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- PDB-7o01: Dimeric Photosystem I of a temperature sensitive mutant Chlamydom... -

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Basic information

Entry
Database: PDB / ID: 7o01
TitleDimeric Photosystem I of a temperature sensitive mutant Chlamydomonas reinhardtii
Components
  • (Chlorophyll a-b binding protein, ...) x 9
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 7
  • PSI subunit V
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / chlamydomonas / photosystem I / temperature sensitive / water molecules
Function / homology
Function and homology information


chloroplast thylakoid lumen / photosynthesis, light harvesting / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chloroplast thylakoid membrane / chlorophyll binding ...chloroplast thylakoid lumen / photosynthesis, light harvesting / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chloroplast thylakoid membrane / chlorophyll binding / response to light stimulus / 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 V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / 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 center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / 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 / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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
Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein, chloroplastic / PSI subunit V / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit IX ...Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein, chloroplastic / PSI subunit V / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 17.1 Å
AuthorsCaspy, I. / Nelson, N.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
German-Israeli Foundation for Research and DevelopmentG-1483-207/2018 Israel
CitationJournal: Commun Biol / Year: 2021
Title: Dimeric and high-resolution structures of Chlamydomonas Photosystem I from a temperature-sensitive Photosystem II mutant.
Authors: Ido Caspy / Tom Schwartz / Vinzenz Bayro-Kaiser / Mariia Fadeeva / Amit Kessel / Nir Ben-Tal / Nathan Nelson /
Abstract: Water molecules play a pivotal functional role in photosynthesis, primarily as the substrate for Photosystem II (PSII). However, their importance and contribution to Photosystem I (PSI) activity ...Water molecules play a pivotal functional role in photosynthesis, primarily as the substrate for Photosystem II (PSII). However, their importance and contribution to Photosystem I (PSI) activity remains obscure. Using a high-resolution cryogenic electron microscopy (cryo-EM) PSI structure from a Chlamydomonas reinhardtii temperature-sensitive photoautotrophic PSII mutant (TSP4), a conserved network of water molecules - dating back to cyanobacteria - was uncovered, mainly in the vicinity of the electron transport chain (ETC). The high-resolution structure illustrated that the water molecules served as a ligand in every chlorophyll that was missing a fifth magnesium coordination in the PSI core and in the light-harvesting complexes (LHC). The asymmetric distribution of the water molecules near the ETC branches modulated their electrostatic landscape, distinctly in the space between the quinones and FX. The data also disclosed the first observation of eukaryotic PSI oligomerisation through a low-resolution PSI dimer that was comprised of PSI-10LHC and PSI-8LHC.
History
DepositionMar 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release

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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, chloroplastic
E: Photosystem I reaction center subunit IV, chloroplastic
F: Photosystem I reaction center subunit III, chloroplastic
G: Photosystem I reaction center subunit V, chloroplastic
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit psaK, chloroplastic
L: PSI subunit V
1: Chlorophyll a-b binding protein, chloroplastic
Z: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
7: Chlorophyll a-b binding protein, chloroplastic
8: Chlorophyll a-b binding protein, chloroplastic
4: Chlorophyll a-b binding protein, chloroplastic
5: Chlorophyll a-b binding protein, chloroplastic
6: Chlorophyll a-b binding protein, chloroplastic
2: Chlorophyll a-b binding protein, chloroplastic
9: Chlorophyll a-b binding protein, chloroplastic
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, chloroplastic
e: Photosystem I reaction center subunit IV, chloroplastic
f: Photosystem I reaction center subunit III, chloroplastic
g: Photosystem I reaction center subunit V, chloroplastic
i: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
k: Photosystem I reaction center subunit psaK, chloroplastic
l: PSI subunit V
p: Chlorophyll a-b binding protein, chloroplastic
z: Chlorophyll a-b binding protein, chloroplastic
q: Chlorophyll a-b binding protein, chloroplastic
r: Chlorophyll a-b binding protein, chloroplastic
s: Chlorophyll a-b binding protein, chloroplastic
t: Chlorophyll a-b binding protein, chloroplastic
u: Chlorophyll a-b binding protein, chloroplastic
v: Chlorophyll a-b binding protein, chloroplastic


Theoretical massNumber of molelcules
Total (without water)918,44240
Polymers918,44240
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area93270 Å2
ΔGint-563 kcal/mol
Surface area447340 Å2
MethodPISA

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 4 molecules AaBb

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


Mass: 82121.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12154, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 81996.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P09144, photosystem I

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Protein , 2 types, 4 molecules CcLl

#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8738.130 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q00914, photosystem I
#11: Protein PSI subunit V


Mass: 14130.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IL32

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Photosystem I reaction center subunit ... , 7 types, 14 molecules DdEeFfGgIiJjKk

#4: Protein Photosystem I reaction center subunit II, chloroplastic / Photosystem I 20 kDa subunit / PSI-D


Mass: 16152.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39615
#5: Protein Photosystem I reaction center subunit IV, chloroplastic / PSI-E / P30 protein / Photosystem I 8.1 kDa protein


Mass: 7021.877 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12352
#6: Protein Photosystem I reaction center subunit III, chloroplastic / Light-harvesting complex I 17 kDa protein / P21 protein / PSI-F


Mass: 17957.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12356
#7: Protein Photosystem I reaction center subunit V, chloroplastic / Light-harvesting complex I 10 kDa protein / P35 protein / PSI-G


Mass: 9572.677 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P14224
#8: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 3970.731 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IFG7
#9: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4516.257 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P59777
#10: Protein Photosystem I reaction center subunit psaK, chloroplastic / Light-harvesting complex I 8.4 kDa protein / P37 protein / PSI-K / Photosystem I subunit X


Mass: 8146.467 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P14225

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Chlorophyll a-b binding protein, ... , 9 types, 18 molecules 1Zpz3q7r8s4t5u6v29

#12: Protein
Chlorophyll a-b binding protein, chloroplastic


Mass: 20368.023 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q7DM26
#13: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23689.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY9
#14: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23304.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q84Y02
#15: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23293.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY7
#16: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23018.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VZ0
#17: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 25122.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY8
#18: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24937.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY6
#19: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 21658.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IKC8
#20: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 19929.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8S567

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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 of temperature sensitive Chlamydomonas reinhardtii
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.89 MDa / Experimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 8
SpecimenEmbedding 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 / Nominal magnification: 165000 X
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 46.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 12418

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.1_4122refinement
PHENIX1.19.1_4122refinement
EM software
IDNameVersionCategory
1RELION3.0.7particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
10RELION3.0.7initial Euler assignment
11RELION3.0.7final Euler assignment
12RELIONclassification
13RELION3.0.73D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1208518
3D reconstructionResolution: 17.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5707 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6JO5

6jo5

RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 999.99 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004666547
ELECTRON MICROSCOPYf_angle_d0.767390660
ELECTRON MICROSCOPYf_chiral_restr0.04959689
ELECTRON MICROSCOPYf_plane_restr0.005911655
ELECTRON MICROSCOPYf_dihedral_angle_d13.253923088

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