[English] 日本語
Yorodumi
- PDB-8jw0: PSI-AcpPCI supercomplex from Amphidinium carterae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jw0
TitlePSI-AcpPCI supercomplex from Amphidinium carterae
Components
  • (Chlorophyll a-chlorophyll c-peridinin-protein-complex I- ...) x 17
  • (Photosystem I ...) x 11
KeywordsPHOTOSYNTHESIS / Photosysrem I / Dinoflagellate
Function / homology
Function and homology information


BETA-CAROTENE / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PERIDININ / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...BETA-CAROTENE / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PERIDININ / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / :
Similarity search - Component
Biological speciesAmphidinium carterae (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLi, Z.H. / Li, X.Y. / Wang, W.D.
Funding support China, 8items
OrganizationGrant numberCountry
Chinese Academy of Sciences2021YFA1300403 China
Chinese Academy of Sciences2019YFA0906300 China
Chinese Academy of SciencesXDA26050402 China
Chinese Academy of SciencesXDB17000000 China
Chinese Academy of Sciences2020081 China
Chinese Academy of SciencesJCTD-2020-06 China
Chinese Academy of Sciences31970260 China
Chinese Academy of Sciences32222007 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structures and organizations of PSI-AcpPCI supercomplexes from red tidal and coral symbiotic photosynthetic dinoflagellates.
Authors: Xiaoyi Li / Zhenhua Li / Fangfang Wang / Songhao Zhao / Caizhe Xu / Zhiyuan Mao / Jialin Duan / Yue Feng / Yang Yang / Lili Shen / Guanglei Wang / Yanyan Yang / Long-Jiang Yu / Min Sang / ...Authors: Xiaoyi Li / Zhenhua Li / Fangfang Wang / Songhao Zhao / Caizhe Xu / Zhiyuan Mao / Jialin Duan / Yue Feng / Yang Yang / Lili Shen / Guanglei Wang / Yanyan Yang / Long-Jiang Yu / Min Sang / Guangye Han / Xuchu Wang / Tingyun Kuang / Jian-Ren Shen / Wenda Wang /
Abstract: Marine photosynthetic dinoflagellates are a group of successful phytoplankton that can form red tides in the ocean and also symbiosis with corals. These features are closely related to the ...Marine photosynthetic dinoflagellates are a group of successful phytoplankton that can form red tides in the ocean and also symbiosis with corals. These features are closely related to the photosynthetic properties of dinoflagellates. We report here three structures of photosystem I (PSI)-chlorophylls (Chls) /-peridinin protein complex (PSI-AcpPCI) from two species of dinoflagellates by single-particle cryoelectron microscopy. The crucial PsaA/B subunits of a red tidal dinoflagellate are remarkably smaller and hence losing over 20 pigment-binding sites, whereas its PsaD/F/I/J/L/M/R subunits are larger and coordinate some additional pigment sites compared to other eukaryotic photosynthetic organisms, which may compensate for the smaller PsaA/B subunits. Similar modifications are observed in a coral symbiotic dinoflagellate species, where two additional core proteins and fewer AcpPCIs are identified in the PSI-AcpPCI supercomplex. The antenna proteins AcpPCIs in dinoflagellates developed some loops and pigment sites as a result to accommodate the changed PSI core, therefore the structures of PSI-AcpPCI supercomplex of dinoflagellates reveal an unusual protein assembly pattern. A huge pigment network comprising Chls and and various carotenoids is revealed from the structural analysis, which provides the basis for our deeper understanding of the energy transfer and dissipation within the PSI-AcpPCI supercomplex, as well as the evolution of photosynthetic organisms.
History
DepositionJun 28, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
a: Photosystem I PsaA
b: Photosystem I PsaB
c: Photosystem I PsaC
d: Photosystem I PsaD
e: Photosystem I PsaE
f: Photosystem I PsaF
h: Photosystem I PsaR
i: Photosystem I PsaI
j: Photosystem I PsaJ
l: Photosystem I PsaL
m: Photosystem I PsaM
A: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-10, acpPCI-10
G: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-8, acpPCI-8
I: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-7, acpPCI-7
K: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-6, acpPCI-6
F: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-2, acpPCI-2
J: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-3, acpPCI-3
M: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-4, acpPCI-4
L: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-5, acpPCI-5
D: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-9, acpPCI-9
B: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-11, acpPCI-11
H: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-12, acpPCI-12
N: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-13, acpPCI-13
O: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-15, acpPCI-15
T: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-16, acpPCI-16
Q: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-17, acpPCI-17
C: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-16, acpPCI-16
P: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-14, acpPCI-14
E: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-1, acpPCI-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)931,225440
Polymers614,00129
Non-polymers317,224411
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Photosystem I ... , 11 types, 11 molecules abcdefhijlm

