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- PDB-6kig: Structure of cyanobacterial photosystem I-IsiA supercomplex -

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Basic information

Entry
Database: PDB / ID: 6kig
TitleStructure of cyanobacterial photosystem I-IsiA supercomplex
Components
  • (Photosystem I ...) x 10
  • Iron stress-induced chlorophyll-binding protein
  • PsaM
KeywordsPHOTOSYNTHESIS / Photosystem / Antenna / Chlorophyll-binding protein / Membrane protein / iron stress-induced protein A
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosynthetic electron transport chain / 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 / photosystem I / photosynthetic electron transport chain / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / 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 center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / 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 PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / 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 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Iron stress-induced chlorophyll-binding protein / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII ...BETA-CAROTENE / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Iron stress-induced chlorophyll-binding protein / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit PsaK / Photosystem I iron-sulfur center
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsCao, P. / Cao, D.F. / Si, L. / Su, X.D. / Chang, W.R. / Liu, Z.F. / Zhang, X.Z. / Li, M.
CitationJournal: Nat Plants / Year: 2020
Title: Structural basis for energy and electron transfer of the photosystem I-IsiA-flavodoxin supercomplex.
Authors: Peng Cao / Duanfang Cao / Long Si / Xiaodong Su / Lijin Tian / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li /
Abstract: Under iron-deficiency stress, which occurs frequently in natural aquatic environments, cyanobacteria reduce the amount of iron-enriched proteins, including photosystem I (PSI) and ferredoxin (Fd), ...Under iron-deficiency stress, which occurs frequently in natural aquatic environments, cyanobacteria reduce the amount of iron-enriched proteins, including photosystem I (PSI) and ferredoxin (Fd), and upregulate the expression of iron-stress-induced proteins A and B (IsiA and flavodoxin (Fld)). Multiple IsiAs function as the peripheral antennae that encircle the PSI core, whereas Fld replaces Fd as the electron receptor of PSI. Here, we report the structures of the PSI-IsiA-Fld and PSI-IsiA supercomplexes from Synechococcus sp. PCC 7942, revealing features that are different from the previously reported PSI structures, and a sophisticated pigment network that involves previously unobserved pigment molecules. Spectroscopic results demonstrated that IsiAs are efficient light harvesters for PSI. Three Flds bind symmetrically to the trimeric PSI core-we reveal the detailed interaction and the electron transport path between PSI and Fld. Our results provide a structural basis for understanding the mechanisms of light harvesting, energy transfer and electron transport of cyanobacterial PSI under stressed conditions.
History
DepositionJul 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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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
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I PsaI protein
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: PsaM
1: Iron stress-induced chlorophyll-binding protein
2: Iron stress-induced chlorophyll-binding protein
3: Iron stress-induced chlorophyll-binding protein
4: Iron stress-induced chlorophyll-binding protein
5: Iron stress-induced chlorophyll-binding protein
6: Iron stress-induced chlorophyll-binding protein
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 reaction center subunit II
Q: Photosystem I reaction center subunit IV
R: Photosystem I reaction center subunit III
S: Photosystem I PsaI protein
T: Photosystem I reaction center subunit IX
U: Photosystem I reaction center subunit PsaK
V: Photosystem I reaction center subunit XI
W: PsaM
Y: Iron stress-induced chlorophyll-binding protein
Z: Iron stress-induced chlorophyll-binding protein
a: Iron stress-induced chlorophyll-binding protein
b: Iron stress-induced chlorophyll-binding protein
c: Iron stress-induced chlorophyll-binding protein
d: Iron stress-induced chlorophyll-binding protein
e: Photosystem I P700 chlorophyll a apoprotein A1
f: Photosystem I P700 chlorophyll a apoprotein A2
g: Photosystem I iron-sulfur center
h: Photosystem I reaction center subunit II
i: Photosystem I reaction center subunit IV
j: Photosystem I reaction center subunit III
k: Photosystem I PsaI protein
l: Photosystem I reaction center subunit IX
m: Photosystem I reaction center subunit PsaK
n: Photosystem I reaction center subunit XI
o: PsaM
q: Iron stress-induced chlorophyll-binding protein
r: Iron stress-induced chlorophyll-binding protein
s: Iron stress-induced chlorophyll-binding protein
t: Iron stress-induced chlorophyll-binding protein
u: Iron stress-induced chlorophyll-binding protein
v: Iron stress-induced chlorophyll-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,103,987897
Polymers1,424,54551
Non-polymers679,442846
Water97354
1


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

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Components

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

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


Mass: 83994.336 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / References: UniProt: Q31LJ0, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 81554.742 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / References: UniProt: Q31LJ1, photosystem I
#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8807.235 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / References: UniProt: Q31QV2, photosystem I
#4: Protein Photosystem I reaction center subunit II / PsaD


Mass: 15536.583 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / References: UniProt: Q31PI7
#5: Protein Photosystem I reaction center subunit IV


Mass: 8147.134 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / References: UniProt: Q31NL7
#6: Protein Photosystem I reaction center subunit III


Mass: 17125.742 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / References: UniProt: Q31NT9
#7: Protein/peptide Photosystem I PsaI protein / PsaI / Photosystem I subunit VIII


Mass: 4002.733 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / References: UniProt: P95823
#8: Protein/peptide Photosystem I reaction center subunit IX / PsaJ


Mass: 4713.585 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / References: UniProt: Q31NU0
#9: Protein Photosystem I reaction center subunit PsaK / Photosystem I subunit X


Mass: 8397.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / References: UniProt: Q31PR9
#10: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 17302.688 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / References: UniProt: P95822

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Protein/peptide / Protein / Sugars , 3 types, 39 molecules MWo123456YZabcdqrstuv

#11: Protein/peptide PsaM


Mass: 3239.867 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / References: photosystem I
#12: Protein
Iron stress-induced chlorophyll-binding protein / CP43'


Mass: 37004.453 Da / Num. of mol.: 18 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / References: UniProt: P15347
#18: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 8 types, 882 molecules

#13: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 594 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: 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
#15: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 536.873 Da / Num. of mol.: 144 / Source method: obtained synthetically / Formula: C40H56
#17: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#19: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C45H86O10
#20: 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.: 24 / Source method: obtained synthetically / Formula: C41H78O12S
#21: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: Photosystem I-IsiA supercomplex / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Synechococcus elongatus PCC 7942 (bacteria) / Strain: PCC 7942
Buffer solutionpH: 7.5
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63332 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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