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- PDB-7ymm: PSII-Pcb Tetramer of Acaryochloris Marina -

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Basic information

Entry
Database: PDB / ID: 7ymm
TitlePSII-Pcb Tetramer of Acaryochloris Marina
Components
  • (High light inducible ...) x 4
  • (Photosystem II ...) x 14
  • Cytochrome b559 subunit alpha
  • Unknown protein
KeywordsPHOTOSYNTHESIS / Photosystem II / Pcb
Function / homology
Function and homology information


photosystem / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / plasma membrane-derived thylakoid membrane ...photosystem / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthetic electron transport in photosystem II / photosynthesis / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbY / Photosystem II PsbX, type 1 subfamily / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) ...Photosystem II PsbY / Photosystem II PsbX, type 1 subfamily / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II CP43 reaction centre protein / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / 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 reaction centre protein H superfamily / 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 / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Chem-8CT / BICARBONATE ION / CHLOROPHYLL D / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / Chem-PL9 ...Chem-8CT / BICARBONATE ION / CHLOROPHYLL D / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Chem-ZEX / Photosystem II protein D1 2 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II D2 protein 1 / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein Y / High light inducible protein / High light inducible protein / High light inducible protein / Photosystem II protein PsbI / Photosystem II protein PsbT / High light inducible protein / Photosystem II reaction center protein L / Cytochrome b559 subunit alpha / Photosystem II reaction center protein K / Photosystem II 10 kDa phosphoprotein PsbH / Photosystem II reaction center protein M / Photosystem II CP47 reaction center protein
Similarity search - Component
Biological speciesAcaryochloris marina MBIC11017 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsShen, L.L. / Gao, Y.Z. / Wang, W.D. / Zhang, X. / Shen, J.R. / Wang, P.Y. / Han, G.Y.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDY-SSW-SMC003 China
Chinese Academy of SciencesXDB17000000 China
National Basic Research Program of China (973 Program)2015CB150100 China
CitationJournal: To Be Published
Title: Structure of a large photosystem II supercomplex from Acaryochloris marina.
Authors: Shen, L.L. / Gao, Y.Z. / Wang, W.D. / Zhang, X. / Shen, J.R. / Wang, P.Y. / Han, G.Y.
History
DepositionJul 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1A: Photosystem II protein D1 2
1B: Photosystem II CP47 reaction center protein
1C: Photosystem II CP43 reaction center protein
1D: Photosystem II D2 protein 1
1E: Cytochrome b559 subunit alpha
1F: Photosystem II protein Y
1H: Photosystem II 10 kDa phosphoprotein PsbH
1I: Photosystem II protein PsbI
1K: Photosystem II reaction center protein K
1L: Photosystem II reaction center protein L
1M: Photosystem II reaction center protein M
1T: Photosystem II reaction center protein T
1X: Photosystem II reaction center X protein
1Y: Photosystem II reaction center protein Ycf12
1Z: Photosystem II reaction center protein Z
12: High light inducible protein
1G: Unknown protein
11: High light inducible protein
13: High light inducible protein
14: High light inducible protein
2A: Photosystem II protein D1 2
2B: Photosystem II CP47 reaction center protein
2C: Photosystem II CP43 reaction center protein
2D: Photosystem II D2 protein 1
2E: Cytochrome b559 subunit alpha
2F: Photosystem II protein Y
2H: Photosystem II 10 kDa phosphoprotein PsbH
2I: Photosystem II protein PsbI
2K: Photosystem II reaction center protein K
2L: Photosystem II reaction center protein L
2M: Photosystem II reaction center protein M
2T: Photosystem II reaction center protein T
2X: Photosystem II reaction center X protein
2Y: Photosystem II reaction center protein Ycf12
2Z: Photosystem II reaction center protein Z
22: High light inducible protein
2G: Unknown protein
21: High light inducible protein
23: High light inducible protein
24: High light inducible protein
3A: Photosystem II protein D1 2
3B: Photosystem II CP47 reaction center protein
3C: Photosystem II CP43 reaction center protein
3D: Photosystem II D2 protein 1
3E: Cytochrome b559 subunit alpha
3F: Photosystem II protein Y
3H: Photosystem II 10 kDa phosphoprotein PsbH
3I: Photosystem II protein PsbI
3K: Photosystem II reaction center protein K
3L: Photosystem II reaction center protein L
3M: Photosystem II reaction center protein M
3T: Photosystem II reaction center protein T
3X: Photosystem II reaction center X protein
3Y: Photosystem II reaction center protein Ycf12
3Z: Photosystem II reaction center protein Z
32: High light inducible protein
3G: Unknown protein
31: High light inducible protein
33: High light inducible protein
34: High light inducible protein
4A: Photosystem II protein D1 2
4B: Photosystem II CP47 reaction center protein
4C: Photosystem II CP43 reaction center protein
4D: Photosystem II D2 protein 1
4E: Cytochrome b559 subunit alpha
4F: Photosystem II protein Y
4H: Photosystem II 10 kDa phosphoprotein PsbH
4I: Photosystem II protein PsbI
4K: Photosystem II reaction center protein K
4L: Photosystem II reaction center protein L
4M: Photosystem II reaction center protein M
4T: Photosystem II reaction center protein T
4X: Photosystem II reaction center X protein
4Y: Photosystem II reaction center protein Ycf12
4Z: Photosystem II reaction center protein Z
42: High light inducible protein
4G: Unknown protein
41: High light inducible protein
43: High light inducible protein
44: High light inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,158,031704
Polymers1,650,17280
Non-polymers507,858624
Water00
1


