[English] 日本語
Yorodumi
- PDB-9kqp: PSI-LHCI supercomplex binding with 10 Lhcas from C. subellipsoidea -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kqp
TitlePSI-LHCI supercomplex binding with 10 Lhcas from C. subellipsoidea
Components
  • (Chlorophyll a-b binding protein, ...) x 9
  • (Photosystem I ...) x 12
  • PSI subunit V
  • PSI-K
KeywordsPHOTOSYNTHESIS / Photosystem I / Thylakoid membrane
Function / homology
Function and homology information


plastid thylakoid membrane / thylakoid membrane / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid ...plastid thylakoid membrane / thylakoid membrane / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / protein domain specific binding / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I PsaO / PsaO transmembrane domain / 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 PsaO / PsaO transmembrane domain / 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 PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / 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
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / ASTAXANTHIN / BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-LAP / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / ASTAXANTHIN / BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-LAP / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / PHOSPHATIDYLETHANOLAMINE / Chem-QTB / IRON/SULFUR CLUSTER / Chem-SQD / Unknown ligand / Chem-XAT / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit XII / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction centre subunit IV/PsaE / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSI-K / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit II, chloroplastic / Photosystem I PsaO / Photosystem I reaction centre subunit VI / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit III
Similarity search - Component
Biological speciesCoccomyxa subellipsoidea C-169 (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 1.92 Å
AuthorsTsai, P.-C. / Kato, K. / Shen, J.-R. / Akita, F.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22H04916 Japan
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2025
Title: Structural study of the chlorophyll between Lhca8 and PsaJ in an Antarctica green algal photosystem I-LHCI supercomplex revealed by its atomic structure.
Authors: Pi-Cheng Tsai / Koji Kato / Jian-Ren Shen / Fusamichi Akita /
Abstract: Coccomyxa subellipsoidea is an oleaginous, non-motile unicellular green microalga isolated from Antarctica, and is an attractive candidate for CO fixation and biomass production. C. subellipsoidea is ...Coccomyxa subellipsoidea is an oleaginous, non-motile unicellular green microalga isolated from Antarctica, and is an attractive candidate for CO fixation and biomass production. C. subellipsoidea is the first polar green alga whose genome has been sequenced. Understanding the structure of photosystems from C. subellipsoidea can provide more information about the conversion of light energy into chemical energy under extreme environments. Photosystems I (PSI) is one of the two photosystems highly conserved from cyanobacteria to vascular plants, and associates with a large amount of outer light-harvesting complex (LHC) which absorb light energy and transfer them to the core complex. Here, we determined the structure of the PSI-10 LHCIs and PSI-8 LHCIs supercomplexes from C. subellipsoidea at 1.92 Å and 2.06 Å resolutions by cryo-electron microscopy, respectively. The supercomplex is similar to PSI-LHCI from other green algae, whereas a large amount of water molecules is observed in our structure because of the high-resolution map. Two novel chlorophylls (Chls), Chl a321 in Lhca4 and Chl a314 in Lhca8, are observed at the lumenal side in our structure, in which Lhca8-Chl a314 provides a potential excitation energy transfer (EET) pathway between the inner-belt of LHCI and the core at the lumenal side. A total of three major EET pathways from LHCIs to PSI core are proposed, and C. subellipsoidea might adapt to the extreme environment by transferring energy in these three different EET pathways instead of by two major pathways proposed in other organisms.
History
DepositionNov 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
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, chloroplastic
E: Photosystem I reaction centre subunit IV/PsaE
F: Photosystem I reaction center subunit III
G: Photosystem I reaction center subunit V, chloroplastic
H: Photosystem I reaction centre subunit VI
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: PSI-K
M: Photosystem I reaction center subunit XII
a: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
7: Chlorophyll a-b binding protein, chloroplastic
8: Chlorophyll a-b binding protein, chloroplastic
9: Chlorophyll a-b binding protein, chloroplastic
L: PSI subunit V
O: Photosystem I PsaO
b: Chlorophyll a-b binding protein, chloroplastic
2: Chlorophyll a-b binding protein, chloroplastic/Lhca2
4: Chlorophyll a-b binding protein, chloroplastic
5: Chlorophyll a-b binding protein, chloroplastic
6: Chlorophyll a-b binding protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)868,971378
Polymers590,78624
Non-polymers278,185354
Water19,0961060
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Photosystem I ... , 12 types, 12 molecules ABCDEFGHIJMO

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


Mass: 83220.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: E9NPS7, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 81886.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: E9NPS8, photosystem I
#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8797.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: E9NPV2, photosystem I
#4: Protein Photosystem I reaction center subunit II, chloroplastic


Mass: 20872.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0YVS7
#5: Protein Photosystem I reaction centre subunit IV/PsaE


Mass: 8261.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0YQ13
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 25876.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0Z7V3
#7: Protein Photosystem I reaction center subunit V, chloroplastic / PSI-G


Mass: 14552.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0YTK4
#8: Protein Photosystem I reaction centre subunit VI


Mass: 14596.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0Z284
#9: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 3852.663 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: E9NPX1
#10: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4731.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: E9NPW6
#12: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3380.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: E9NPZ7
#19: Protein Photosystem I PsaO


Mass: 15303.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0YWK6

-
Protein , 2 types, 2 molecules KL

#11: Protein PSI-K


Mass: 13330.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0YST3
#18: Protein PSI subunit V


Mass: 21881.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0Z687

-
Chlorophyll a-b binding protein, ... , 9 types, 10 molecules ab37892456

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


Mass: 24076.436 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0YQ45
#14: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 26877.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0YPL4
#15: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 27493.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0YQ44
#16: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 27499.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0YQ46
#17: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24696.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0YP72
#20: Protein Chlorophyll a-b binding protein, chloroplastic/Lhca2


Mass: 29998.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: photosystem I
#21: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 26938.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0Z7A7
#22: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 29447.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0Z2Y0
#23: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 29137.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coccomyxa subellipsoidea C-169 (plant) / References: UniProt: I0Z7A6

-
Sugars , 2 types, 6 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#33: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

-
Non-polymers , 19 types, 1408 molecules

#24: 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
#25: 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
#26: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#29: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Mass: 254.494 Da / Num. of mol.: 17 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 218 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical ChemComp-LAP / [2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETHYL]-TRIMETHYLAMMONIUM / L-ALFA-LYSOPHOSPHATIDYLCHOLINE, LAUROYL


Mass: 440.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H43NO7P / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical
ChemComp-QTB / (3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one


Mass: 260.414 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H28O / Feature type: SUBJECT OF INVESTIGATION
#36: 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


Mass: 568.871 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#37: 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
#38: Chemical ChemComp-AXT / ASTAXANTHIN / 3,3'-DIHYDROXY-BETA,BETA-CAROTENE-4,4'-DIONE


Mass: 596.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H52O4 / Feature type: SUBJECT OF INVESTIGATION
#39: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H77O8P / Feature type: SUBJECT OF INVESTIGATION
#40: Chemical ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#41: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5 / Feature type: SUBJECT OF INVESTIGATION
#42: 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.: 1 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#43: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#44: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1060 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Green alga photosystem I LHCI supercomplex binding with 10 Lhcas
Type: COMPLEX / Entity ID: #1-#23 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Coccomyxa subellipsoidea C-169 (plant)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 3.42 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 14766

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1489274
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224674 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Atomic model buildingPDB-ID: 6zzx

6zzx


Accession code: 6zzx / Source name: PDB / Type: experimental model
RefinementHighest resolution: 1.92 Å

+
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