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- EMDB-6710: Structure of the 30S small subunit of chloroplast ribosome from s... -

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Entry
Database: EMDB / ID: 6710
TitleStructure of the 30S small subunit of chloroplast ribosome from spinach
Map data
Sample30S small subunit of chloroplast ribosome from spinach:
(30S ribosomal protein ...) x 17 / protein S10 / protein S17 / protein S20 / protein S21 / protein plastid pY / nucleic-acidNucleic acid / protein cS23 / protein cS22 / protein bTHXc
Function / homologyRibosome hibernation promotion factor-like / Ribosomal protein S12/S23 / RNA-binding S4 domain superfamily / Ribosomal protein S21 superfamily / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / PSRP-3/Ycf65 superfamily / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S18 superfamily ...Ribosome hibernation promotion factor-like / Ribosomal protein S12/S23 / RNA-binding S4 domain superfamily / Ribosomal protein S21 superfamily / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / PSRP-3/Ycf65 superfamily / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S18 superfamily / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S2 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S10p/S20e / Ribosomal protein S11 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S9/S16 / Ribosomal protein S10 domain / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / 30s ribosomal protein S13, C-terminal / 30S ribosomal protein / Ribosomal protein S7 domain superfamily / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Ribosome hibernation promoting factor, long/plastid / RNA-binding domain superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S17 / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal protein S4 signature. / Ribosomal protein S9 signature. / Ribosomal protein S10 signature. / Ribosomal protein S15 signature. / Ribosomal protein S14 signature. / Ribosomal protein S3 signature. / Ribosomal protein S5 signature. / Ribosomal protein S13 signature. / Ribosomal protein S18 signature. / Ribosomal protein S16 signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S2 signature 2. / Eukaryotic RNA Recognition Motif (RRM) profile. / S1 domain profile. / Ribosomal protein S13 family profile. / Type-2 KH domain profile. / Ribosomal protein S19 signature. / Ribosomal protein S17 signature. / Ribosomal protein S11 / S4 domain / Ribosomal protein S13/S18 / S1 RNA binding domain / Ribosomal protein S16 / Ribosomal protein S18 / Ribosomal protein S21 / Ribosomal protein S6 / Ribosomal protein S20 / Ribosomal protein S12 signature. / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein S5, C-terminal domain / Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S9, bacterial/plastid / RNA-binding domain, S1 / Ribosomal protein S4/S9 / Ribosomal protein S21 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S3, bacterial / Ribosomal protein S19 conserved site / Ribosomal protein S5, C-terminal / Ribosomal protein S15, bacterial-type / K Homology domain, type 2 / Ribosome hibernation promoting factor/RaiA / S1 domain / RNA-binding S4 domain / Ribosomal protein S20 / Ribosomal protein S19/S15 / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S5, bacterial-type / Ribosomal protein S2 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S3, C-terminal / Ribosomal protein S14 / Ribosomal protein S5 / Ribosomal protein S9
Function and homology information
SourceSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsAhmed T / Shi J
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation.
Authors: Tofayel Ahmed / Jian Shi / Shashi Bhushan
Abstract: Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, ...Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, cS23, bTHXc, cL37 and cL38) which have been suggested to play important regulatory roles in translation. However, their exact locations on the chloroplast ribosome remain elusive due to lack of a high-resolution structure, hindering our progress to understand their possible roles. Here we present a cryo-EM structure of the 70S chloroplast ribosome from spinach resolved to 3.4 Å and focus our discussion mainly on the architecture of the 30S small subunit (SSU) which is resolved to 3.7 Å. cS22 localizes at the SSU foot where it seems to compensate for the deletions in 16S rRNA. The mRNA exit site is highly remodeled due to the presence of cS23 suggesting an alternative mode of translation initiation. bTHXc is positioned at the SSU head and appears to stabilize the intersubunit bridge B1b during thermal fluctuations. The translation factor plastid pY binds to the SSU on the intersubunit side and interacts with the conserved nucleotide bases involved in decoding. Most of the intersubunit bridges are conserved compared to the bacteria, except for a new bridge involving uL2c and bS6c.
Validation ReportPDB-ID: 5x8r

