4V61

Homology model for the Spinach chloroplast 30S subunit fitted to 9.4A cryo-EM map of the 70S chlororibosome.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins

Sharma, M.R.Wilson, D.N.Datta, P.P.Barat, C.Schluenzen, F.Fucini, P.Agrawal, R.K.

(2007) Proc.Natl.Acad.Sci.Usa 104: 19315-19320

  • DOI: 10.1073/pnas.0709856104
  • Primary Citation of Related Structures:  3BBN, 3BBO

  • PubMed Abstract: 
  • Protein synthesis in the chloroplast is carried out by chloroplast ribosomes (chloro-ribosome) and regulated in a light-dependent manner. Chloroplast or plastid ribosomal proteins (PRPs) generally are larger than their bacterial counterparts, and chl ...

    Protein synthesis in the chloroplast is carried out by chloroplast ribosomes (chloro-ribosome) and regulated in a light-dependent manner. Chloroplast or plastid ribosomal proteins (PRPs) generally are larger than their bacterial counterparts, and chloro-ribosomes contain additional plastid-specific ribosomal proteins (PSRPs); however, it is unclear to what extent these proteins play structural or regulatory roles during translation. We have obtained a three-dimensional cryo-EM map of the spinach 70S chloro-ribosome, revealing the overall structural organization to be similar to bacterial ribosomes. Fitting of the conserved portions of the x-ray crystallographic structure of the bacterial 70S ribosome into our cryo-EM map of the chloro-ribosome reveals the positions of PRP extensions and the locations of the PSRPs. Surprisingly, PSRP1 binds in the decoding region of the small (30S) ribosomal subunit, in a manner that would preclude the binding of messenger and transfer RNAs to the ribosome, suggesting that PSRP1 is a translation factor rather than a ribosomal protein. PSRP2 and PSRP3 appear to structurally compensate for missing segments of the 16S rRNA within the 30S subunit, whereas PSRP4 occupies a position buried within the head of the 30S subunit. One of the two PSRPs in the large (50S) ribosomal subunit lies near the tRNA exit site. Furthermore, we find a mass of density corresponding to chloro-ribosome recycling factor; domain II of this factor appears to interact with the flexible C-terminal domain of PSRP1. Our study provides evolutionary insights into the structural and functional roles that the PSRPs play during protein synthesis in chloroplasts.


