6ERI

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 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


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2, chloroplastic
AC
246Spinacia oleraceaMutation(s): 0 
Gene Names: rpl2-A, rpl2-B
Find proteins for P06509 (Spinacia oleracea)
Go to UniProtKB:  P06509
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3, chloroplastic
AD
221Spinacia oleraceaMutation(s): 0 
Gene Names: RPL3
Find proteins for P82191 (Spinacia oleracea)
Go to Gene View: RPL3
Go to UniProtKB:  P82191
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4, chloroplastic
AE
212Spinacia oleraceaMutation(s): 0 
Gene Names: RPL4
Find proteins for O49937 (Spinacia oleracea)
Go to Gene View: RPL4
Go to UniProtKB:  O49937
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5, chloroplastic
AF
207Spinacia oleraceaMutation(s): 0 
Gene Names: RPL5 (PrpL5)
Find proteins for P82192 (Spinacia oleracea)
Go to Gene View: RPL5
Go to UniProtKB:  P82192
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6, chloroplastic
AG
172Spinacia oleraceaMutation(s): 0 
Gene Names: RPL6
Find proteins for P82193 (Spinacia oleracea)
Go to Gene View: RPL6
Go to UniProtKB:  P82193
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9, chloroplastic
AH
46Spinacia oleraceaMutation(s): 0 
Gene Names: RPL9
Find proteins for P82180 (Spinacia oleracea)
Go to Gene View: RPL9
Go to UniProtKB:  P82180
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13, chloroplastic
AJ
200Spinacia oleraceaMutation(s): 0 
Gene Names: RPL13
Find proteins for P12629 (Spinacia oleracea)
Go to Gene View: RPL13
Go to UniProtKB:  P12629
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14, chloroplastic
AK
121Spinacia oleraceaMutation(s): 0 
Gene Names: rpl14
Find proteins for P09596 (Spinacia oleracea)
Go to UniProtKB:  P09596
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15, chloroplastic
AL
184Spinacia oleraceaMutation(s): 0 
Gene Names: RPL15
Find proteins for P22798 (Spinacia oleracea)
Go to Gene View: RPL15
Go to UniProtKB:  P22798
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16, chloroplastic
AM
134Spinacia oleraceaMutation(s): 0 
Gene Names: rpl16
Find proteins for P17353 (Spinacia oleracea)
Go to UniProtKB:  P17353
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17, chloroplastic
AN
116Spinacia oleraceaMutation(s): 0 
Gene Names: RPL17
Find proteins for P82194 (Spinacia oleracea)
Go to Gene View: RPL17
Go to UniProtKB:  P82194
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18, chloroplastic
AO
121Spinacia oleraceaMutation(s): 0 
Gene Names: RPL18 (PRPL18)
Find proteins for P82195 (Spinacia oleracea)
Go to Gene View: RPL18
Go to UniProtKB:  P82195
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19, chloroplastic
AP
118Spinacia oleraceaMutation(s): 0 
Gene Names: RPL19 (PRPL19)
Find proteins for P82413 (Spinacia oleracea)
Go to Gene View: RPL19
Go to UniProtKB:  P82413
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20, chloroplastic
AQ
115Spinacia oleraceaMutation(s): 0 
Gene Names: rpl20
Find proteins for P28803 (Spinacia oleracea)
Go to UniProtKB:  P28803
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21, chloroplastic
AR
165Spinacia oleraceaMutation(s): 0 
Gene Names: RPL21
Find proteins for P24613 (Spinacia oleracea)
Go to Gene View: RPL21
Go to UniProtKB:  P24613
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22, chloroplastic
AS
171Spinacia oleraceaMutation(s): 0 
Gene Names: rpl22
Find proteins for P09594 (Spinacia oleracea)
Go to UniProtKB:  P09594
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23, chloroplastic
AT
92Spinacia oleraceaMutation(s): 0 
Gene Names: RPL23
Find proteins for Q9LWB5 (Spinacia oleracea)
Go to Gene View: RPL23
Go to UniProtKB:  Q9LWB5
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24, chloroplastic
AU
127Spinacia oleraceaMutation(s): 0 
Gene Names: RPL24
Find proteins for P27683 (Spinacia oleracea)
