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- PDB-7liz: LR6 rod linker and scaffolded phycoerythrin beta subunits from th... -

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Basic information

Entry
Database: PDB / ID: 7liz
TitleLR6 rod linker and scaffolded phycoerythrin beta subunits from the phycobilisome of Porphyridium purpureum
Components
  • B-phycoerythrin beta chain
  • LR6
KeywordsPHOTOSYNTHESIS / linker / phycobilisome / PBS / light harvesting / red algae / scaffolding
Function / homology
Function and homology information


phycobilisome / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanins / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like / Globin-like superfamily ...Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanins / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHYCOERYTHROBILIN / Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod / B-phycoerythrin beta chain
Similarity search - Component
Biological speciesPorphyridium purpureum (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRathbone, H.W. / Landsberg, M.J. / Michie, K.A. / Green, B.R. / Curmi, P.M.G.
Funding support Australia, United States, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP180103964 Australia
Australian Research Council (ARC)LIEF190100165 Australia
Department of Defense (DOD, United States)FA2386-17-1-4101 United States
CitationJournal: Nature / Year: 2020
Title: Structural basis of energy transfer in Porphyridium purpureum phycobilisome.
Authors: Jianfei Ma / Xin You / Shan Sun / Xiaoxiao Wang / Song Qin / Sen-Fang Sui /
Abstract: Photosynthetic organisms have developed various light-harvesting systems to adapt to their environments. Phycobilisomes are large light-harvesting protein complexes found in cyanobacteria and red ...Photosynthetic organisms have developed various light-harvesting systems to adapt to their environments. Phycobilisomes are large light-harvesting protein complexes found in cyanobacteria and red algae, although how the energies of the chromophores within these complexes are modulated by their environment is unclear. Here we report the cryo-electron microscopy structure of a 14.7-megadalton phycobilisome with a hemiellipsoidal shape from the red alga Porphyridium purpureum. Within this complex we determine the structures of 706 protein subunits, including 528 phycoerythrin, 72 phycocyanin, 46 allophycocyanin and 60 linker proteins. In addition, 1,598 chromophores are resolved comprising 1,430 phycoerythrobilin, 48 phycourobilin and 120 phycocyanobilin molecules. The markedly improved resolution of our structure compared with that of the phycobilisome of Griffithsia pacifica enabled us to build an accurate atomic model of the P. purpureum phycobilisome system. The model reveals how the linker proteins affect the microenvironment of the chromophores, and suggests that interactions of the aromatic amino acids of the linker proteins with the chromophores may be a key factor in fine-tuning the energy states of the chromophores to ensure the efficient unidirectional transfer of energy.
History
DepositionJan 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_entry_details.has_protein_modification
Remark 0THIS DEPOSITION 7LIZ PROVIDES A STRUCTURAL MODEL FOR PREVIOUSLY UNMODELED EM MAP DENSITY IN EMD- ...THIS DEPOSITION 7LIZ PROVIDES A STRUCTURAL MODEL FOR PREVIOUSLY UNMODELED EM MAP DENSITY IN EMD-9976. THIS IS NOT A REPLACEMENT, ONLY AN ADDITION. ORIGINAL AUTHORS OF EMD-9976 ARE SUI, S.F., MA, J.F., YOU, X., SUN, S.

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-9976
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  • Superimposition on EM map
  • EMDB-9976
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Structure viewerMolecule:
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Assembly

Deposited unit
A: LR6
B: B-phycoerythrin beta chain
C: B-phycoerythrin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9969
Polymers83,4643
Non-polymers3,5326
Water00
1


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

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Components

#1: Protein LR6


Mass: 46295.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: A0A5J4YMI8
#2: Protein B-phycoerythrin beta chain


Mass: 18584.182 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: P11393
#3: Chemical
ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H40N4O6
Has ligand of interestN
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: Phycobilisome / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Buffer solutionpH: 8
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: ice
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
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategoryDetails
13PHENIX1.18model refinementreal.space.refine used for refinement
14Coot0.8.9.2model refinementmodel building
15ISOLDE1.1model refinementmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191825 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDPdb chain residue range
14LMX

4lmx

B4LMX11-30
23V57

3v57

D3V57231-177
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 51.38 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01453773
ELECTRON MICROSCOPYf_angle_d0.95215136
ELECTRON MICROSCOPYf_chiral_restr0.0518576
ELECTRON MICROSCOPYf_plane_restr0.0042648
ELECTRON MICROSCOPYf_dihedral_angle_d15.04841349

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