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- PDB-7lx0: Quantitative assessment of chlorophyll types in cryo-EM maps of p... -

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Basic information

Entry
Database: PDB / ID: 7lx0
TitleQuantitative assessment of chlorophyll types in cryo-EM maps of photosystem I acclimated to far-red light
Components
  • (Photosystem I ...) x 10
  • PSI subunit V
  • Photosystem one PsaX
KeywordsPHOTOSYNTHESIS / Photosystem I / Far-red light / Chlorophyll f
Function / homology
Function and homology information


: / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / membrane => GO:0016020 / photosynthesis / 4 iron, 4 sulfur cluster binding ...: / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / membrane => GO:0016020 / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 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 PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / 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 / Chlorophyll F / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit XI ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / Chlorophyll F / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit XI / Uncharacterized protein / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV / Photosystem one PsaX / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesFischerella thermalis PCC 7521 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsGisriel, C.J. / Wang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
CitationJournal: BBA Adv / Year: 2021
Title: Quantitative assessment of chlorophyll types in cryo-EM maps of photosystem I acclimated to far-red light
Authors: Gisriel, C.J. / Huang, H.L. / Reiss, K.M. / Flesher, D.A. / Batista, V.S. / Bryant, D.A. / Brudvig, G.W. / Wang, J.
History
DepositionMar 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-23563
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Photosystem I P700 chlorophyll a apoprotein A1
H: Photosystem I P700 chlorophyll a apoprotein A2
N: Photosystem I iron-sulfur center
O: Photosystem I protein PsaD
P: Photosystem I reaction center subunit IV
Q: Photosystem I reaction center protein PsaF subunit III
R: photosystem I subunit VIII
S: Photosystem I reaction centre subunit IX / PsaJ
T: Photosystem I reaction center subunit PsaK
U: PSI subunit V
V: Photosystem I reaction center subunit XII
W: Photosystem one PsaX
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 protein PsaD
e: Photosystem I reaction center subunit IV
f: Photosystem I reaction center protein PsaF subunit III
i: photosystem I subunit VIII
j: Photosystem I reaction centre subunit IX / PsaJ
k: Photosystem I reaction center subunit PsaK
l: PSI subunit V
m: Photosystem I reaction center subunit XII
x: Photosystem one PsaX
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 protein PsaD
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center protein PsaF subunit III
I: photosystem I subunit VIII
J: Photosystem I reaction centre subunit IX / PsaJ
K: Photosystem I reaction center subunit PsaK
L: PSI subunit V
M: Photosystem I reaction center subunit XII
X: Photosystem one PsaX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,119,610408
Polymers823,13936
Non-polymers296,471372
Water00
1


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

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Components

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Photosystem I ... , 10 types, 30 molecules GaAHbBNcCOdDPeEQfFRiISjJTkKVmM

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


Mass: 87627.914 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FME9, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB / photosystem I core protein PsaB


Mass: 83450.969 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: A0A2N6KXB6, photosystem I
#3: Protein Photosystem I iron-sulfur center / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8853.221 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FW50, photosystem I
#4: Protein Photosystem I protein PsaD


Mass: 17776.348 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FW99
#5: Protein Photosystem I reaction center subunit IV


Mass: 8070.138 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FQU3
#6: Protein Photosystem I reaction center protein PsaF subunit III


Mass: 17788.021 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FMD3
#7: Protein photosystem I subunit VIII


Mass: 7735.956 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: A0A2N6MR25
#8: Protein/peptide Photosystem I reaction centre subunit IX / PsaJ


Mass: 5435.492 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FMD2
#9: Protein/peptide Photosystem I reaction center subunit PsaK


Mass: 4494.526 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria)
#11: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3471.115 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FWT6

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Protein , 2 types, 6 molecules UlLWxX

#10: Protein PSI subunit V / PSI-L / Photosystem I reaction center subunit XI


Mass: 18543.229 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: A0A2N6L446
#12: Protein Photosystem one PsaX


Mass: 11132.814 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FSH2

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Sugars , 1 types, 6 molecules

#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 , 9 types, 366 molecules

#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 252 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#15: Chemical
ChemComp-F6C / Chlorophyll F / [methyl 9-ethenyl-14-ethyl-8-formyl-4,13,18-trimethyl-20-oxo-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,23,25-tetradehydro-24,26-dihydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]magnesium


Mass: 905.457 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C55H68MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H46O2
#17: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#18: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C40H56
#19: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#20: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C45H86O10
#22: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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Details

Has ligand of interestY
Has protein modificationY
Sequence detailsThe full sequence of PsaK is MSSILLAAAATVPPTAEWSPKVALIISISCLVAVLLSFRIEKPKVGPKMPGLPLSIPTFV ...The full sequence of PsaK is MSSILLAAAATVPPTAEWSPKVALIISISCLVAVLLSFRIEKPKVGPKMPGLPLSIPTFV AAMAFGHVIGVAIVLGLTNIGKI

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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: Photosystem I adapted to far-red light / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Source (natural)Organism: Fischerella thermalis PCC 7521 (bacteria)
Buffer solutionpH: 7
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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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 FIELD
Image recordingElectron dose: 57.328 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201104 / Symmetry type: POINT

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