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- PDB-7y8a: Cryo-EM structure of cryptophyte photosystem I -

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Basic information

Entry
Database: PDB / ID: 7y8a
TitleCryo-EM structure of cryptophyte photosystem I
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • ACPI-1
  • ACPI-12
  • ACPI-13
  • ACPI-14
  • ACPI-2
  • ACPI-3
  • ACPI-4
  • ACPI-5
  • ACPI-6
  • ACPI-7
  • ACPI-8
  • ACPI-S
  • Photosystem I iron-sulfur center
  • PsaO
  • PsaR
  • Unk1
KeywordsPHOTOSYNTHESIS / Cryptophyte / Photosystem I / evolution
Function / homology
Function and homology information


thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding ...thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI ...Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Chem-8CT / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-IHT / Chem-II0 / Chem-II3 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE ...Chem-8CT / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-IHT / Chem-II0 / Chem-II3 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV
Similarity search - Component
Biological speciesChroomonas placoidea (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsZhao, L.S. / Zhang, Y.Z. / Liu, L.N. / Li, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Plant Cell / Year: 2023
Title: Structural basis and evolution of the photosystem I-light-harvesting supercomplex of cryptophyte algae.
Authors: Long-Sheng Zhao / Peng Wang / Kang Li / Quan-Bao Zhang / Fei-Yu He / Chun-Yang Li / Hai-Nan Su / Xiu-Lan Chen / Lu-Ning Liu / Yu-Zhong Zhang /
Abstract: Cryptophyte plastids originated from a red algal ancestor through secondary endosymbiosis. Cryptophyte photosystem I (PSI) associates with transmembrane alloxanthin-chlorophyll a/c proteins (ACPIs) ...Cryptophyte plastids originated from a red algal ancestor through secondary endosymbiosis. Cryptophyte photosystem I (PSI) associates with transmembrane alloxanthin-chlorophyll a/c proteins (ACPIs) as light-harvesting complexes (LHCs). Here, we report the structure of the photosynthetic PSI-ACPI supercomplex from the cryptophyte Chroomonas placoidea at 2.7-Å resolution obtained by crygenic electron microscopy. Cryptophyte PSI-ACPI represents a unique PSI-LHCI intermediate in the evolution from red algal to diatom PSI-LHCI. The PSI-ACPI supercomplex is composed of a monomeric PSI core containing 14 subunits, 12 of which originated in red algae, 1 diatom PsaR homolog, and an additional peptide. The PSI core is surrounded by 14 ACPI subunits that form 2 antenna layers: an inner layer with 11 ACPIs surrounding the PSI core and an outer layer containing 3 ACPIs. A pigment-binding subunit that is not present in any other previously characterized PSI-LHCI complexes, ACPI-S, mediates the association and energy transfer between the outer and inner ACPIs. The extensive pigment network of PSI-ACPI ensures efficient light harvesting, energy transfer, and dissipation. Overall, the PSI-LHCI structure identified in this study provides a framework for delineating the mechanisms of energy transfer in cryptophyte PSI-LHCI and for understanding the evolution of photosynthesis in the red lineage, which occurred via secondary endosymbiosis.
History
DepositionJun 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 26, 2023Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.3Jul 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: ACPI-1
2: ACPI-2
3: ACPI-3
4: ACPI-4
5: ACPI-5
6: ACPI-6
7: ACPI-7
8: ACPI-8
9: ACPI-12
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
O: PsaO
R: PsaR
X: Unk1
Z: ACPI-S
a: ACPI-13
b: ACPI-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)863,764383
Polymers584,58626
Non-polymers279,178357
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 16 types, 16 molecules 123456789CORXZab

#1: Protein ACPI-1


Mass: 23479.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#2: Protein ACPI-2


Mass: 23400.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#3: Protein ACPI-3


Mass: 24966.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#4: Protein ACPI-4


Mass: 23548.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#5: Protein ACPI-5


Mass: 24055.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#6: Protein ACPI-6


Mass: 22688.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#7: Protein ACPI-7


Mass: 24550.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#8: Protein ACPI-8


Mass: 23700.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#9: Protein ACPI-12


Mass: 23223.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#12: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8743.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI25, photosystem I
#21: Protein PsaO


Mass: 16253.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#22: Protein PsaR


Mass: 13867.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#23: Protein Unk1


Mass: 13975.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Authors do not know how the coordinates align with the sequence and the residue numbering is arbitrary.
Source: (natural) Chroomonas placoidea (eukaryote)
#24: Protein ACPI-S


Mass: 25645.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#25: Protein ACPI-13


Mass: 22270.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#26: Protein ACPI-14


Mass: 23755.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#10: Protein Photosystem I P700 chlorophyll a apoprotein A1 / / PsaA


Mass: 83493.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AIB4, photosystem I
#11: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PsaB


Mass: 82219.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI95, photosystem I

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Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFIJKLM

#13: Protein Photosystem I reaction center subunit II /


Mass: 15590.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AIA6
#14: Protein Photosystem I reaction center subunit IV /


Mass: 7352.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AIF3
#15: Protein Photosystem I reaction center subunit III / / PSI-F


Mass: 20393.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI52
#16: Protein/peptide Photosystem I reaction center subunit VIII /


Mass: 3975.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI78
#17: Protein/peptide Photosystem I reaction center subunit IX /


Mass: 4862.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI55
#18: Protein Photosystem I reaction center subunit PsaK / / Photosystem I subunit X


Mass: 8836.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI34
#19: Protein Photosystem I reaction center subunit XI / / PSI subunit V / PSI-L


Mass: 16490.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI68
#20: Protein/peptide Photosystem I reaction center subunit XII / / PSI-M


Mass: 3247.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI28

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Sugars , 2 types, 5 molecules

#36: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#39: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 11 types, 352 molecules

#27: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 222 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical
ChemComp-KC2 / Chlorophyll c2 / Chlorophyll c


Mass: 608.926 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C35H28MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical...
ChemComp-II0 / (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol / Alloxanthin


Mass: 564.840 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: C40H52O2 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical ChemComp-II3 / (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol / Monadoxanthin


Mass: 566.856 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H54O2 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical
ChemComp-IHT / (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol / Allobetaxanthin


Mass: 550.856 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H54O / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C45H86O10
#33: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#34: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78O12S
#35: Chemical...
ChemComp-8CT / (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene


Mass: 536.873 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#37: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#38: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: photosystem I of cryptophyte / Type: COMPLEX / Entity ID: #1-#26 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118810 / Symmetry type: POINT

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