[English] 日本語
Yorodumi
- PDB-4v61: Homology model for the Spinach chloroplast 30S subunit fitted to ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v61
TitleHomology model for the Spinach chloroplast 30S subunit fitted to 9.4A cryo-EM map of the 70S chlororibosome.
Components
  • (Ribosomal Protein ...) x 49
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 4.8S rRNA
  • 5S rRNA5S ribosomal RNA
KeywordsRIBOSOME / SMALL RIBOSOMAL SUBUNIT / SPINACH CHLOROPLAST RIBOSOME / RIBONUCLEOPROTEIN PARTICLE / MACROMOLECULAR COMPLEX
Function / homology
Function and homology information


plastid small ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / mitochondrial large ribosomal subunit / maturation of LSU-rRNA / ribosome assembly / DNA-templated transcription, termination / chloroplast / positive regulation of translational fidelity / ribosomal small subunit assembly ...plastid small ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / mitochondrial large ribosomal subunit / maturation of LSU-rRNA / ribosome assembly / DNA-templated transcription, termination / chloroplast / positive regulation of translational fidelity / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / cytosolic small ribosomal subunit / small ribosomal subunit / transferase activity / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / mitochondrion / RNA binding
KOW motif / Ribosomal protein L2, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L5, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein S19 conserved site / Ribosomal protein L35 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal ...KOW motif / Ribosomal protein L2, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L5, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein S19 conserved site / Ribosomal protein L35 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein S4/S9 / Ribosomal protein L11, N-terminal / Ribosomal protein L5 domain superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein L1, conserved site / Ribosomal protein L1-like / Ribosomal protein L11, conserved site / Ribosomal protein L11, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein L33, conserved site / K homology domain-like, alpha/beta / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L10e/L16 / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein S11, bacterial-type / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S7 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein L2, domain 2 / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / S4 domain / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S6 / Ribosomal protein S8 / Ribosomal protein S9/S16 / Ribosomal protein S11 / Ribosomal protein S13/S18 / Ribosomal protein S14/S29 / Ribosomal protein S15 / Ribosomal protein S16 / Ribosomal protein L33 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L4/L1 family / Ribosomal protein L5 / ribosomal L5P family C-terminus / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein S3, C-terminal domain / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L21-like / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L20, C-terminal / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / L21-like superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L19 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L2, domain 3 / Ribosomal protein S13, bacterial-type / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S18 / RNA-binding S4 domain / Ribosomal protein S19/S15 / Ribosomal protein L2 / Ribosomal protein L4/L1e
30S ribosomal protein S5, chloroplastic / gb:7636084: / embl:sol400848: / 30S ribosomal protein S11, chloroplastic / 30S ribosomal protein S14, chloroplastic / 30S ribosomal protein S15, chloroplastic / 50S ribosomal protein L4, chloroplastic / 30S ribosomal protein S18, chloroplastic / 30S ribosomal protein S19, chloroplastic / 50S ribosomal protein L2, chloroplastic ...30S ribosomal protein S5, chloroplastic / gb:7636084: / embl:sol400848: / 30S ribosomal protein S11, chloroplastic / 30S ribosomal protein S14, chloroplastic / 30S ribosomal protein S15, chloroplastic / 50S ribosomal protein L4, chloroplastic / 30S ribosomal protein S18, chloroplastic / 30S ribosomal protein S19, chloroplastic / 50S ribosomal protein L2, chloroplastic / 50S ribosomal protein L20, chloroplastic / 30S ribosomal protein S2, chloroplastic / 50S ribosomal protein L22, chloroplastic / 30S ribosomal protein S3, chloroplastic / 50S ribosomal protein L14, chloroplastic / 30S ribosomal protein S8, chloroplastic / 50S ribosomal protein L13, chloroplastic / 30S ribosomal protein S4, chloroplastic / 50S ribosomal protein L16, chloroplastic / 50S ribosomal protein L35, chloroplastic / 50S ribosomal protein L21, chloroplastic / 50S ribosomal protein L24, chloroplastic / 50S ribosomal protein L32, chloroplastic / 50S ribosomal protein L1, chloroplastic / 50S ribosomal protein L33, chloroplastic / 30S ribosomal protein S16, chloroplastic / 50S ribosomal protein L11, chloroplastic / 30S ribosomal protein S12, chloroplastic / 30S ribosomal protein S7, chloroplastic / 30S ribosomal protein S13, chloroplastic / 50S ribosomal protein L5, chloroplastic / 50S ribosomal protein L34, chloroplastic / 30S ribosomal protein S9, chloroplastic / 30S ribosomal protein S6 alpha, chloroplastic / 50S ribosomal protein L19, chloroplastic / 50S ribosomal protein L23, chloroplastic
Biological speciesSpinacea oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.4 Å
AuthorsSharma, M.R. / Wilson, D.N. / Datta, P.P. / Barat, C. / Schluenzen, F. / Fucini, P. / Agrawal, R.K.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2007
Title: Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins.
Authors: Manjuli R Sharma / Daniel N Wilson / Partha P Datta / Chandana Barat / Frank Schluenzen / Paola Fucini / Rajendra K Agrawal /
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 ...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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3BBO, 3BBN
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 25, 2015Group: Other
Revision 1.3Dec 18, 2019Group: Data collection / Database references / Other
Category: atom_sites / em_image_scans ...atom_sites / em_image_scans / struct_ref_seq / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1417
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: 16S rRNA
AB: Ribosomal Protein S2
AC: Ribosomal Protein S3
AD: Ribosomal Protein S4
AE: Ribosomal Protein S5
AF: Ribosomal Protein S6
AG: Ribosomal Protein S7
AH: Ribosomal Protein S8
AI: Ribosomal Protein S9
AJ: Ribosomal Protein S10
AK: Ribosomal Protein S11
AL: Ribosomal Protein S12
AM: Ribosomal Protein S13
AN: Ribosomal Protein S14
AO: Ribosomal Protein S15
AP: Ribosomal Protein S16
AQ: Ribosomal Protein S17
AR: Ribosomal Protein S18
AS: Ribosomal Protein S19
AT: Ribosomal Protein S20
AU: Ribosomal Protein S21
BA: 23S rRNA
BB: 5S rRNA
BC: 4.8S rRNA
BD: Ribosomal Protein L1
BE: Ribosomal Protein L2
BF: Ribosomal Protein L3
BG: Ribosomal Protein L4
BH: Ribosomal Protein L5
BI: Ribosomal Protein L6
BJ: Ribosomal Protein L9
BK: Ribosomal Protein L11
BL: Ribosomal Protein L13
BM: Ribosomal Protein L14
BN: Ribosomal Protein L15
BO: Ribosomal Protein L16
BP: Ribosomal Protein L17
BQ: Ribosomal Protein L18
BR: Ribosomal Protein L19
BS: Ribosomal Protein L20
BT: Ribosomal Protein L21
BU: Ribosomal Protein L22
BV: Ribosomal Protein L23
BW: Ribosomal Protein L24
BX: Ribosomal Protein L27
BY: Ribosomal Protein L28
BZ: Ribosomal Protein L29
B1: Ribosomal Protein L31
B2: Ribosomal Protein L32
B3: Ribosomal Protein L33
B4: Ribosomal Protein L34
B5: Ribosomal Protein L35
B6: Ribosomal Protein L36


