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- PDB-6pnj: Structure of Photosystem I Acclimated to Far-red Light -

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Basic information

Entry
Database: PDB / ID: 6pnj
TitleStructure of Photosystem I Acclimated to Far-red Light
Components
  • (Photosystem I ...) x 11
  • Photosystem one PsaX
KeywordsPHOTOSYNTHESIS / trimeric alpha helical complex
Function / homology
Function and homology information


: / thylakoid membrane / 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 ...: / thylakoid membrane / 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 / endomembrane system / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI ...Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / Single helix bin / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / SH3 type barrels. - #50 / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / 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 / Alpha-Beta Plaits - #20 / 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 PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / 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 / Helicase, Ruva Protein; domain 3 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
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 protein 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 protein subunit XI / Uncharacterized protein / Uncharacterized protein / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit IV / Photosystem one PsaX / Photosystem I reaction center subunit PsaK / 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: 3.19 Å
AuthorsGisriel, C.J. / Shen, G. / Kurashov, V. / Ho, M. / Zhang, S. / Williams, D. / Golbeck, J.H. / Fromme, P. / Bryant, D.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1613022 United States
National Science Foundation (NSF, United States)1531991 United States
Department of Energy (DOE, United States)DE-SC 0001035 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41-GM103311 United States
CitationJournal: Sci Adv / Year: 2020
Title: The structure of Photosystem I acclimated to far-red light illuminates an ecologically important acclimation process in photosynthesis.
Authors: Christopher Gisriel / Gaozhong Shen / Vasily Kurashov / Ming-Yang Ho / Shangji Zhang / Dewight Williams / John H Golbeck / Petra Fromme / Donald A Bryant /
Abstract: Phototrophic organisms are superbly adapted to different light environments but often must acclimate to challenging competition for visible light wavelengths in their niches. Some cyanobacteria ...Phototrophic organisms are superbly adapted to different light environments but often must acclimate to challenging competition for visible light wavelengths in their niches. Some cyanobacteria overcome this challenge by expressing paralogous photosynthetic proteins and by synthesizing and incorporating ~8% chlorophyll f into their Photosystem I (PSI) complexes, enabling them to grow under far-red light (FRL). We solved the structure of FRL-acclimated PSI from the cyanobacterium PCC 7521 by single-particle, cryo-electron microscopy to understand its structural and functional differences. Four binding sites occupied by chlorophyll f are proposed. Subtle structural changes enable FRL-adapted PSI to extend light utilization for oxygenic photosynthesis to nearly 800 nm. This structure provides a platform for understanding FRL-driven photosynthesis and illustrates the robustness of adaptive and acclimation mechanisms in nature.
History
DepositionJul 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 2.0Feb 26, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 3.0Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral / refine
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _refine.ls_d_res_high / _refine.ls_d_res_low

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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 protein PsaD
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center protein PsaF subunit III
G: Photosystem I P700 chlorophyll a apoprotein A1
H: Photosystem I P700 chlorophyll a apoprotein A2
I: photosystem I subunit VIII
J: Photosystem I reaction centre subunit IX / PsaJ
K: photosystem I reaction center subunit PsaK
L: Photosystem I reaction center protein subunit XI
M: Photosystem I reaction center subunit XII
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: Photosystem I reaction center protein subunit XI
V: Photosystem I reaction center subunit XII
W: Photosystem one PsaX
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: Photosystem I reaction center protein subunit XI
m: Photosystem I reaction center subunit XII
x: Photosystem one PsaX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,115,867408
Polymers820,50236
Non-polymers295,365372
Water00
1


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

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Components

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Photosystem I ... , 11 types, 33 molecules AGaBHbCNcDOdEPeFQfIRiJSjKTkLUl...

#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, UniProt: G6FMF0*PLUS, 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, UniProt: A0A2N6M8S7*PLUS
#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: 3615.425 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Fischerella thermalis PCC 7521 (bacteria) / References: UniProt: G6FV28
#10: Protein Photosystem I reaction center protein 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: A0A2N6M3Z9, UniProt: G6FMF1*PLUS
#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 / Sugars , 2 types, 9 molecules WXx

#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
#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.: 12 / Source method: obtained synthetically / Formula: C55H68MgN4O6
#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.: 63 / 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

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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 from far-red light-adapted Fischerella thermalis PCC 7521
Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Source (natural)Organism: Fischerella thermalis PCC 7521 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1300 mMtricineC6H13NO51
250 mMsodium chlorideNaCl1
30.02 %BDDM1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

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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: 1.5252 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.refine1.16_3549refinement
PHENIX1.16_3549refinement
EM software
IDNameVersionCategory
2SerialEM3.7image acquisition
4Gctf1.06CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178666 / Symmetry type: POINT
RefinementResolution: 3.19→3.19 Å / SU ML: 0.9762 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 44.0042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3845 1994 0.04 %
Rwork0.3914 4868372 -
obs0.3914 4870366 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.23 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0175438
ELECTRON MICROSCOPYf_angle_d1.92106725
ELECTRON MICROSCOPYf_chiral_restr0.07949558
ELECTRON MICROSCOPYf_plane_restr0.012212768
ELECTRON MICROSCOPYf_dihedral_angle_d27.849429226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.55771440.5435348767ELECTRON MICROSCOPY100
3.28-3.370.54031440.5333348698ELECTRON MICROSCOPY100
3.37-3.470.51641560.5167346889ELECTRON MICROSCOPY100
3.47-3.580.45911320.4898347726ELECTRON MICROSCOPY100
3.58-3.710.44291440.4584348122ELECTRON MICROSCOPY100
3.71-3.860.39171110.4193347330ELECTRON MICROSCOPY100
3.86-4.030.36311440.3727348382ELECTRON MICROSCOPY100
4.03-4.240.32161440.3336347776ELECTRON MICROSCOPY100
4.24-4.510.31641440.3011348159ELECTRON MICROSCOPY100
4.51-4.860.27071440.2931347568ELECTRON MICROSCOPY99.99
4.86-5.350.32421430.2992347688ELECTRON MICROSCOPY99.96
5.35-6.120.31831440.3273348078ELECTRON MICROSCOPY100
6.12-7.710.30651440.3108347676ELECTRON MICROSCOPY100
7.71-427.770.23151560.2675345513ELECTRON MICROSCOPY99.34

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