5MMI

Structure of the large subunit of the chloroplast ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.

Bieri, P.Leibundgut, M.Saurer, M.Boehringer, D.Ban, N.

(2017) EMBO J 36: 475-486

  • DOI: https://doi.org/10.15252/embj.201695959

  • PubMed Abstract: 

    Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid-specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light- and temperature-dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A-site and P-site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non-rotated state, in which the intersubunit bridges to the large subunit are stabilized.


  • Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31A [auth 0]130Spinacia oleraceaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32, chloroplasticB [auth 1]57Spinacia oleraceaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33, chloroplasticC [auth 2]66Spinacia oleraceaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34, chloroplasticD [auth 3]152Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35, chloroplasticE [auth 4]159Spinacia oleraceaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36, chloroplasticF [auth 5]37Spinacia oleraceaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein cL37, PSRP5G [auth 6]142Spinacia oleraceaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein 6, chloroplasticH [auth 7]116Spinacia oleraceaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2, chloroplasticK [auth C]272Spinacia oleraceaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein uL3cL [auth D]305Spinacia oleraceaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein uL4cM [auth E]293Spinacia oleraceaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein uL5cN [auth F]258Spinacia oleraceaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein uL6cO [auth G]220Spinacia oleraceaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein bL9cP [auth H]196Spinacia oleraceaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein uL10cQ [auth I]232Spinacia oleraceaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11, chloroplasticR [auth J]224Spinacia oleraceaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13, chloroplasticS [auth K]250Spinacia oleraceaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14, chloroplasticT [auth L]121Spinacia oleraceaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein uL15cU [auth M]271Spinacia oleraceaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16, chloroplasticV [auth N]135Spinacia oleraceaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein bL17cW [auth O]126Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein uL18cX [auth P]166Spinacia oleraceaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19, chloroplasticY [auth Q]233Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20, chloroplasticZ [auth R]128Spinacia oleraceaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21, chloroplasticAA [auth S]256Spinacia oleraceaMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22, chloroplasticBA [auth T]199Spinacia oleraceaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23, chloroplasticCA [auth U]198Spinacia oleraceaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein uL24cDA [auth V]192Spinacia oleraceaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein bL27cFA [auth X]194Spinacia oleraceaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein bL28cGA [auth Y]148Spinacia oleraceaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein uL29cHA [auth Z]168Spinacia oleraceaMutation(s): 0 
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Entity ID: 9
MoleculeChains LengthOrganismImage
23S ribosomal RNAI [auth A]2,810Spinacia oleracea
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Entity ID: 10
MoleculeChains LengthOrganismImage
5S ribosomal RNAJ [auth B]121Spinacia oleracea
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Entity ID: 31
MoleculeChains LengthOrganismImage
4.5S ribosomal RNAEA [auth W]106Spinacia oleracea
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Entity ID: 35
MoleculeChains LengthOrganismImage
E-site tRNAIA [auth z]2Spinacia 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 
JA [auth 2],
LA [auth 5]
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 B],
AT [auth V],
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 B],
BT [auth V],
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 B],
CT [auth W],
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 B],
DT [auth W],
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],
ET [auth W],
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 B],
FT [auth W],
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],
GS [auth B],
GT [auth W],
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],
HS [auth B],
HT [auth W],
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],
IS [auth B],
IT [auth W],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
JH [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],
JS [auth B],
JT [auth W],
KA [auth 4],
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],
KS [auth B],
KT [auth W],
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],
LS [auth B],
LT [auth W],
MA [auth 6],
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],
MS [auth B],
MT [auth W],
NA [auth 7],
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],
NS [auth B],
NT [auth W],
OA [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],
OS [auth C],
OT [auth W],
PA [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],
PS [auth D],
PT [auth W],
QA [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],
QS [auth D],
QT [auth X],
RA [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],
RS [auth E],
RT [auth Y],
SA [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],
SS [auth H],
TA [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],
TS [auth M],
UA [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],
US [auth M],
VA [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],
VS [auth N],
WA [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],
WS [auth P],
XA [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],
XS [auth R],
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],
YS [auth T],
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 B],
ZS [auth U]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIX1.11.1

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.3: 2018-10-17
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2019-12-11
    Changes: Other
  • Version 1.5: 2024-05-15
    Changes: Data collection, Database references, Derived calculations, Refinement description