6ERI

Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor


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 1.0 of the entry. See complete history


Literature

Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.

Boerema, A.P.Aibara, S.Paul, B.Tobiasson, V.Kimanius, D.Forsberg, B.O.Wallden, K.Lindahl, E.Amunts, A.

(2018) Nat Plants 4: 212-217

  • DOI: https://doi.org/10.1038/s41477-018-0129-6
  • Primary Citation of Related Structures:  
    6ERI

  • PubMed Abstract: 

    Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome 1,2 . Despite recent structural information 3-6 , some of these aspects remained elusive. To provide new insights into the structural specialities and evolution, we report a comprehensive analysis of the 2.9-3.1 Å resolution electron cryo-microscopy structure of the spinach chlororibosome in complex with its recycling factor and hibernation-promoting factor. The model reveals a prominent channel extending from the exit tunnel to the chlororibosome exterior, structural re-arrangements that lead to increased surface area for translocon binding, and experimental evidence for parallel and convergent evolution of chloro- and mitoribosomes.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2, chloroplasticC [auth AC]246Spinacia oleraceaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3, chloroplasticD [auth AD]221Spinacia oleraceaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4, chloroplasticE [auth AE]212Spinacia oleraceaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5, chloroplasticF [auth AF]207Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6, chloroplasticG [auth AG]172Spinacia oleraceaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9, chloroplasticH [auth AH]46Spinacia oleraceaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13, chloroplasticI [auth AJ]200Spinacia oleraceaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14, chloroplasticJ [auth AK]121Spinacia oleraceaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15, chloroplasticK [auth AL]184Spinacia oleraceaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16, chloroplasticL [auth AM]134Spinacia oleraceaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17, chloroplasticM [auth AN]116Spinacia oleraceaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18, chloroplasticN [auth AO]121Spinacia oleraceaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19, chloroplasticO [auth AP]118Spinacia oleraceaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20, chloroplasticP [auth AQ]115Spinacia oleraceaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21, chloroplasticQ [auth AR]165Spinacia oleraceaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22, chloroplasticR [auth AS]171Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23, chloroplasticS [auth AT]92Spinacia oleraceaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24, chloroplasticT [auth AU]127Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27, chloroplasticU [auth AW]114Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28, chloroplasticV [auth AX]76Spinacia oleraceaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29, chloroplasticW [auth AY]99Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31, chloroplasticX [auth AZ]66Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32, chloroplasticY [auth Aa]48Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33, chloroplasticZ [auth Ab]60Spinacia oleraceaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34, chloroplasticAA [auth Ac]61Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35, chloroplasticBA [auth Ad]72Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36, chloroplasticCA [auth Ae]37Spinacia oleraceaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein 6, chloroplasticDA [auth Af]47Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein 5 alpha, chloroplasticEA [auth Aw]49Spinacia oleraceaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome-recycling factor, chloroplasticGA [auth Az]191Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2, chloroplasticIA [auth BB]215Spinacia oleraceaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3, chloroplasticJA [auth BC]217Spinacia oleraceaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4, chloroplasticKA [auth BD]200Spinacia oleraceaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5, chloroplasticLA [auth BE]158Spinacia oleraceaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6 alpha, chloroplasticMA [auth BF]113Spinacia oleraceaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7, chloroplasticNA [auth BG]151Spinacia oleraceaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8, chloroplasticOA [auth BH]134Spinacia oleraceaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9, chloroplasticPA [auth BI]141Spinacia oleraceaMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10 alpha, chloroplasticQA [auth BJ]98Spinacia oleraceaMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11, chloroplasticRA [auth BK]110Spinacia oleraceaMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12, chloroplasticSA [auth BL]122Spinacia oleraceaMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13, chloroplasticTA [auth BM]111Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14, chloroplasticUA [auth BN]99Spinacia oleraceaMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15, chloroplasticVA [auth BO]72Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16, chloroplasticWA [auth BP]81Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17, chloroplasticXA [auth BQ]84Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18, chloroplasticYA [auth BR]53Spinacia oleraceaMutation(s): 0 
UniProt
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UniProt GroupQ9M3K7
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19, chloroplasticZA [auth BS]81Spinacia oleraceaMutation(s): 0 
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Find proteins for P06508 (Spinacia oleracea)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20, chloroplasticAB [auth BT]102Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82130 (Spinacia oleracea)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21, chloroplasticBB [auth BU]59Spinacia oleraceaMutation(s): 0 
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Find proteins for P82024 (Spinacia oleracea)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome-binding factor PSRP1, chloroplasticCB [auth BV]106Spinacia oleraceaMutation(s): 0 
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Find proteins for P19954 (Spinacia oleracea)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S31, chloroplasticDB [auth BW]37Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P47910 (Spinacia oleracea)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
bS1cEB [auth BY]170Spinacia oleraceaMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth AA]2,810Spinacia oleracea
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Entity ID: 2
MoleculeChains LengthOrganismImage
4.5S ribosomal RNAB [auth AB]106Spinacia oleracea
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Entity ID: 32
MoleculeChains LengthOrganismImage
5S ribosomal RNAFA [auth Ax]118Spinacia oleracea
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Entity ID: 34
MoleculeChains LengthOrganismImage
16S ribosomal RNAHA [auth BA]1,481Spinacia oleracea
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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 
BL [auth Ab],
CL [auth Ae]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth AA]
AD [auth AA]
AE [auth AA]
AF [auth AA]
AG [auth AA]
AC [auth AA],
AD [auth AA],
AE [auth AA],
AF [auth AA],
AG [auth AA],
AH [auth AA],
AI [auth AA],
AJ [auth AA],
AK [auth AA],
AL [auth AB],
AM [auth BA],
AN [auth BA],
AO [auth BA],
BC [auth AA],
BD [auth AA],
BE [auth AA],
BF [auth AA],
BG [auth AA],
BH [auth AA],
BI [auth AA],
BJ [auth AA],
BK [auth AA],
BM [auth BA],
BN [auth BA],
BO [auth BA],
CC [auth AA],
CD [auth AA],
CE [auth AA],
CF [auth AA],
CG [auth AA],
CH [auth AA],
CI [auth AA],
CJ [auth AA],
CK [auth AA],
CM [auth BA],
CN [auth BA],
CO [auth BA],
DC [auth AA],
DD [auth AA],
DE [auth AA],
DF [auth AA],
DG [auth AA],
DH [auth AA],
DI [auth AA],
DJ [auth AA],
DK [auth AA],
DL [auth Af],
DM [auth BA],
DN [auth BA],
DO [auth BA],
EC [auth AA],
ED [auth AA],
EE [auth AA],
EF [auth AA],
EG [auth AA],
EH [auth AA],
EI [auth AA],
EJ [auth AA],
EK [auth AA],
EL [auth Aw],
EM [auth BA],
EN [auth BA],
EO [auth BA],
