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- PDB-5xno: Structure of M-LHCII and CP24 complexes in the unstacked C2S2M2-t... -

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Entry
Database: PDB / ID: 5xno
TitleStructure of M-LHCII and CP24 complexes in the unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Components
  • (Chlorophyll a-b binding ...) x 2
  • Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24
KeywordsMEMBRANE PROTEIN / Photosystem II / M-LHCII and CP24 complexes / PSII-LHCII / C2S2M2 supercomplex
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / metal ion binding
Similarity search - Function
Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-LUT / Chem-NEX / Chem-XAT / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein 8, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSu, X.D. / Ma, J. / Wei, X.P. / Cao, P. / Zhu, D.J. / Chang, W.R. / Liu, Z.F. / Zhang, X.Z. / Li, M.
Funding support China, 4items
OrganizationGrant numberCountry
The Strategic Priority Research Program of CASXDB08020302 China
The Key Research Program of Frontier Sciences of CASQYZDB-SSW-SMC005 China
National 973 project grant2011CBA00900 China
National Natural Science Foundation of China31570724 and 31270793 China
CitationJournal: Science / Year: 2017
Title: Structure and assembly mechanism of plant CSM-type PSII-LHCII supercomplex.
Authors: Xiaodong Su / Jun Ma / Xuepeng Wei / Peng Cao / Dongjie Zhu / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li /
Abstract: In plants, the photosynthetic machinery photosystem II (PSII) consists of a core complex associated with variable numbers of light-harvesting complexes II (LHCIIs). The supercomplex, comprising a ...In plants, the photosynthetic machinery photosystem II (PSII) consists of a core complex associated with variable numbers of light-harvesting complexes II (LHCIIs). The supercomplex, comprising a dimeric core and two strongly bound and two moderately bound LHCIIs (CSM), is the dominant form in plants acclimated to limited light. Here we report cryo-electron microscopy structures of two forms of CSM (termed stacked and unstacked) from at 2.7- and 3.2-angstrom resolution, respectively. In each CSM, the moderately bound LHCII assembles specifically with a peripheral antenna complex CP24-CP29 heterodimer and the strongly bound LHCII, to establish a pigment network that facilitates light harvesting at the periphery and energy transfer into the core. The high mobility of peripheral antennae, including the moderately bound LHCII and CP24, provides insights into functional regulation of plant PSII.
History
DepositionMay 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Structure summary
Category: cell / database_PDB_caveat ...cell / database_PDB_caveat / em_entity_assembly / em_software / pdbx_validate_chiral
Item: _cell.Z_PDB / _cell.length_a ..._cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _em_entity_assembly.entity_id_list / _em_software.name
Revision 2.0Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _chem_comp.formula / _chem_comp.pdbx_synonyms ..._chem_comp.formula / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
1: Chlorophyll a-b binding protein 8, chloroplastic
2: Chlorophyll a-b binding protein 8, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
4: Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,60276
Polymers99,3084
Non-polymers59,29372
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area88430 Å2
ΔGint-897 kcal/mol
Surface area38190 Å2

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Components

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Chlorophyll a-b binding ... , 2 types, 3 molecules 123

#1: Protein Chlorophyll a-b binding protein 8, chloroplastic / LHCII type I CAB-8


Mass: 24952.113 Da / Num. of mol.: 2 / Fragment: UNP residues 37-268 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P27490
#2: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 26545.240 Da / Num. of mol.: 1 / Fragment: UNP residues 23-265 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q04918

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Protein , 1 types, 1 molecules 4

#3: Protein Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24


Mass: 22858.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A2D0TCJ3*PLUS

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Non-polymers , 7 types, 72 molecules

#4: Chemical...
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#5: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#6: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN / Lutein


Mass: 568.871 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C40H56O2
#7: Chemical
ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN / Violaxanthin


Mass: 600.870 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56O4
#8: Chemical ChemComp-NEX / (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL / 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H56O4
#9: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#10: Chemical ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56

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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: M-LHCII and CP24 complexes in the unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Pisum sativum (garden pea)
Buffer solutionpH: 7.5
SpecimenConc.: 3 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 FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2747: / Classification: refinement
EM software
IDNameCategory
7Chimeramodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50237 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01110674
ELECTRON MICROSCOPYf_angle_d3.41915419
ELECTRON MICROSCOPYf_dihedral_angle_d15.1125110
ELECTRON MICROSCOPYf_chiral_restr0.1191238
ELECTRON MICROSCOPYf_plane_restr0.0091991

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