#1: Protein Photosystem I PsaA /


Mass: 70529.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#2: Protein Photosystem I PsaB /


Mass: 67962.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#3: Protein Photosystem I PsaC /


Mass: 9409.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#4: Protein Photosystem I PsaD /


Mass: 28754.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#5: Protein Photosystem I PsaE /


Mass: 8617.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#6: Protein Photosystem I PsaF /


Mass: 20761.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#7: Protein Photosystem I PsaR /


Mass: 14937.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#8: Protein Photosystem I PsaI /


Mass: 14184.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#9: Protein Photosystem I PsaJ /


Mass: 7757.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#10: Protein Photosystem I PsaL /


Mass: 27994.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#11: Protein Photosystem I PsaM /


Mass: 9634.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)

-
Chlorophyll a-chlorophyll c-peridinin-protein-complex I- ... , 17 types, 18 molecules AGIKFJMLDBHNOTCQPE

#12: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-10, acpPCI-10


Mass: 19554.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#13: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-8, acpPCI-8


Mass: 23780.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#14: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-7, acpPCI-7


Mass: 21347.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#15: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-6, acpPCI-6


Mass: 19171.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#16: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-2, acpPCI-2


Mass: 19335.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#17: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-3, acpPCI-3


Mass: 18231.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#18: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-4, acpPCI-4


Mass: 18956.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#19: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-5, acpPCI-5


Mass: 20585.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#20: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-9, acpPCI-9


Mass: 17068.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#21: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-11, acpPCI-11


Mass: 19562.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#22: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-12, acpPCI-12


Mass: 17109.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#23: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-13, acpPCI-13


Mass: 17119.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#24: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-15, acpPCI-15


Mass: 17422.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#25: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-16, acpPCI-16


Mass: 17109.498 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#26: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-17, acpPCI-17


Mass: 17357.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#27: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-14, acpPCI-14


Mass: 17355.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)
#28: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-1, acpPCI-1


Mass: 15280.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Amphidinium carterae (eukaryote)

-
Sugars , 1 types, 8 molecules

#35: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

-
Non-polymers , 11 types, 403 molecules

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


Mass: 893.489 Da / Num. of mol.: 223 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#30: 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
#31: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#32: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#34: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#36: 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 / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: C40H54O3 / Feature type: SUBJECT OF INVESTIGATION
#37: Chemical...
ChemComp-PID / PERIDININ / Peridinin


Mass: 630.810 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: C39H50O7 / Feature type: SUBJECT OF INVESTIGATION
#38: Chemical
ChemComp-UIX / [(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate / Dinoxanthin


Mass: 642.907 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C42H58O5 / Feature type: SUBJECT OF INVESTIGATION
#39: Chemical...
ChemComp-KC1 / Chlorophyll c1 / Chlorophyll c


Mass: 610.941 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C35H30MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#40: 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 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: PSI-AcpPCI supercomplex from Amphidinium carterae / Type: COMPLEX / Entity ID: #1-#24, #26, #25, #27-#28 / Source: NATURAL
Source (natural)Organism: Amphidinium carterae (eukaryote)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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 / Nominal defocus max: 2200 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 356838 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00666688
ELECTRON MICROSCOPYf_angle_d1.47295434
ELECTRON MICROSCOPYf_dihedral_angle_d17.34521907
ELECTRON MICROSCOPYf_chiral_restr0.0498201
ELECTRON MICROSCOPYf_plane_restr0.00512212

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

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. 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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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