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

+
Open data


ID or keywords:

Loading...

no data

-
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
  • PsaKPosek
  • PsaL
KeywordsPHOTOSYNTHESIS / photosynthesis / complex / photosystem I / light harvesting complex / Physcomitrella
Specimen sourcePhyscomitrella patens (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 11.6 Å resolution
AuthorsIwai, M. / Grob, P.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 6, 2018 / Release: Nov 21, 2018

-
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
Polyers420,50924
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

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

#1: Protein/peptide Chlorophyll A/B binding protein 1


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


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


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


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


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


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


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


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


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


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


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


Mass: 19166.555 Da / Num. of mol.: 1 / Source: (natural) Physcomitrella patens (plant)

-
Protein/peptide , 12 types, 12 molecules JLNPQRSTUVWX

#10: Protein/peptide PsaA


Mass: 63250.809 Da / Num. of mol.: 1 / Source: (natural) Physcomitrella patens (plant)
#12: Protein/peptide PsaB


Mass: 62399.789 Da / Num. of mol.: 1 / Source: (natural) Physcomitrella patens (plant)
#14: Protein/peptide PsaC


Mass: 6826.406 Da / Num. of mol.: 1 / Source: (natural) Physcomitrella patens (plant)
#16: Protein/peptide PsaD


Mass: 12188.016 Da / Num. of mol.: 1 / Source: (natural) Physcomitrella patens (plant)
#17: Protein/peptide PsaE


Mass: 5634.938 Da / Num. of mol.: 1 / Source: (natural) Physcomitrella patens (plant)
#18: Protein/peptide PsaF


Mass: 13124.170 Da / Num. of mol.: 1 / Source: (natural) Physcomitrella patens (plant)
#19: Protein/peptide PsaG


Mass: 8273.189 Da / Num. of mol.: 1 / Source: (natural) Physcomitrella patens (plant)
#20: Protein/peptide PsaH


Mass: 7507.245 Da / Num. of mol.: 1 / Source: (natural) Physcomitrella patens (plant)
#21: Protein/peptide PsaI


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


Mass: 3592.419 Da / Num. of mol.: 1 / Source: (natural) Physcomitrella patens (plant)
#23: Protein/peptide PsaK / Posek


Mass: 6571.091 Da / Num. of mol.: 1 / Source: (natural) Physcomitrella patens (plant)
#24: Protein/peptide PsaL


Mass: 13379.484 Da / Num. of mol.: 1 / Source: (natural) Physcomitrella patens (plant)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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: 1,2,3,4,5,6,8,9,10,11,12,14,16,17,18,19,20,21,22,23,24,7,13,15
Source: NATURAL
Molecular weightValue: 0.94 MDa / Experimental value: NO
Source (natural)Cellular location: chloroplast / Organelle: chloroplast / Organism: Physcomitrella patens (plant) / Strain: Gransden 2004 / 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 kelvins / Details: Lights off, blot 4.5 seconds before plunging.

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 80000 / Calibrated magnification: 107140 / 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 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Temperature (max): 93 kelvins / Temperature (min): 93 kelvins
Image recordingAverage exposure time: 0.5 sec. / Electron dose: 25 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number of grids imaged: 3 / Number of real images: 361
Image scansSampling size: 15 microns / 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 selectionNumber of particles selected: 55780
SymmetryPoint symmetry: C1
3D reconstructionResolution: 11.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 14412 / Algorithm: FOURIER SPACE / Number of class averages: 5 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT
Least-squares processHighest resolution: 11.6 Å

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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