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- PDB-7y3f: Structure of the Anabaena PSI-monomer-IsiA supercomplex -

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Basic information

Entry
Database: PDB / ID: 7y3f
TitleStructure of the Anabaena PSI-monomer-IsiA supercomplex
Components
  • (Photosystem I ...) x 10
  • Iron stress-induced chlorophyll-binding protein
  • IsiA
  • PsaM
  • Unknown
KeywordsPHOTOSYNTHESIS / Photosystem I / ELECTRON TRANSPORT / isiA
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosynthetic electron transport chain / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosynthetic electron transport chain / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / 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 PsaX / Photosystem I PsaX superfamily / PsaX family / 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 PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / 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
BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A2 1 / Photosystem I 4.8 kDa protein / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XI / Iron stress-induced chlorophyll-binding protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsNagao, R. / Kato, K. / Hamaguchi, T. / Kawakami, K. / Yonekura, K. / Shen, J.R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20H02914 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120
Authors: Nagao, R. / Kato, K. / Hamaguchi, T. / Ueno, Y. / Tsuboshita, N. / Shimizu, S. / Furutani, M. / Ehira, S. / Nakajima, Y. / Kawakami, K. / Suzuki, T. / Dohmae, N. / Akimoto, S. / Yonekura, K. / Shen, J.R.
History
DepositionJun 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2 1
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Unknown
M: PsaM
X: Photosystem I 4.8 kDa protein
1: Photosystem I reaction center subunit XI
2: IsiA
3: IsiA
4: Iron stress-induced chlorophyll-binding protein
5: Iron stress-induced chlorophyll-binding protein
6: IsiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)617,160218
Polymers453,50717
Non-polymers163,653201
Water46826
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I ... , 10 types, 10 molecules ABCDEFIJX1

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


Mass: 83289.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria) / References: UniProt: P58576, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 1 / / PsaB 1


Mass: 83457.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria) / References: UniProt: P58565, photosystem I
#3: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8825.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria) / References: UniProt: P0A410, photosystem I
#4: Protein Photosystem I reaction center subunit II /


Mass: 15176.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria) / References: UniProt: P58573
#5: Protein Photosystem I reaction center subunit IV /


Mass: 7897.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria) / References: UniProt: P58575
#6: Protein Photosystem I reaction center subunit III / / PSI-F


Mass: 17850.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria) / References: UniProt: P58564
#7: Protein/peptide Photosystem I reaction center subunit VIII /


Mass: 5066.925 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria) / References: UniProt: P58560
#8: Protein/peptide Photosystem I reaction center subunit IX /


Mass: 5499.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria) / References: UniProt: P58568
#11: Protein/peptide Photosystem I 4.8 kDa protein /


Mass: 4872.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria) / References: UniProt: P58566
#12: Protein Photosystem I reaction center subunit XI / / PSI subunit V / PSI-L


Mass: 51717.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria) / References: UniProt: Q8YQ34

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Protein , 3 types, 6 molecules K23645

#9: Protein Unknown


Mass: 6996.616 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Authors do not know the sequence. / Source: (natural) Nostoc sp. (bacteria)
#13: Protein IsiA


Mass: 27676.963 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: Authors do not know the sequence. / Source: (natural) Nostoc sp. (bacteria)
#14: Protein Iron stress-induced chlorophyll-binding protein / CP43'


Mass: 37701.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria) / References: UniProt: Q8YQ35

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Protein/peptide / Sugars , 2 types, 7 molecules M

#10: Protein/peptide PsaM


Mass: 4424.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria)
#21: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 8 types, 221 molecules

#15: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#16: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 155 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#17: 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
#18: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#19: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C40H56
#20: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#22: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10
#23: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: PSI-monomer-IsiA / Type: COMPLEX / Entity ID: #1-#8, #10-#14 / Source: NATURAL
Molecular weightValue: 0.64 MDa / Experimental value: NO
Source (natural)Organism: Nostoc sp. (bacteria)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMMESMES-NaOH1
20.03 %DDMDDM1
SpecimenConc.: 1.68 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 11.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
7UCSF Chimera1.12model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13REFMAC5.8.0267model refinement
14PHENIX1.13_2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47602 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL

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