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- PDB-8z11: Cryo-EM structure of haptophyte photosystem I -

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Entry
Database: PDB / ID: 8z11
TitleCryo-EM structure of haptophyte photosystem I
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 6
  • L-iFP
  • Photosystem I iron-sulfur center
  • PsaE
  • PsaK
  • PsaR
  • iFCPI-1
  • iFCPI-10
  • iFCPI-11
  • iFCPI-12
  • iFCPI-13
  • iFCPI-15/14/16
  • iFCPI-17
  • iFCPI-18
  • iFCPI-2
  • iFCPI-20/19/21
  • iFCPI-22
  • iFCPI-3
  • iFCPI-4
  • iFCPI-5
  • iFCPI-6
  • iFCPI-7
  • iFCPI-8
  • iFCPI-9
KeywordsPHOTOSYNTHESIS / Haptophyte / Photosystem I / evolution
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / 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 / 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-A86 / BETA-CAROTENE / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...Chem-A86 / BETA-CAROTENE / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 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 VIII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit XI
Similarity search - Component
Biological speciesIsochrysis galbana (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsHe, F.Y. / Zhao, L.S. / Li, K. / Zhang, Y.Z. / Liu, L.N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2023YFA0914600 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structural insights into the assembly and energy transfer of haptophyte photosystem I-light-harvesting supercomplex.
Authors: Fei-Yu He / Long-Sheng Zhao / Xin-Xiao Qu / Kang Li / Jian-Ping Guo / Fang Zhao / Ning Wang / Bing-Yue Qin / Xiu-Lan Chen / Jun Gao / Lu-Ning Liu / Yu-Zhong Zhang /
Abstract: Haptophyta represents a major taxonomic group, with plastids derived from the primary plastids of red algae. Here, we elucidated the cryoelectron microscopy structure of the photosystem I-light- ...Haptophyta represents a major taxonomic group, with plastids derived from the primary plastids of red algae. Here, we elucidated the cryoelectron microscopy structure of the photosystem I-light-harvesting complex I (PSI-LHCI) supercomplex from the haptophyte . The PSI core comprises 12 subunits, which have evolved differently from red algae and cryptophytes by losing the PsaO subunit while incorporating the PsaK subunit, which is absent in diatoms and dinoflagellates. The PSI core is encircled by 22 fucoxanthin-chlorophyll /-binding light-harvesting antenna proteins (iFCPIs) that form a trilayered antenna arrangement. Moreover, a pigment-binding subunit, L, which has not been identified in any other previously characterized PSI-LHCI supercomplexes, was determined in PSI-iFCPI, presumably facilitating the interactions and energy transfer between peripheral iFCPIs and the PSI core. Calculation of excitation energy transfer rates by computational simulations revealed that the intricate pigment network formed within PSI-iFCPI ensures efficient transfer of excitation energy. Overall, our study provides a solid structural foundation for understanding the light-harvesting and energy transfer mechanisms in haptophyte PSI-iFCPI and provides insights into the evolution and structural variations of red-lineage PSI-LHCIs.
History
DepositionApr 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iFCPI-7
B: iFCPI-1
C: iFCPI-11
D: iFCPI-6
E: iFCPI-5
F: iFCPI-8
G: iFCPI-13
H: iFCPI-10
I: iFCPI-3
J: iFCPI-9
K: iFCPI-4
L: iFCPI-12
M: iFCPI-15/14/16
N: iFCPI-17
O: iFCPI-20/19/21
P: iFCPI-15/14/16
Q: iFCPI-18
R: iFCPI-20/19/21
S: iFCPI-22
T: iFCPI-20/19/21
U: iFCPI-2
V: L-iFP
W: iFCPI-15/14/16
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: PsaE
f: Photosystem I reaction center subunit III
i: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
k: PsaK
l: Photosystem I reaction center subunit XI
m: Photosystem I reaction center subunit XII
r: PsaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,180,902552
Polymers781,61935
Non-polymers399,283517
Water00
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 , 23 types, 27 molecules ABCDEFGHIJKLMPWNORTQSUVcekr

#1: Protein iFCPI-7


Mass: 22841.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#2: Protein iFCPI-1


Mass: 22262.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#3: Protein iFCPI-11


Mass: 21889.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#4: Protein iFCPI-6


Mass: 26300.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#5: Protein iFCPI-5


Mass: 21683.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#6: Protein iFCPI-8


Mass: 25390.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#7: Protein iFCPI-13


Mass: 20749.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#8: Protein iFCPI-10


Mass: 21410.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#9: Protein iFCPI-3


Mass: 21055.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#10: Protein iFCPI-9


Mass: 20788.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#11: Protein iFCPI-4


Mass: 21735.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#12: Protein iFCPI-12


Mass: 24225.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#13: Protein iFCPI-15/14/16


Mass: 23142.912 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#14: Protein iFCPI-17


Mass: 23706.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#15: Protein iFCPI-20/19/21


Mass: 21494.846 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#16: Protein iFCPI-18


Mass: 20023.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#17: Protein iFCPI-22


Mass: 25384.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#18: Protein iFCPI-2


Mass: 21908.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#19: Protein L-iFP


Mass: 12567.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#22: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8795.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote) / References: UniProt: A0A7D4X9R7, photosystem I
#24: Protein PsaE


Mass: 12835.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#28: Protein PsaK


Mass: 9484.241 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)
#31: Protein PsaR


Mass: 13750.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote)

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

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


Mass: 83558.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote) / References: UniProt: A0A7D4XMT1, photosystem I
#21: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82181.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote) / References: UniProt: A0A7D4X9X4, photosystem I

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Photosystem I reaction center subunit ... , 6 types, 6 molecules dfijlm

#23: Protein Photosystem I reaction center subunit II


Mass: 15882.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote) / References: UniProt: A0A7D4XG42
#25: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 20218.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote) / References: UniProt: A0A7D4XMU0
#26: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3943.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote) / References: UniProt: A0A7D4X9U5
#27: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4506.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote) / References: UniProt: A0A7D4X9Y3
#29: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 15477.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote) / References: UniProt: A0A7D5B6G5
#30: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3149.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Isochrysis galbana (eukaryote) / References: UniProt: A0A7D4XMW6

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Sugars , 2 types, 7 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#40: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


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

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Non-polymers , 10 types, 510 molecules

#32: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 280 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical...
ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 62 / Source method: obtained synthetically / Formula: C35H28MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical...
ChemComp-DD6 / (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: C40H54O3 / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#36: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C45H86O10
#37: Chemical...
ChemComp-A86 / (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate / Fucoxanthin


Mass: 658.906 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C42H58O6 / Feature type: SUBJECT OF INVESTIGATION
#39: 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
#41: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#42: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#43: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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 haptophyte / Type: COMPLEX / Entity ID: #1-#31 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Isochrysis galbana (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: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / 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: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148236 / Symmetry type: POINT

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