[English] 日本語
Yorodumi
- PDB-6mem: A unique supramolecular organization of photosystem I in the moss... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mem
TitleA unique supramolecular organization of photosystem I in the moss Physcomitrella patens
Components
  • (Chlorophyll A/B binding protein ...) x 12
  • PsaA
  • PsaB
  • PsaC
  • PsaD
  • PsaE
  • PsaF
  • PsaG
  • PsaH
  • PsaI
  • PsaJ
  • PsaK
  • PsaL
KeywordsPHOTOSYNTHESIS / complex / photosystem I / light harvesting complex / Physcomitrella
Biological speciesPhyscomitrella patens (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.6 Å
AuthorsIwai, M. / Grob, P.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)1S10OD020062-01 United States
CitationJournal: Nat Plants / Year: 2018
Title: A unique supramolecular organization of photosystem I in the moss Physcomitrella patens.
Authors: Masakazu Iwai / Patricia Grob / Anthony T Iavarone / Eva Nogales / Krishna K Niyogi /
Abstract: The photosynthesis machinery in chloroplast thylakoid membranes is comprised of multiple protein complexes and supercomplexes. Here, we show a novel supramolecular organization of photosystem I (PSI) ...The photosynthesis machinery in chloroplast thylakoid membranes is comprised of multiple protein complexes and supercomplexes. Here, we show a novel supramolecular organization of photosystem I (PSI) in the moss Physcomitrella patens by single-particle cryo-electron microscopy. The moss-specific light-harvesting complex (LHC) protein Lhcb9 is involved in this PSI supercomplex, which has been shown to have a molecular density similar to that of the green alga Chlamydomonas reinhardtii. Our results show that the structural organization is unexpectedly different-two rows of the LHCI belt exist as in C. reinhardtii, but the outer one is shifted toward the PsaK side. Furthermore, one trimeric LHC protein and one monomeric LHC protein position alongside PsaL/K, filling the gap between these subunits and the outer LHCI belt. We provide evidence showing that Lhcb9 is a key factor, acting as a linkage between the PSI core and the outer LHCI belt to form the unique supramolecular organization of the PSI supercomplex in P. patens.
History
DepositionSep 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9107
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chlorophyll A/B binding protein 1
B: Chlorophyll A/B binding protein 5
C: Chlorophyll A/B binding protein 3
D: Chlorophyll A/B binding protein 7
E: Chlorophyll A/B binding protein 4
F: Chlorophyll A/B binding protein 9
G: Chlorophyll A/B binding protein 8
H: Chlorophyll A/B binding protein 2
I: Chlorophyll A/B binding protein 6
J: PsaA
K: Chlorophyll A/B binding protein 10
L: PsaB
M: Chlorophyll A/B binding protein 11
N: PsaC
O: Chlorophyll A/B binding protein 12
P: PsaD
Q: PsaE
R: PsaF
S: PsaG
T: PsaH
U: PsaI
V: PsaJ
W: PsaK
X: PsaL


Theoretical massNumber of molelcules
Total (without water)420,50924
Polymers420,50924
Non-polymers00
Water00
1


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

-
Components

-
Chlorophyll A/B binding protein ... , 12 types, 12 molecules ABCDEFGHIKMO

#1: Protein Chlorophyll A/B binding protein 1


Mass: 16443.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#2: Protein Chlorophyll A/B binding protein 5


Mass: 16613.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#3: Protein Chlorophyll A/B binding protein 3


Mass: 17719.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#4: Protein Chlorophyll A/B binding protein 7


Mass: 17549.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#5: Protein Chlorophyll A/B binding protein 4


Mass: 18826.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#6: Protein Chlorophyll A/B binding protein 9


Mass: 18570.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#7: Protein Chlorophyll A/B binding protein 8


Mass: 18655.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#8: Protein Chlorophyll A/B binding protein 2


Mass: 16868.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#9: Protein Chlorophyll A/B binding protein 6


Mass: 16698.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#11: Protein Chlorophyll A/B binding protein 10


Mass: 18996.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#13: Protein Chlorophyll A/B binding protein 11


Mass: 19081.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#15: Protein Chlorophyll A/B binding protein 12


Mass: 19166.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)

-
Protein , 10 types, 10 molecules JLNPQRSTWX

#10: Protein PsaA


Mass: 63250.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#12: Protein PsaB


Mass: 62399.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#14: Protein PsaC


Mass: 6826.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#16: Protein PsaD


Mass: 12188.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#17: Protein PsaE


Mass: 5634.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#18: Protein PsaF


Mass: 13124.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#19: Protein PsaG


Mass: 8273.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#20: Protein PsaH


Mass: 7507.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#23: Protein PsaK


Mass: 6571.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#24: Protein PsaL


Mass: 13379.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)

-
Protein/peptide , 2 types, 2 molecules UV

#21: Protein/peptide PsaI


Mass: 2571.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)
#22: Protein/peptide PsaJ


Mass: 3592.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrella patens (plant)

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Large PSI-LHCI supercomplex / Type: COMPLEX
Details: A protein supercomplex isolated by gentle detergent solubilization of thylakoid membranes and maltose density gradient centrifugation
Entity ID: #1-#6, #8-#12, #14, #16-#24, #7, #13, #15 / Source: NATURAL
Molecular weightValue: 0.94 MDa / Experimental value: NO
Source (natural)Organism: Physcomitrella patens (plant) / Strain: Gransden 2004 / Cellular location: chloroplast / Organelle: chloroplast / Tissue: protonema
Buffer solutionpH: 6.5
Buffer component
IDConc.FormulaBuffer-ID
125 mMMES1
20.03 %DDM1
30.5 %trehalose1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K / Details: Lights off, blot 4.5 seconds before plunging.

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 80000 X / Calibrated magnification: 107140 X / Nominal defocus max: -1800 nm / Nominal defocus min: -2500 nm / Calibrated defocus min: -1900 nm / Calibrated defocus max: -4200 nm / Cs: 2.2 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Temperature (max): 93 K / Temperature (min): 93 K
Image recordingAverage exposure time: 0.5 sec. / Electron dose: 25 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 361
Image scansSampling size: 15 µm / Width: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2Leginonimage acquisition
3Gautomatchimage acquisition
5CTFFIND3CTF correction
8UCSF Chimeramodel fitting
11RELION1.4initial Euler assignment
12RELION1.4final Euler assignment
13RELION1.4classification
14RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 55780
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 11.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14412 / Algorithm: FOURIER SPACE / Num. of class averages: 5 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementHighest resolution: 11.6 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