SummaryFull reportAbout validation report
DateDeposition: Mar 3, 2017 / Header (metadata) release: Jun 7, 2017 / Map release: Jun 7, 2017 / Last update: Jun 6, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
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  • Surface view colored by height
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: : PDB-5x8r
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6710.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.05 Å/pix.
= 403.2 Å
384 pix
1.05 Å/pix.
= 403.2 Å
384 pix
1.05 Å/pix.
= 403.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.17213282 - 0.3157689
Average (Standard dev.)0.0006205938 (0.008562695)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z403.200403.200403.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1720.3160.001

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Supplemental data

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Sample components

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Entire 30S small subunit of chloroplast ribosome from spinach

EntireName: 30S small subunit of chloroplast ribosome from spinach
Number of components: 27
MassTheoretical: 1.7 MDa

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Component #1: protein, 30S small subunit of chloroplast ribosome from spinach

ProteinName: 30S small subunit of chloroplast ribosome from spinach
Recombinant expression: No
MassTheoretical: 1.7 MDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #2: protein, 30S ribosomal protein S2, chloroplastic

ProteinName: 30S ribosomal protein S2, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 26.736141 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #3: protein, 30S ribosomal protein S3, chloroplastic

ProteinName: 30S ribosomal protein S3, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 24.965156 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #4: protein, 30S ribosomal protein S5, chloroplastic

ProteinName: 30S ribosomal protein S5, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 27.69658 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #5: protein, 30S ribosomal protein S6 alpha, chloroplastic

ProteinName: 30S ribosomal protein S6 alpha, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 16.341423 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #6: protein, 30S ribosomal protein S7, chloroplastic

ProteinName: 30S ribosomal protein S7, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 17.378309 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #7: protein, 30S ribosomal protein S8, chloroplastic

ProteinName: 30S ribosomal protein S8, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 15.527256 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #8: protein, 30S ribosomal protein S9, chloroplastic

ProteinName: 30S ribosomal protein S9, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 17.092791 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #9: protein, protein S10

ProteinName: protein S10 / Recombinant expression: No
MassTheoretical: 13.882167 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #10: protein, 30S ribosomal protein S11, chloroplastic

ProteinName: 30S ribosomal protein S11, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 14.927551 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #11: protein, 30S ribosomal protein S12, chloroplastic

ProteinName: 30S ribosomal protein S12, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 13.794261 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #12: protein, 30S ribosomal protein S13, chloroplastic

ProteinName: 30S ribosomal protein S13, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 14.418822 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #13: protein, 30S ribosomal protein S15, chloroplastic

ProteinName: 30S ribosomal protein S15, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 10.778763 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #14: protein, 30S ribosomal protein S16, chloroplastic

ProteinName: 30S ribosomal protein S16, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 10.454237 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #15: protein, protein S17

ProteinName: protein S17 / Recombinant expression: No
MassTheoretical: 12.195099 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #16: protein, 30S ribosomal protein S18, chloroplastic

ProteinName: 30S ribosomal protein S18, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 12.079137 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #17: protein, 30S ribosomal protein S19 alpha, chloroplastic

ProteinName: 30S ribosomal protein S19 alpha, chloroplasticRibosome
Recombinant expression: No
MassTheoretical: 10.6325 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #18: protein, protein S20

ProteinName: protein S20 / Recombinant expression: No
MassTheoretical: 12.17809 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #19: protein, protein S21

ProteinName: protein S21 / Recombinant expression: No
MassTheoretical: 16.096171 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #20: protein, protein plastid pY

ProteinName: protein plastid pY / Recombinant expression: No
MassTheoretical: 26.85133 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #21: nucleic-acid, 16S rRNA

