth A],
DS [auth A],
EB [auth a],
EC [auth a],
ED [auth a],
EE [auth a],
EF [auth a],
EG [auth a],
EH [auth a],
EI [auth A],
EJ [auth A],
EK [auth A],
EL [auth A],
EM [auth A],
EN [auth A],
EO [auth A],
EP [auth A],
EQ [auth A],
ER [auth A],
ES [auth B],
FB [auth a],
FC [auth a],
FD [auth a],
FE [auth a],
FF [auth a],
FG [auth a],
FH [auth a],
FI [auth A],
FJ [auth A],
FK [auth A],
FL [auth A],
FM [auth A],
FN [auth A],
FO [auth A],
FP [auth A],
FQ [auth A],
FR [auth A],
FS [auth C],
GB [auth a],
GC [auth a],
GD [auth a],
GE [auth a],
GF [auth a],
GG [auth a],
GH [auth a],
GI [auth A],
GJ [auth A],
GK [auth A],
GL [auth A],
GM [auth A],
GN [auth A],
GO [auth A],
GP [auth A],
GQ [auth A],
GR [auth A],
HB [auth a],
HC [auth a],
HD [auth a],
HE [auth a],
HF [auth a],
HG [auth a],
HH [auth a],
HI [auth A],
HJ [auth A],
HK [auth A],
HL [auth A],
HM [auth A],
HN [auth A],
HO [auth A],
HP [auth A],
HQ [auth A],
HR [auth A],
IB [auth a],
IC [auth a],
ID [auth a],
IE [auth a],
IF [auth a],
IG [auth a],
IH [auth a],
II [auth A],
IJ [auth A],
IK [auth A],
IL [auth A],
IM [auth A],
IN [auth A],
IO [auth A],
IP [auth A],
IQ [auth A],
IR [auth A],
JB [auth a],
JC [auth a],
JD [auth a],
JE [auth a],
JF [auth a],
JG [auth a],
JI [auth A],
JJ [auth A],
JK [auth A],
JL [auth A],
JM [auth A],
JN [auth A],
JO [auth A],
JP [auth A],
JQ [auth A],
JR [auth A],
KB [auth a],
KC [auth a],
KD [auth a],
KE [auth a],
KF [auth a],
KG [auth a],
KH [auth A],
KI [auth A],
KJ [auth A],
KK [auth A],
KL [auth A],
KM [auth A],
KN [auth A],
KO [auth A],
KP [auth A],
KQ [auth A],
KR [auth A],
LB [auth a],
LC [auth a],
LD [auth a],
LE [auth a],
LF [auth a],
LG [auth a],
LH [auth A],
LI [auth A],
LJ [auth A],
LK [auth A],
LL [auth A],
LM [auth A],
LN [auth A],
LO [auth A],
LP [auth A],
LQ [auth A],
LR [auth A],
MB [auth a],
MC [auth a],
MD [auth a],
ME [auth a],
MF [auth a],
MG [auth a],
MH [auth A],
MI [auth A],
MJ [auth A],
MK [auth A],
ML [auth A],
MM [auth A],
MN [auth A],
MO [auth A],
MP [auth A],
MQ [auth A],
MR [auth A],
NB [auth a],
NC [auth a],
ND [auth a],
NE [auth a],
NF [auth a],
NG [auth a],
NH [auth A],
NI [auth A],
NJ [auth A],
NK [auth A],
NL [auth A],
NM [auth A],
NN [auth A],
NO [auth A],
NP [auth A],
NQ [auth A],
NR [auth A],
OB [auth a],
OC [auth a],
OD [auth a],
OE [auth a],
OF [auth a],
OG [auth a],
OH [auth A],
OI [auth A],
OJ [auth A],
OK [auth A],
OL [auth A],
OM [auth A],
ON [auth A],
OO [auth A],
OP [auth A],
OQ [auth A],
OR [auth A],
PB [auth a],
PC [auth a],
PD [auth a],
PE [auth a],
PF [auth a],
PG [auth a],
PH [auth A],
PI [auth A],
PJ [auth A],
PK [auth A],
PL [auth A],
PM [auth A],