Go to Gene View: RPL24
Go to UniProtKB:  P27683
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27, chloroplastic
AW
114Spinacia oleraceaMutation(s): 0 
Gene Names: RPL27
Find proteins for P82190 (Spinacia oleracea)
Go to Gene View: RPL27
Go to UniProtKB:  P82190
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28, chloroplastic
AX
76Spinacia oleraceaMutation(s): 0 
Gene Names: RPL28
Find proteins for P82245 (Spinacia oleracea)
Go to Gene View: RPL28
Go to UniProtKB:  P82245
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29, chloroplastic
AY
99Spinacia oleraceaMutation(s): 0 
Gene Names: RPL29
Find proteins for P82248 (Spinacia oleracea)
Go to Gene View: RPL29
Go to UniProtKB:  P82248
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31, chloroplastic
AZ
66Spinacia oleraceaMutation(s): 0 
Gene Names: RPL31
Find proteins for P82249 (Spinacia oleracea)
Go to Gene View: RPL31
Go to UniProtKB:  P82249
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32, chloroplastic
Aa
48Spinacia oleraceaMutation(s): 0 
Gene Names: rpl32
Find proteins for P28804 (Spinacia oleracea)
Go to UniProtKB:  P28804
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33, chloroplastic
Ab
60Spinacia oleraceaMutation(s): 0 
Gene Names: rpl33
Find proteins for P28805 (Spinacia oleracea)
Go to UniProtKB:  P28805
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34, chloroplastic
Ac
61Spinacia oleraceaMutation(s): 0 
Gene Names: RPL34
Find proteins for P82244 (Spinacia oleracea)
Go to Gene View: RPL34
Go to UniProtKB:  P82244
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35, chloroplastic
Ad
72Spinacia oleraceaMutation(s): 0 
Gene Names: RPL35
Find proteins for P23326 (Spinacia oleracea)
Go to Gene View: RPL35
Go to UniProtKB:  P23326
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36, chloroplastic
Ae
37Spinacia oleraceaMutation(s): 0 
Gene Names: rpl36
Find proteins for P12230 (Spinacia oleracea)
Go to UniProtKB:  P12230
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein 6, chloroplastic
Af
47Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP6
Find proteins for P82411 (Spinacia oleracea)
Go to UniProtKB:  P82411
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein 5 alpha, chloroplastic
Aw
49Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP5 (RPL40)
Find proteins for P27684 (Spinacia oleracea)
Go to UniProtKB:  P27684
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Ribosome-recycling factor, chloroplastic
Az
191Spinacia oleraceaMutation(s): 0 
Gene Names: RRF (FRRHCP)
Find proteins for P82231 (Spinacia oleracea)
Go to UniProtKB:  P82231
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2, chloroplastic
BB
215Spinacia oleraceaMutation(s): 0 
Gene Names: rps2
Find proteins for P08242 (Spinacia oleracea)
Go to UniProtKB:  P08242
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3, chloroplastic
BC
217Spinacia oleraceaMutation(s): 0 
Gene Names: rps3
Find proteins for P09595 (Spinacia oleracea)
Go to UniProtKB:  P09595
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4, chloroplastic
BD
200Spinacia oleraceaMutation(s): 0 
Gene Names: rps4
Find proteins for P13788 (Spinacia oleracea)
Go to UniProtKB:  P13788
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5, chloroplastic
BE
158Spinacia oleraceaMutation(s): 0 
Gene Names: rps5
Find proteins for Q9ST69 (Spinacia oleracea)
Go to UniProtKB:  Q9ST69
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6 alpha, chloroplastic
BF
113Spinacia oleraceaMutation(s): 0 
Gene Names: RPS6
Find proteins for P82403 (Spinacia oleracea)
Go to Gene View: RPS6
Go to UniProtKB:  P82403
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7, chloroplastic
BG
151Spinacia oleraceaMutation(s): 0 
Gene Names: rps7-A, rps7-B
Find proteins for P82129 (Spinacia oleracea)
Go to UniProtKB:  P82129
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8, chloroplastic
BH
134Spinacia oleraceaMutation(s): 0 
