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Yorodumi- PDB-5xnn: Structure of M-LHCII and CP24 complexes in the stacked C2S2M2-typ... -
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-Basic information
Entry | Database: PDB / ID: 5xnn | |||||||||||||||
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Title | Structure of M-LHCII and CP24 complexes in the stacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum | |||||||||||||||
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Keywords | MEMBRANE PROTEIN / Photosystem II / M-LHCII and CP24 complexes / PSII-LHCII / C2S2M2 supercomplex | |||||||||||||||
Function / homology | Function and homology information photosynthesis, light harvesting in photosystem II / PSII associated light-harvesting complex II / response to high light intensity / regulation of stomatal movement / plastoglobule / response to abscisic acid / photosynthesis, light harvesting in photosystem I / chloroplast envelope / photosystem I / response to herbicide ...photosynthesis, light harvesting in photosystem II / PSII associated light-harvesting complex II / response to high light intensity / regulation of stomatal movement / plastoglobule / response to abscisic acid / photosynthesis, light harvesting in photosystem I / chloroplast envelope / photosystem I / response to herbicide / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / protein domain specific binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Pisum sativum (garden pea) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
Authors | Su, 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
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Citation | Journal: 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 |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 5xnn.cif.gz | 253 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xnn.ent.gz | 208.3 KB | Display | PDB format |
PDBx/mmJSON format | 5xnn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xnn_validation.pdf.gz | 4.7 MB | Display | wwPDB validaton report |
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Full document | 5xnn_full_validation.pdf.gz | 4.9 MB | Display | |
Data in XML | 5xnn_validation.xml.gz | 65.5 KB | Display | |
Data in CIF | 5xnn_validation.cif.gz | 78.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/5xnn ftp://data.pdbj.org/pub/pdb/validation_reports/xn/5xnn | HTTPS FTP |
-Related structure data
Related structure data | 6743MC 6741C 6742C 6744C 5xnlC 5xnmC 5xnoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Chlorophyll a-b binding ... , 2 types, 3 molecules 123
#1: Protein | 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 | | 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 | 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 / #5: Chemical | ChemComp-CLA / #6: Chemical | ChemComp-LUT / ( #7: Chemical | ChemComp-XAT / ( #8: Chemical | #9: Chemical | ChemComp-LHG / #10: Chemical | ChemComp-BCR / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: M-LHCII and CP24 complexes in the stacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL |
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Source (natural) | Organism: Pisum sativum (garden pea) |
Buffer solution | pH: 5.7 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_2747: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136521 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||
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