6ERI image
Deposition Date 2017-10-18
Release Date 2018-04-18
Last Version Date 2024-11-13
Entry Detail
PDB ID:
6ERI
Keywords:
Title:
Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:A (auth: AA)
Chain Length:48
Number of Molecules:1
Biological Source:Spinacia oleracea
Polymer Type:polyribonucleotide
Molecule:4.5S ribosomal RNA
Chain IDs:B (auth: AB)
Chain Length:60
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2, chloroplastic
Gene (Uniprot):rpl2-A, rpl2-B
Chain IDs:C (auth: AC)
Chain Length:246
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3, chloroplastic
Gene (Uniprot):RPL3
Chain IDs:D (auth: AD)
Chain Length:221
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4, chloroplastic
Gene (Uniprot):RPL4
Chain IDs:E (auth: AE)
Chain Length:212
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5, chloroplastic
Gene (Uniprot):RPL5
Chain IDs:F (auth: AF)
Chain Length:47
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6, chloroplastic
Gene (Uniprot):RPL6
Chain IDs:G (auth: AG)
Chain Length:172
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9, chloroplastic
Gene (Uniprot):RPL9
Chain IDs:H (auth: AH)
Chain Length:46
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13, chloroplastic
Gene (Uniprot):RPL13
Chain IDs:I (auth: AJ)
Chain Length:200
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14, chloroplastic
Gene (Uniprot):rpl14
Chain IDs:J (auth: AK)
Chain Length:121
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15, chloroplastic
Gene (Uniprot):RPL15
Chain IDs:K (auth: AL)
Chain Length:184
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16, chloroplastic
Gene (Uniprot):rpl16
Chain IDs:L (auth: AM)
Chain Length:134
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17, chloroplastic
Gene (Uniprot):RPL17
Chain IDs:M (auth: AN)
Chain Length:116
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18, chloroplastic
Gene (Uniprot):RPL18
Chain IDs:N (auth: AO)
Chain Length:121
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19, chloroplastic
Gene (Uniprot):RPL19
Chain IDs:O (auth: AP)
Chain Length:118
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20, chloroplastic
Gene (Uniprot):rpl20
Chain IDs:P (auth: AQ)
Chain Length:115
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21, chloroplastic
Gene (Uniprot):RPL21
Chain IDs:Q (auth: AR)
Chain Length:165
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22, chloroplastic
Gene (Uniprot):rpl22
Chain IDs:R (auth: AS)
Chain Length:171
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23, chloroplastic
Gene (Uniprot):RPL23
Chain IDs:S (auth: AT)
Chain Length:92
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24, chloroplastic
Gene (Uniprot):RPL24
Chain IDs:T (auth: AU)
Chain Length:127
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27, chloroplastic
Gene (Uniprot):RPL27
Chain IDs:U (auth: AW)
Chain Length:49
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28, chloroplastic
Gene (Uniprot):RPL28
Chain IDs:V (auth: AX)
Chain Length:76
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29, chloroplastic
Gene (Uniprot):RPL29
Chain IDs:W (auth: AY)
Chain Length:99
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31, chloroplastic
Gene (Uniprot):RPL31
Chain IDs:X (auth: AZ)
Chain Length:191
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32, chloroplastic
Gene (Uniprot):rpl32
Chain IDs:Y (auth: Aa)
Chain Length:48
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33, chloroplastic
Gene (Uniprot):rpl33
Chain IDs:Z (auth: Ab)
Chain Length:60
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34, chloroplastic
Gene (Uniprot):RPL34
Chain IDs:AA (auth: Ac)
Chain Length:246
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35, chloroplastic
Gene (Uniprot):RPL35
Chain IDs:BA (auth: Ad)
Chain Length:221
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36, chloroplastic
Gene (Uniprot):rpl36
Chain IDs:CA (auth: Ae)
Chain Length:212
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein 6, chloroplastic
Gene (Uniprot):PSRP6
Chain IDs:DA (auth: Af)
Chain Length:47
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein 5 alpha, chloroplastic