Gene Names: rps8
Find proteins for P09597 (Spinacia oleracea)
Go to UniProtKB:  P09597
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9, chloroplastic
BI
141Spinacia oleraceaMutation(s): 0 
Gene Names: PRPS9
Find proteins for P82278 (Spinacia oleracea)
Go to UniProtKB:  P82278
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10 alpha, chloroplastic
BJ
98Spinacia oleraceaMutation(s): 0 
Gene Names: RPS10
Find proteins for P82162 (Spinacia oleracea)
Go to Gene View: RPS10
Go to UniProtKB:  P82162
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11, chloroplastic
BK
110Spinacia oleraceaMutation(s): 0 
Gene Names: rps11
Find proteins for P06506 (Spinacia oleracea)
Go to UniProtKB:  P06506
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12, chloroplastic
BL
122Spinacia oleraceaMutation(s): 0 
Gene Names: rps12-A, rps12-B
Find proteins for P62128 (Spinacia oleracea)
Go to UniProtKB:  P62128
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13, chloroplastic
BM
111Spinacia oleraceaMutation(s): 0 
Gene Names: RPS13
Find proteins for P82163 (Spinacia oleracea)
Go to Gene View: RPS13
Go to UniProtKB:  P82163
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14, chloroplastic
BN
99Spinacia oleraceaMutation(s): 0 
Gene Names: rps14
Find proteins for P06507 (Spinacia oleracea)
Go to UniProtKB:  P06507
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15, chloroplastic
BO
72Spinacia oleraceaMutation(s): 0 
Gene Names: rps15
Find proteins for Q9M3I4 (Spinacia oleracea)
Go to UniProtKB:  Q9M3I4
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16, chloroplastic
BP
81Spinacia oleraceaMutation(s): 0 
Gene Names: rps16
Find proteins for P28807 (Spinacia oleracea)
Go to UniProtKB:  P28807
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17, chloroplastic
BQ
84Spinacia oleraceaMutation(s): 0 
Gene Names: RPS17
Find proteins for P82137 (Spinacia oleracea)
Go to Gene View: RPS17
Go to UniProtKB:  P82137
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18, chloroplastic
BR
53Spinacia oleraceaMutation(s): 0 
Gene Names: RPS18
Find proteins for Q9M3K7 (Spinacia oleracea)
Go to Gene View: RPS18
Go to UniProtKB:  Q9M3K7
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19, chloroplastic
BS
81Spinacia oleraceaMutation(s): 0 
Gene Names: rps19
Find proteins for P06508 (Spinacia oleracea)
Go to UniProtKB:  P06508
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20, chloroplastic
BT
102Spinacia oleraceaMutation(s): 0 
Gene Names: RPS20
Find proteins for P82130 (Spinacia oleracea)
Go to Gene View: RPS20
Go to UniProtKB:  P82130
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21, chloroplastic
BU
59Spinacia oleraceaMutation(s): 0 
Gene Names: rps21
Find proteins for P82024 (Spinacia oleracea)
Go to UniProtKB:  P82024
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Ribosome-binding factor PSRP1, chloroplastic
BV
106Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP1 (RPS22, RPS30)
Find proteins for P19954 (Spinacia oleracea)
Go to UniProtKB:  P19954
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S31, chloroplastic
BW
37Spinacia oleraceaMutation(s): 0 
Gene Names: RPS31 (PSRP4)
Find proteins for P47910 (Spinacia oleracea)
Go to UniProtKB:  P47910
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
bS1c
BY
170N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNAAA2810Spinacia oleracea
Entity ID: 2
MoleculeChainsLengthOrganism
4.5S ribosomal RNAAB106Spinacia oleracea
Entity ID: 32
MoleculeChainsLengthOrganism
5S ribosomal RNAAx118Spinacia oleracea
Entity ID: 34
MoleculeChainsLengthOrganism
16S ribosomal RNABA1481Spinacia oleracea
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
Ab, Ae
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
AA, AB, Af, Aw, Ax, BA, BN
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
BY
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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