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- PDB-8eqm: Structure of a dimeric photosystem II complex acclimated to far-r... -

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Entry
Database: PDB / ID: 8eqm
TitleStructure of a dimeric photosystem II complex acclimated to far-red light
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 13
  • Cytochrome c-550
KeywordsPHOTOSYNTHESIS / Far-red / photosystem II / cyanobacteria / chlorophyll
Function / homology
Function and homology information


photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II / extrinsic component of membrane / chlorophyll binding ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II / extrinsic component of membrane / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / : / phosphate ion binding / photosynthesis, light reaction / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like ...Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL D / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll F / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL D / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll F / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / (3R)-beta,beta-caroten-3-ol / Chem-SQD / Photosystem II reaction center protein T / Photosystem II extrinsic protein V / Cytochrome b559 subunit alpha / Photosystem II reaction center protein L / Photosystem II reaction center protein X / Photosystem II 10 kDa phosphoprotein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II extrinsic protein O / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II extrinsic protein U / Photosystem II reaction center protein K
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7335 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGisriel, C.J. / Shen, G. / Flesher, D.A. / Kurashov, V. / Golbeck, J.H. / Brudvig, G.W. / Amin, M. / Bryant, D.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM140174 United States
National Science Foundation (NSF, United States)MCB-1613022 United States
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
CitationJournal: J Biol Chem / Year: 2023
Title: Structure of a dimeric photosystem II complex from a cyanobacterium acclimated to far-red light.
Authors: Christopher J Gisriel / Gaozhong Shen / David A Flesher / Vasily Kurashov / John H Golbeck / Gary W Brudvig / Muhamed Amin / Donald A Bryant /
Abstract: Photosystem II (PSII) is the water-splitting enzyme central to oxygenic photosynthesis. To drive water oxidation, light is harvested by accessory pigments, mostly chlorophyll (Chl) a molecules, which ...Photosystem II (PSII) is the water-splitting enzyme central to oxygenic photosynthesis. To drive water oxidation, light is harvested by accessory pigments, mostly chlorophyll (Chl) a molecules, which absorb visible light (400-700 nm). Some cyanobacteria facultatively acclimate to shaded environments by altering their photosynthetic machinery to additionally absorb far-red light (FRL, 700-800 nm), a process termed far-red light photoacclimation or FaRLiP. During far-red light photoacclimation, FRL-PSII is assembled with FRL-specific isoforms of the subunits PsbA, PsbB, PsbC, PsbD, and PsbH, and some Chl-binding sites contain Chls d or f instead of the usual Chl a. The structure of an apo-FRL-PSII monomer lacking the FRL-specific PsbH subunit has previously been determined, but visualization of the dimeric complex has remained elusive. Here, we report the cryo-EM structure of a dimeric FRL-PSII complex. The site assignments for Chls d and f are consistent with those assigned in the previous apo-FRL-PSII monomeric structure. All sites that bind Chl d or Chl f at high occupancy exhibit a FRL-specific interaction of the formyl moiety of the Chl d or Chl f with the protein environment, which in some cases involves a phenylalanine sidechain. The structure retains the FRL-specific PsbH2 subunit, which appears to alter the energetic landscape of FRL-PSII, redirecting energy transfer from the phycobiliprotein complex to a Chl f molecule bound by PsbB2 that acts as a bridge for energy transfer to the electron transfer chain. Collectively, these observations extend our previous understanding of the structure-function relationship that allows PSII to function using lower energy FRL.
History
DepositionOct 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 25, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem II protein D1
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Photosystem II manganese-stabilizing polypeptide
T: Photosystem II reaction center protein T
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
X: Photosystem II reaction center X protein
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Photosystem II manganese-stabilizing polypeptide
t: Photosystem II reaction center protein T
u: Photosystem II 12 kDa extrinsic protein
v: Cytochrome c-550
x: Photosystem II reaction center X protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)702,028164
Polymers601,92932
Non-polymers100,099132
Water10,629590
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 II ... , 13 types, 26 molecules AaBbCcDdHhIiKkLlMmOoTtUuXx

#1: Protein Photosystem II protein D1


Mass: 39958.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56440.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKI1
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa proteinPSII 43 kDa protein / Protein CP-43


Mass: 52375.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKI2
#4: Protein Photosystem II D2 protein / Photosystem Q(A) protein


Mass: 39596.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKI3
#7: Protein Photosystem II reaction center protein H


Mass: 7247.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKI0
#8: Protein/peptide Photosystem II reaction center protein I / PSII 4.4 kDa protein


Mass: 4229.917 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WM03
#9: Protein/peptide Photosystem II reaction center protein K


Mass: 5069.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WR12
#10: Protein/peptide Photosystem II reaction center protein L


Mass: 4566.261 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WII3
#11: Protein/peptide Photosystem II reaction center protein M


Mass: 3980.772 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
#12: Protein Photosystem II manganese-stabilizing polypeptide


Mass: 29319.096 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKJ1
#13: Protein/peptide Photosystem II reaction center protein T


Mass: 3606.362 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: A0A2W4UG77
#14: Protein Photosystem II 12 kDa extrinsic protein / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 17325.834 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WMT5
#16: Protein/peptide Photosystem II reaction center X protein


Mass: 4273.182 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WIZ7

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#5: Protein Cytochrome b559 subunit alpha / PSII reaction center subunit V


Mass: 9136.276 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WII1
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 5023.960 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WKJ2

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Protein , 1 types, 2 molecules Vv

#15: Protein Cytochrome c-550 / Low-potential cytochrome c


Mass: 18814.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WI32

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Sugars , 2 types, 8 molecules

#28: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C51H96O15
#33: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 16 types, 714 molecules

#17: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#18: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#19: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#20: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#21: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#22: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C40H56
#23: 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.: 4 / Source method: obtained synthetically / Formula: C41H78O12S
#24: Chemical
ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#25: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#26: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#27: 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.: 8 / Source method: obtained synthetically / Formula: C55H68MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical ChemComp-CL7 / CHLOROPHYLL D


Mass: 895.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C54H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10
#31: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#32: Chemical ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O
#34: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: Far-red light-acclimated photosystem II / Type: COMPLEX / Entity ID: #3, #1-#2, #4-#16 / Source: NATURAL
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Buffer solutionpH: 6.5
SpecimenConc.: 0.65 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 / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 41.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90191 / Symmetry type: POINT

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