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- PDB-7ksq: The Structure of the moss PSI-LHCI reveals the evolution of the L... -

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Basic information

Entry
Database: PDB / ID: 7ksq
TitleThe Structure of the moss PSI-LHCI reveals the evolution of the LHCI antenna
Components
  • (Chlorophyll a-b binding protein, ...Light-harvesting complexes of green plants) x 4
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 3
  • PSI subunit V
  • PSI-F
  • PSI-G
  • Photosystem I iron-sulfur center
  • PsaD
  • PsaE
  • PsaH
  • PsaK
  • PsaO
KeywordsPHOTOSYNTHESIS / PSI / electron transport / chlorophyll / Antenna / light harvesting / membrane protein
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane ...photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaO / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) ...Photosystem I PsaO / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit III / Chlorophyll a-b binding protein, chloroplastic / Photosystem I subunit O / Photosystem I subunit X / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSI subunit V / Photosystem I reaction center subunit V, chloroplastic / Predicted protein / Chlorophyll a-b binding protein, chloroplastic / Predicted protein / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1
Similarity search - Component
Biological speciesPhyscomitrium patens (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRiddle, R. / Gorski, C. / Toporik, H. / Dobson, Z. / Da, Z. / Williams, D. / Mazor, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Plants / Year: 2022
Title: The structure of the Physcomitrium patens photosystem I reveals a unique Lhca2 paralogue replacing Lhca4.
Authors: C Gorski / R Riddle / H Toporik / Z Da / Z Dobson / D Williams / Y Mazor /
Abstract: The moss Physcomitrium patens diverged from green algae shortly after the colonization of land by ancient plants. This colonization posed new environmental challenges, which drove evolutionary ...The moss Physcomitrium patens diverged from green algae shortly after the colonization of land by ancient plants. This colonization posed new environmental challenges, which drove evolutionary processes. The photosynthetic machinery of modern flowering plants is adapted to the high light conditions on land. Red-shifted Lhca4 antennae are present in the photosystem I light-harvesting complex of many green-lineage plants but absent in P. patens. The cryo-EM structure of the P. patens photosystem I light-harvesting complex I supercomplex (PSI-LHCI) at 2.8 Å reveals that Lhca4 is replaced by a unique Lhca2 paralogue in moss. This PSI-LHCI supercomplex also retains the PsaM subunit, present in Cyanobacteria and several algal species but lost in vascular plants, and the PsaO subunit responsible for binding light-harvesting complex II. The blue-shifted Lhca2 paralogue and chlorophyll b enrichment relative to flowering plants make the P. patens PSI-LHCI spectroscopically unique among other green-lineage supercomplexes. Overall, the structure represents an evolutionary intermediate PSI with the crescent-shaped LHCI common in vascular plants, and contains a unique Lhca2 paralogue that facilitates the moss's adaptation to low-light niches.
History
DepositionNov 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
1: Chlorophyll a-b binding protein, chloroplastic
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
4: Chlorophyll a-b binding protein, chloroplastic
C: Photosystem I iron-sulfur center
D: PsaD
E: PsaE
F: PSI-F
G: PSI-G
H: PsaH
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: PsaK
L: PSI subunit V
M: Photosystem I reaction center subunit XII
O: PsaO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)544,742237
Polymers368,11818
Non-polymers176,624219
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / / PSI-A / PsaA


Mass: 82313.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q8MFA3, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 82245.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q8MFA2, photosystem I

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Chlorophyll a-b binding protein, ... , 4 types, 4 molecules 1234

#3: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 20761.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9T399
#4: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 22124.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1IW94
#5: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23834.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9TEM8
#6: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 22305.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9RW10

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Protein , 9 types, 9 molecules CDEFGHKLO

#7: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8649.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q6YXQ2, photosystem I
#8: Protein PsaD


Mass: 15789.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9REG3
#9: Protein PsaE


Mass: 7081.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9SPD7
#10: Protein PSI-F / PsaF


Mass: 17646.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1IN36
#11: Protein PSI-G / PsaG / Photosystem I reaction center subunit V / chloroplastic


Mass: 9728.970 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9SJ10
#12: Protein PsaH


Mass: 9491.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9TCU9
#15: Protein PsaK


Mass: 8106.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1JLW2
#16: Protein PSI subunit V / PsaL


Mass: 16692.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9S1E1
#18: Protein PsaO


Mass: 9778.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1JDE1

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Photosystem I reaction center subunit ... , 3 types, 3 molecules IJM

#13: Protein/peptide Photosystem I reaction center subunit VIII / / PSI-I / PsaI


Mass: 3791.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q6YXR3
#14: Protein/peptide Photosystem I reaction center subunit IX / / PSI-J / PsaJ


Mass: 4597.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q6YXM2
#17: Protein/peptide Photosystem I reaction center subunit XII / / PSI-M / PsaM


Mass: 3179.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q6YXK4

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Sugars , 2 types, 7 molecules

#26: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#27: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 10 types, 257 molecules

#19: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C31H46O2
#22: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Fe4S4
#23: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#25: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN / Lutein


Mass: 568.871 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#30: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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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: PSI / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL
Source (natural)Organism: Physcomitrium patens (plant)
Buffer solutionpH: 8
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3.1 / Category: final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114608 / Symmetry type: POINT

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