FB [auth AA],
FC [auth AA],
FD [auth AA],
FE [auth AA],
FF [auth AA],
FG [auth AA],
FH [auth AA],
FI [auth AA],
FJ [auth AA],
FK [auth AA],
FL [auth Ax],
FM [auth BA],
FN [auth BA],
FO [auth BA],
GB [auth AA],
GC [auth AA],
GD [auth AA],
GE [auth AA],
GF [auth AA],
GG [auth AA],
GH [auth AA],
GI [auth AA],
GJ [auth AA],
GK [auth AA],
GL [auth Ax],
GM [auth BA],
GN [auth BA],
GO [auth BA],
HB [auth AA],
HC [auth AA],
HD [auth AA],
HE [auth AA],
HF [auth AA],
HG [auth AA],
HH [auth AA],
HI [auth AA],
HJ [auth AA],
HK [auth AA],
HL [auth BA],
HM [auth BA],
HN [auth BA],
HO [auth BA],
IB [auth AA],
IC [auth AA],
ID [auth AA],
IE [auth AA],
IF [auth AA],
IG [auth AA],
IH [auth AA],
II [auth AA],
IJ [auth AA],
IK [auth AA],
IL [auth BA],
IM [auth BA],
IN [auth BA],
IO [auth BA],
JB [auth AA],
JC [auth AA],
JD [auth AA],
JE [auth AA],
JF [auth AA],
JG [auth AA],
JH [auth AA],
JI [auth AA],
JJ [auth AA],
JK [auth AA],
JL [auth BA],
JM [auth BA],
JN [auth BA],
JO [auth BA],
KB [auth AA],
KC [auth AA],
KD [auth AA],
KE [auth AA],
KF [auth AA],
KG [auth AA],
KH [auth AA],
KI [auth AA],
KJ [auth AA],
KK [auth AA],
KL [auth BA],
KM [auth BA],
KN [auth BA],
KO [auth BA],
LB [auth AA],
LC [auth AA],
LD [auth AA],
LE [auth AA],
LF [auth AA],
LG [auth AA],
LH [auth AA],
LI [auth AA],
LJ [auth AA],
LK [auth AA],
LL [auth BA],
LM [auth BA],
LN [auth BA],
LO [auth BN],
MB [auth AA],
MC [auth AA],
MD [auth AA],
ME [auth AA],
MF [auth AA],
MG [auth AA],
MH [auth AA],
MI [auth AA],
MJ [auth AA],
MK [auth AA],
ML [auth BA],
MM [auth BA],
MN [auth BA],
NB [auth AA],
NC [auth AA],
ND [auth AA],
NE [auth AA],
NF [auth AA],
NG [auth AA],
NH [auth AA],
NI [auth AA],
NJ [auth AA],
NK [auth AA],
NL [auth BA],
NM [auth BA],
NN [auth BA],
OB [auth AA],
OC [auth AA],
OD [auth AA],
OE [auth AA],
OF [auth AA],
OG [auth AA],
OH [auth AA],
OI [auth AA],
OJ [auth AA],
OK [auth AA],
OL [auth BA],
OM [auth BA],
ON [auth BA],
PB [auth AA],
PC [auth AA],
PD [auth AA],
PE [auth AA],
PF [auth AA],
PG [auth AA],
PH [auth AA],
PI [auth AA],
PJ [auth AA],
PK [auth AA],
PL [auth BA],
PM [auth BA],
PN [auth BA],
QB [auth AA],
QC [auth AA],
QD [auth AA],
QE [auth AA],
QF [auth AA],
QG [auth AA],
QH [auth AA],
QI [auth AA],
QJ [auth AA],
QK [auth AA],
QL [auth BA],
QM [auth BA],
QN [auth BA],
RB [auth AA],
RC [auth AA],
RD [auth AA],
RE [auth AA],
RF [auth AA],
RG [auth AA],
RH [auth AA],
RI [auth AA],
RJ [auth AA],
RK [auth AA],
RL [auth BA],
RM [auth BA],
RN [auth BA],
SB [auth AA],
SC [auth AA],
SD [auth AA],
SE [auth AA],
SF [auth AA],
SG [auth AA],
SH [auth AA],
SI [auth AA],
SJ [auth AA],
SK [auth AB],
SL [auth BA],
SM [auth BA],
SN [auth BA],
TB [auth AA],
TC [auth AA],
TD [auth AA],
TE [auth AA],
TF [auth AA],
TG [auth AA],
TH [auth AA],
TI [auth AA],
TJ [auth AA],
TK [auth AB],
TL [auth BA],
TM [auth BA],
TN [auth BA],
UB [auth AA],
UC [auth AA],
UD [auth AA],
UE [auth AA],
UF [auth AA],
UG [auth AA],
UH [auth AA],
UI [auth AA],
UJ [auth AA],
UK [auth AB],
UL [auth BA],
UM [auth BA],
UN [auth BA],
VB [auth AA],
VC [auth AA],
VD [auth AA],
VE [auth AA],
VF [auth AA],
VG [auth AA],
VH [auth AA],
VI [auth AA],
VJ [auth AA],
VK [auth AB],
VL [auth BA],
VM [auth BA],
VN [auth BA],
WB [auth AA],
WC [auth AA],
WD [auth AA],
WE [auth AA],
WF [auth AA],
WG [auth AA],
WH [auth AA],
WI [auth AA],
WJ [auth AA],
WK [auth AB],
WL [auth BA],
WM [auth BA],
WN [auth BA],
XB [auth AA],
XC [auth AA],
XD [auth AA],
XE [auth AA],
XF [auth AA],
XG [auth AA],
XH [auth AA],
XI [auth AA],
XJ [auth AA],
XK [auth AB],
XL [auth BA],
XM [auth BA],
XN [auth BA],
YB [auth AA],
YC [auth AA],
YD [auth AA],
YE [auth AA],
YF [auth AA],
YG [auth AA],
YH [auth AA],
YI [auth AA],
YJ [auth AA],
YK [auth AB],
YL [auth BA],
YM [auth BA],
YN [auth BA],
ZB [auth AA],
ZC [auth AA],
ZD [auth AA],
ZE [auth AA],
ZF [auth AA],
ZG [auth AA],
ZH [auth AA],
ZI [auth AA],
ZJ [auth AA],
ZK [auth AB],
ZL [auth BA],
ZM [auth BA],
ZN [auth BA]
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 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Foundation for Strategic ResearchSwedenFuture Leaders Grant FFL15:0325
Ragnar Soderberg FoundationSwedenM44/16
Swedish Research CouncilSwedenNT-2016-04107
Swedish Research CouncilSwedenNT-2013-5901

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release