PN [auth A],
PO [auth A],
PP [auth A],
PQ [auth A],
PR [auth A],
QB [auth a],
QC [auth a],
QD [auth a],
QE [auth a],
QF [auth a],
QG [auth a],
QH [auth A],
QI [auth A],
QJ [auth A],
QK [auth A],
QL [auth A],
QM [auth A],
QN [auth A],
QO [auth A],
QP [auth A],
QQ [auth A],
QR [auth A],
RB [auth a],
RC [auth a],
RD [auth a],
RE [auth a],
RF [auth a],
RG [auth a],
RH [auth A],
RI [auth A],
RJ [auth A],
RK [auth A],
RL [auth A],
RM [auth A],
RN [auth A],
RO [auth A],
RP [auth A],
RQ [auth A],
RR [auth A],
SB [auth a],
SC [auth a],
SD [auth a],
SE [auth a],
SF [auth a],
SG [auth a],
SH [auth A],
SI [auth A],
SJ [auth A],
SK [auth A],
SL [auth A],
SM [auth A],
SN [auth A],
SO [auth A],
SP [auth A],
SQ [auth A],
SR [auth A],
TB [auth a],
TC [auth a],
TD [auth a],
TE [auth a],
TF [auth a],
TG [auth a],
TH [auth A],
TI [auth A],
TJ [auth A],
TK [auth A],
TL [auth A],
TM [auth A],
TN [auth A],
TO [auth A],
TP [auth A],
TQ [auth A],
TR [auth A],
UB [auth a],
UC [auth a],
UD [auth a],
UE [auth a],
UF [auth a],
UG [auth a],
UH [auth A],
UI [auth A],
UJ [auth A],
UK [auth A],
UL [auth A],
UM [auth A],
UN [auth A],
UO [auth A],
UP [auth A],
UQ [auth A],
UR [auth A],
VB [auth a],
VC [auth a],
VD [auth a],
VE [auth a],
VF [auth a],
VG [auth a],
VH [auth A],
VI [auth A],
VJ [auth A],
VK [auth A],
VL [auth A],
VM [auth A],
VN [auth A],
VO [auth A],
VP [auth A],
VQ [auth A],
VR [auth A],
WB [auth a],
WC [auth a],
WD [auth a],
WE [auth a],
WF [auth a],
WG [auth a],
WH [auth A],
WI [auth A],
WJ [auth A],
WK [auth A],
WL [auth A],
WM [auth A],
WN [auth A],
WO [auth A],
WP [auth A],
WQ [auth A],
WR [auth A],
XB [auth a],
XC [auth a],
XD [auth a],
XE [auth a],
XF [auth a],
XG [auth a],
XH [auth A],
XI [auth A],
XJ [auth A],
XK [auth A],
XL [auth A],
XM [auth A],
XN [auth A],
XO [auth A],
XP [auth A],
XQ [auth A],
XR [auth A],
YA [auth a],
YB [auth a],
YC [auth a],
YD [auth a],
YE [auth a],
YF [auth a],
YG [auth a],
YH [auth A],
YI [auth A],
YJ [auth A],
YK [auth A],
YL [auth A],
YM [auth A],
YN [auth A],
YO [auth A],
YP [auth A],
YQ [auth A],
YR [auth A],
ZA [auth a],
ZB [auth a],
ZC [auth a],
ZD [auth a],
ZE [auth a],
ZF [auth a],
ZG [auth a],
ZH [auth A],
ZI [auth A],
ZJ [auth A],
ZK [auth A],
ZL [auth A],
ZM [auth A],
ZN [auth A],
ZO [auth A],
ZP [auth A],
ZQ [auth A],
ZR [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentUnited StatesUniversity of Texas
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM136936
Welch FoundationUnited StatesH-2032-20230405
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM008280

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references