Theoretical massNumber of molelcules
Total (without water)2,447,89153
Polymers2,447,89153
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

-
Components

-
RNA chain , 4 types, 4 molecules AABABBBC

#1: RNA chain 16S rRNA


Mass: 483490.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: GenBank: 7636084
#22: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 911368.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: EMBL: SOL400848
#23: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 37743.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: EMBL: SOL400848
#24: RNA chain 4.8S rRNA


Mass: 33330.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: EMBL: SOL400848

+
Ribosomal Protein ... , 49 types, 49 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUBDBEBFBGBHBIBJBKBLBM...

#2: Protein Ribosomal Protein S2 /


Mass: 26092.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P08242
#3: Protein Ribosomal Protein S3 /


Mass: 24965.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P09595
#4: Protein Ribosomal Protein S4 /


Mass: 23454.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P13788
#5: Protein Ribosomal Protein S5 /


Mass: 33626.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: Q9ST69
#6: Protein Ribosomal Protein S6 /


Mass: 18870.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P82403
#7: Protein Ribosomal Protein S7 /


Mass: 17378.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P82129
#8: Protein Ribosomal Protein S8 /


Mass: 15527.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P09597
#9: Protein Ribosomal Protein S9 /


Mass: 21350.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P82278
#10: Protein Ribosomal Protein S10 /


Mass: 21632.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast
#11: Protein Ribosomal Protein S11 /


Mass: 15085.706 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P06506
#12: Protein Ribosomal Protein S12 /


Mass: 13794.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P62128
#13: Protein Ribosomal Protein S13 /


Mass: 16306.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P82163
#14: Protein Ribosomal Protein S14 /


Mass: 11809.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P06507
#15: Protein Ribosomal Protein S15 /


Mass: 10778.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: Q9M3I4
#16: Protein Ribosomal Protein S16 /


Mass: 10454.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P28807
#17: Protein Ribosomal Protein S17 /


Mass: 15828.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast
#18: Protein Ribosomal Protein S18 /