Nucleic-acidName: 16S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UCUCAUGGAG AGUUCGAUCC UGGCUCAGGA UGAACGCUGG CGGCAUGCUU AACACAUGCA AGUCGGACGG GAAGUGGUGU UUCCAGUGGC GGACGGGUGA GUAACGCGUA AGAACCUGCC CUUGGGAGGG GAACAACAGC UGGAAACGGC UGCUAAUACC CCGUAGGCUG AGAAGCAAAA GGAGGAAUCC GCCCGAGGAG GGGCUCGCGU CUGAUUAGCU AGUUGGUGAG GUAAUAGCUU ACCAAGGCGA UGAUCAGUAG CUGGUCCGAG AGGAUGAUCA GCCACACUGG GACUGAGACA CGGCCCAGAC UCCUACGGGA GGCAGCAGUG GGGAAUUUUC CGCAAUGGGC GAAAGCCUGA CGGAGCAAUG CCGCGUGGAG GCAGAAGGCC CACGGGUCGU GAACUUCUUU UCCCGGAGAA GAAGCAAUGA CGGUAUCCGG GGAAUAAGCA UCGGCUAACU CUGUGCCAGC AGCCGCGGUA AGACAGAGGA UGCAAGCGUU AUCCGGAAUG AUUGGGCGUA AAGCGUCUGU AGGUGGCUUU UUAAGUCCGC CGUCAAAUCC CAGGGCUCAA CCCUGGACAG GCGGUGGAAA CUACCAAGCU GGAGUACGGU AGGGGCAGAG GGAAUUUCCG GUGGAGCGGU GAAAUGCGUA GAGAUCGGAA AGAACACCAA CGGCGAAAGC ACUCUGCUGG GCCGACACUG ACACUGAGAG ACGAAAGCUA GGGGAGCGAA UGGGAUUAGA UACCCCAGUA GUCCUAGCCG UAAACGAUGG AUACUAGGCG CUGUGCGUAU CGACCCGUGC AGUGUUGUAG CUAACGCGUU AAGUAUCCCG CCUGGGGAGU ACGUUCGCAA GAAUGAAACU CAAAGGAAUU GACGGGGGCC CGCACAAGCG GUGGAGCAUG UGGUUUAAUU CGAUGCAAAG CGAAGAACCU UACCAGGGCU UGACAUGCCG CGAAUCCUCU UGAAAGAGAG GGGUGCCUUC GGGAACGCGG ACACAGGUGG UGCAUGGCUG UCGUCAGCUC GUGCCGUAAG GUGUUGGGUU AAGUCCCGCA ACGAGCGCAA CCCUCGUGUU UAGUUGCCAA CGUUGAGUUU GGAACCCUGA ACAGACUGCC GGUGAUAAGC CGGAGGAAGG UGAGGAUGAC GUCAAGUCAU CAUGCCCCUU AUGCCCUGGG CGACACACGU GCUACAAUGG CCGGGACAAA GGGUCGCGAU CCCGCGAGGG UGAGCUAACC CCAAAAACCC GUCCUCAGUU CGGAUUGCAG GCUGCAACUC GCCUGCAUGA AGCCGGAAUC GCUAGUAAUC GCCGGUCAGC CAUACGGCGG UGAAUUCGUU CCCGGGCCUU GUACACACCG CCCGUCACAC UAUGGGAGCU GGCCAUGCCC GAAGUCGUUA CCUUAACCGC AAGGAGGGGG AUGCCGAAGG CAGGGCUAGU GACUGGAGUG AAGUCGUAAC AAGGUAGCCG UACUGGAAGG UGCGGCUGGA UCACCUCCUU U
MassTheoretical: 483.4665 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #22: protein, protein cS23

ProteinName: protein cS23 / Recombinant expression: No
MassTheoretical: 13.808066 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #23: protein, 30S ribosomal protein S4, chloroplastic

ProteinName: 30S ribosomal protein S4, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 23.454531 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #24: protein, protein cS22

ProteinName: protein cS22 / Recombinant expression: No
MassTheoretical: 21.691145 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #25: protein, 30S ribosomal protein S14, chloroplastic

ProteinName: 30S ribosomal protein S14, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 11.809832 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #26: protein, protein bTHXc

ProteinName: protein bTHXc / Recombinant expression: No
MassTheoretical: 5.188887 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Component #27: protein, 30S ribosomal protein S1, chloroplastic

ProteinName: 30S ribosomal protein S1, chloroplasticRibosome / Recombinant expression: No
MassTheoretical: 40.472961 kDa
SourceSpecies: Spinacia oleracea (spinach)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 20 mM Tris HCl, pH 7.6, 100 mM KCl, 10 mM MgOAc, 100 mM sucrose, 7 mM 2-mercaptoethanol, 1 unit/ml RNase inhibitor, 0.1% protease inhibitor
pH: 7.6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 1 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 75000 X (nominal), 133333 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 400.0 - 3700.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3161 / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 81305
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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