Gene (Uniprot):PSRP5
Chain IDs:EA (auth: Aw)
Chain Length:49
Number of Molecules:1
Biological Source:Spinacia oleracea
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:FA (auth: Ax)
Chain Length:76
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome-recycling factor, chloroplastic
Gene (Uniprot):RRF
Chain IDs:GA (auth: Az)
Chain Length:191
Number of Molecules:1
Biological Source:Spinacia oleracea
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:HA (auth: BA)
Chain Length:1481
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2, chloroplastic
Gene (Uniprot):rps2
Chain IDs:IA (auth: BB)
Chain Length:215
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3, chloroplastic
Gene (Uniprot):rps3
Chain IDs:JA (auth: BC)
Chain Length:217
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4, chloroplastic
Gene (Uniprot):rps4
Chain IDs:KA (auth: BD)
Chain Length:200
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5, chloroplastic
Gene (Uniprot):rps5
Chain IDs:LA (auth: BE)
Chain Length:158
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6 alpha, chloroplastic
Gene (Uniprot):RPS6
Chain IDs:MA (auth: BF)
Chain Length:113
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7, chloroplastic
Gene (Uniprot):rps7-A, rps7-B
Chain IDs:NA (auth: BG)
Chain Length:151
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8, chloroplastic
Gene (Uniprot):rps8
Chain IDs:OA (auth: BH)
Chain Length:134
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9, chloroplastic
Gene (Uniprot):PRPS9
Chain IDs:PA (auth: BI)
Chain Length:141
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10 alpha, chloroplastic
Gene (Uniprot):RPS10
Chain IDs:QA (auth: BJ)
Chain Length:98
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11, chloroplastic
Gene (Uniprot):rps11
Chain IDs:RA (auth: BK)
Chain Length:110
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12, chloroplastic
Gene (Uniprot):rps12-A, rps12-B
Chain IDs:SA (auth: BL)
Chain Length:122
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13, chloroplastic
Gene (Uniprot):RPS13
Chain IDs:TA (auth: BM)
Chain Length:111
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14, chloroplastic
Gene (Uniprot):rps14
Chain IDs:UA (auth: BN)
Chain Length:99
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15, chloroplastic
Gene (Uniprot):rps15
Chain IDs:VA (auth: BO)
Chain Length:72
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16, chloroplastic
Gene (Uniprot):rps16
Chain IDs:WA (auth: BP)
Chain Length:81
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17, chloroplastic
Gene (Uniprot):RPS17
Chain IDs:XA (auth: BQ)
Chain Length:84
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18, chloroplastic
Gene (Uniprot):RPS18
Chain IDs:YA (auth: BR)
Chain Length:53
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19, chloroplastic
Gene (Uniprot):rps19
Chain IDs:ZA (auth: BS)
Chain Length:81
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20, chloroplastic
Gene (Uniprot):RPS20
Chain IDs:AB (auth: BT)
Chain Length:102
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21, chloroplastic
Gene (Uniprot):rps21
Chain IDs:BB (auth: BU)
Chain Length:59
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome-binding factor PSRP1, chloroplastic
Gene (Uniprot):PSRP1
Chain IDs:CB (auth: BV)
Chain Length:106
Number of Molecules:1
Biological Source:Spinacia oleracea
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S31, chloroplastic
Gene (Uniprot):RPS31
Chain IDs:DB (auth: BW)
Chain Length:37
Number of Molecules:1
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Molecule:bS1c
Chain IDs:EB (auth: BY)
Chain Length:170
Number of Molecules:1
Biological Source:Spinacia oleracea
Primary Citation
Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.
Nat Plants 4 212 217 (2018)
PMID: 29610536 DOI: 10.1038/s41477-018-0129-6

Abstact

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 chlororibosome1,2. Despite recent structural information3-6, 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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
Feedback Form
Name
Email
Institute
Feedback