Mass: 12337.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: Q9M3K7
#19: Protein Ribosomal Protein S19 / 40S ribosomal protein S19


Mass: 10632.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast / References: UniProt: P06508
#20: Protein Ribosomal Protein S20 /


Mass: 21866.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast
#21: Protein Ribosomal Protein S21 /


Mass: 21701.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AVY as template / Source: (natural) Spinacea oleracea (spinach) / Cellular location: chloroplast
#25: Protein Ribosomal Protein L1 /


Mass: 38681.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: Q9LE95
#26: Protein Ribosomal Protein L2 /


Mass: 29480.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P06509
#27: Protein Ribosomal Protein L3 /


Mass: 28423.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#28: Protein Ribosomal Protein L4 / 60S ribosomal protein L4


Mass: 32479.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: O49937
#29: Protein Ribosomal Protein L5 / 60S ribosomal protein L5


Mass: 24248.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P82192
#30: Protein Ribosomal Protein L6 /


Mass: 24747.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#31: Protein Ribosomal Protein L9 /


Mass: 22169.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#32: Protein Ribosomal Protein L11 /


Mass: 23689.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P31164
#33: Protein Ribosomal Protein L13 / 60S ribosomal protein L13


Mass: 28211.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P12629
#34: Protein Ribosomal Protein L14 /


Mass: 13484.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P09596
#35: Protein Ribosomal Protein L15 /


Mass: 27491.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#36: Protein Ribosomal Protein L16 /


Mass: 15328.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P17353
#37: Protein Ribosomal Protein L17 /


Mass: 22983.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#38: Protein Ribosomal Protein L18 /


Mass: 17850.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#39: Protein Ribosomal Protein L19 /


Mass: 26121.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P82413
#40: Protein Ribosomal Protein L20 /


Mass: 14617.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P28803
#41: Protein Ribosomal Protein L21 /


Mass: 28554.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P24613
#42: Protein Ribosomal Protein L22 / 60S ribosomal protein L22


Mass: 23276.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P09594
#43: Protein Ribosomal Protein L23 /


Mass: 21832.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: Q9LWB5
#44: Protein Ribosomal Protein L24 /


Mass: 21481.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P27683
#45: Protein Ribosomal Protein L27 /


Mass: 21771.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#46: Protein Ribosomal Protein L28 /


Mass: 16730.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: modeled using Thermus thermophilus 2J01 as template
Source: (natural) Spinacea oleracea (spinach)
#47: Protein Ribosomal Protein L29 /


Mass: 19415.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)
#48: Protein Ribosomal Protein L31 /


Mass: 16060.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: modeled using Thermus thermophilus 2J01 as template
Source: (natural) Spinacea oleracea (spinach)
#49: Protein Ribosomal Protein L32 /


Mass: 6650.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P28804
#50: Protein Ribosomal Protein L33 /


Mass: 7668.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P28805
#51: Protein Ribosomal Protein L34 /


Mass: 16126.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P82244
#52: Protein Ribosomal Protein L35 /


Mass: 17376.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach) / References: UniProt: P23326
#53: Protein Ribosomal Protein L36 /


Mass: 11509.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modeled using Escherichia coli 2AWB as template / Source: (natural) Spinacea oleracea (spinach)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: spinach 70S chloro-ribosome / Type: RIBOSOME / Details: tight couple chloroplast 70S ribosomes
Buffer solutionName: 10mM Tris-HCL pH 7.6, 50mM KCL, 10mM MgOAc, 7mM 2-ME / pH: 7.6
Details: 10mM Tris-HCL pH 7.6, 50mM KCL, 10mM MgOAc, 7mM 2-ME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: 5 microliters applied to the grid then blotted for 3 seconds with Whatman number 1 filter paper before plunging in liquid ethane.

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 50760 X / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

-
Processing

CTF correctionDetails: CTF correction for each Micrograph
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: The projection matching procedure within the SPIDER software was used to get 3D map
Resolution: 9.4 Å / Num. of particles: 86370 / Actual pixel size: 2.76 Å / Magnification calibration: 50,760
Details: An 11.5 A E.coli 70S ribosome map was used as initial reference and then resulting 18 A map from reconstruction of 70S chloro-ribosome was used as a reference for iterative refinement
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Best visual fit using the program O
Details: METHOD--Cross-Correlation based manual fitting in O REFINEMENT PROTOCOL--Rigid Body
Atomic model building
IDPDB-ID3D fitting-IDDetails
12XYZ12XYZ AND 2ZXY FOR SMALL AND LARGE SUBUNIT RESPECTIVELY
22ZXY12XYZ AND 2ZXY FOR SMALL AND LARGE SUBUNIT RESPECTIVELY
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms19373 31745 0 0 51118

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more