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

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Components

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Photosystem II ... , 14 types, 56 molecules 1A2A3A4A1B2B3B4B1C2C3C4C1D2D3D4D1F2F3F4F1H2H3H4H1I2I3I4I1K2K...

#1: Protein
Photosystem II protein D1 2 / PSII D1 protein 2 / Photosystem II Q(B) protein 2


Mass: 39695.211 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: A5A8K9, photosystem II
#2: Protein
Photosystem II CP47 reaction center protein


Mass: 56518.746 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0CFM2
#3: Protein
Photosystem II CP43 reaction center protein


Mass: 53978.320 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C1V7
#4: Protein
Photosystem II D2 protein 1 / PSII D2 protein 1 / Photosystem Q(A) protein 1


Mass: 39291.852 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C1V6, photosystem II
#6: Protein
Photosystem II protein Y


Mass: 11277.320 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C2V2
#7: Protein
Photosystem II 10 kDa phosphoprotein PsbH


Mass: 7683.901 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0CDZ2
#8: Protein/peptide
Photosystem II protein PsbI


Mass: 3948.692 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C5R5
#9: Protein/peptide
Photosystem II reaction center protein K / PSII-K


Mass: 4939.008 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6Z7
#10: Protein/peptide
Photosystem II reaction center protein L / PSII-L


Mass: 4254.045 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6T1
#11: Protein/peptide
Photosystem II reaction center protein M / PSII-M


Mass: 3614.302 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0CFM0
#12: Protein/peptide
Photosystem II reaction center protein T


Mass: 5442.383 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C605
#13: Protein/peptide
Photosystem II reaction center X protein


Mass: 4443.303 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0BYW9
#14: Protein/peptide
Photosystem II reaction center protein Ycf12


Mass: 4015.932 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria)
#15: Protein
Photosystem II reaction center protein Z / PSII-Z


Mass: 6395.632 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C0S7

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High light inducible ... , 4 types, 16 molecules 12223242112131411323334314243444

#16: Protein
High light inducible protein / Light harvesting chlorophyll d-binding protein 2 (PcbA)


Mass: 38753.934 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C3E5
#18: Protein
High light inducible protein / Light harvesting chlorophyll d-binding protein 1 (PcbA)


Mass: 38612.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C576
#19: Protein
High light inducible protein / Light harvesting chlorophyll d-binding protein 3 (PcbA)


Mass: 38707.781 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6I0
#20: Protein
High light inducible protein / Light harvesting chlorophyll d-binding protein 4 (PcbC)


Mass: 37967.473 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C3E6

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Protein / Protein/peptide / Sugars , 3 types, 16 molecules 1E2E3E4E1G2G3G4G

#17: Protein/peptide
Unknown protein


Mass: 3507.314 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria)
#27: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION
#5: Protein
Cytochrome b559 subunit alpha / PSII reaction center subunit V / PsbE


Mass: 9495.788 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6T2

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Non-polymers , 11 types, 616 molecules

#21: Chemical...
ChemComp-CL7 / CHLOROPHYLL D


Mass: 895.462 Da / Num. of mol.: 424 / Source method: obtained synthetically / Formula: C54H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C55H74N4O5 / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical...
ChemComp-8CT / (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene


Mass: 536.873 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#25: 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.: 28 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#28: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#30: 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 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical...
ChemComp-ZEX / (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: PSII-Pcb Tetramer of Acaryochloris Marina / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Buffer solutionpH: 6.5
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132346 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00871866
ELECTRON MICROSCOPYf_angle_d1.055100892
ELECTRON MICROSCOPYf_dihedral_angle_d20.0823108
ELECTRON MICROSCOPYf_chiral_restr0.0919290
ELECTRON MICROSCOPYf_plane_restr0.00512792

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