    Organizational Affiliation

    Laboratory of Structural Pathology, Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S2
AB
231Spinacia oleraceaGene Names: rps2
Find proteins for P08242 (Spinacia oleracea)
Go to UniProtKB:  P08242
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S3
AC
218Spinacia oleraceaGene Names: rps3
Find proteins for P09595 (Spinacia oleracea)
Go to UniProtKB:  P09595
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S4
AD
201Spinacia oleraceaGene Names: rps4
Find proteins for P13788 (Spinacia oleracea)
Go to UniProtKB:  P13788
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S5
AE
308Spinacia oleraceaGene Names: rps5
Find proteins for Q9ST69 (Spinacia oleracea)
Go to UniProtKB:  Q9ST69
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S6
AF
168Spinacia oleraceaGene Names: RPS6
Find proteins for P82403 (Spinacia oleracea)
Go to Gene View: RPS6
Go to UniProtKB:  P82403
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S7
AG
155Spinacia oleraceaGene Names: rps7-A, rps7-B
Find proteins for P82129 (Spinacia oleracea)
Go to UniProtKB:  P82129
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S8
AH
134Spinacia oleraceaGene Names: rps8
Find proteins for P09597 (Spinacia oleracea)
Go to UniProtKB:  P09597
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S9
AI
197Spinacia oleraceaGene Names: PRPS9
Find proteins for P82278 (Spinacia oleracea)
Go to UniProtKB:  P82278
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S10
AJ
197N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S11
AK
140Spinacia oleraceaGene Names: rps11
Find proteins for P06506 (Spinacia oleracea)
Go to UniProtKB:  P06506
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S12
AL
123Spinacia oleraceaGene Names: rps12-A, rps12-B
Find proteins for P62128 (Spinacia oleracea)
Go to UniProtKB:  P62128
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S13
AM
145Spinacia oleraceaGene Names: RPS13
Find proteins for P82163 (Spinacia oleracea)
Go to Gene View: RPS13
Go to UniProtKB:  P82163
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S14
AN
100Spinacia oleraceaGene Names: rps14
Find proteins for P06507 (Spinacia oleracea)
Go to UniProtKB:  P06507
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S15
AO
90Spinacia oleraceaGene Names: rps15
Find proteins for Q9M3I4 (Spinacia oleracea)
Go to UniProtKB:  Q9M3I4
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S16
AP
88Spinacia oleraceaGene Names: rps16
Find proteins for P28807 (Spinacia oleracea)
Go to UniProtKB:  P28807
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S17
AQ
142N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S18
AR
103Spinacia oleraceaGene Names: RPS18
Find proteins for Q9M3K7 (Spinacia oleracea)
Go to Gene View: RPS18
Go to UniProtKB:  Q9M3K7
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S19
AS
92Spinacia oleraceaGene Names: rps19
Find proteins for P06508 (Spinacia oleracea)
Go to UniProtKB:  P06508
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S20
AT
202N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein S21
AU
190N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L1
BD
352Spinacia oleraceaGene Names: RPL1
Find proteins for Q9LE95 (Spinacia oleracea)
Go to UniProtKB:  Q9LE95
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L2
BE
269Spinacia oleraceaGene Names: rpl2-A, rpl2-B
Find proteins for P06509 (Spinacia oleracea)
Go to UniProtKB:  P06509
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L3
BF
259N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L4
BG
293Spinacia oleraceaGene Names: RPL4
Find proteins for O49937 (Spinacia oleracea)
Go to Gene View: RPL4
Go to UniProtKB:  O49937
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L5
BH
220Spinacia oleraceaGene Names: RPL5 (PrpL5)
Find proteins for P82192 (Spinacia oleracea)
Go to Gene View: RPL5
Go to UniProtKB:  P82192
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L6
BI
223N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L9
BJ
197N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L11
BK
224Spinacia oleraceaGene Names: rpl11
Find proteins for P31164 (Spinacia oleracea)
Go to UniProtKB:  P31164
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L13
BL
250Spinacia oleraceaGene Names: RPL13
Find proteins for P12629 (Spinacia oleracea)
Go to Gene View: RPL13
Go to UniProtKB:  P12629
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L14
BM
121Spinacia oleraceaGene Names: rpl14
Find proteins for P09596 (Spinacia oleracea)
Go to UniProtKB:  P09596
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L15
BN
257N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L16
BO
135Spinacia oleraceaGene Names: rpl16
Find proteins for P17353 (Spinacia oleracea)
Go to UniProtKB:  P17353
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L17
BP
205N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L18
BQ
161N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L19
BR
233Spinacia oleraceaGene Names: RPL19 (PRPL19)
Find proteins for P82413 (Spinacia oleracea)
Go to Gene View: RPL19
Go to UniProtKB:  P82413
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L20
BS
119Spinacia oleraceaGene Names: rpl20
Find proteins for P28803 (Spinacia oleracea)
Go to UniProtKB:  P28803
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L21
BT
257Spinacia oleraceaGene Names: RPL21
Find proteins for P24613 (Spinacia oleracea)
Go to Gene View: RPL21
Go to UniProtKB:  P24613
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L22
BU
199Spinacia oleraceaGene Names: rpl22
Find proteins for P09594 (Spinacia oleracea)
Go to UniProtKB:  P09594
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L23
BV
198Spinacia oleraceaGene Names: RPL23
Find proteins for Q9LWB5 (Spinacia oleracea)
Go to Gene View: RPL23
Go to UniProtKB:  Q9LWB5
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L24
BW
191Spinacia oleraceaGene Names: RPL24
Find proteins for P27683 (Spinacia oleracea)
Go to Gene View: RPL24
Go to UniProtKB:  P27683
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L27
BX
198N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L28
BY
151N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L29
BZ
173N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L31
B1
144N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L32
B2
57Spinacia oleraceaGene Names: rpl32
Find proteins for P28804 (Spinacia oleracea)
Go to UniProtKB:  P28804
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L33
B3
66Spinacia oleraceaGene Names: rpl33
Find proteins for P28805 (Spinacia oleracea)
Go to UniProtKB:  P28805
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L34
B4
152Spinacia oleraceaGene Names: RPL34
Find proteins for P82244 (Spinacia oleracea)
Go to Gene View: RPL34
Go to UniProtKB:  P82244
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L35
B5
159Spinacia oleraceaGene Names: RPL35
Find proteins for P23326 (Spinacia oleracea)
Go to Gene View: RPL35
Go to UniProtKB:  P23326
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Protein L36
B6
104N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAAA1491Spinacia oleracea
Entity ID: 22
MoleculeChainsLengthOrganism
23S rRNABA2810Spinacia oleracea
Entity ID: 23
MoleculeChainsLengthOrganism
5S rRNABB117Spinacia oleracea
Entity ID: 24
MoleculeChainsLengthOrganism
4.8S rRNABC103Spinacia oleracea
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2015-03-25
    Type: Other