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- PDB-8hq8: Bry-LHCII homotrimer of Bryopsis corticulans -

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Basic information

Entry
Database: PDB / ID: 8hq8
TitleBry-LHCII homotrimer of Bryopsis corticulans
Componentssiphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
KeywordsPHOTOSYNTHESIS / Light-harvesting complexes / siphonaxanthin / siphonein
Function / homologySiphonaxanthin / Siphonein / TRIMETHYL GLYCINE / CHLOROPHYLL B / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-NEX
Function and homology information
Biological speciesBryopsis corticulans (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, Z.H. / Shen, J.R. / Wang, W.D.
Funding support China, 9items
OrganizationGrant numberCountry
Chinese Academy of Sciences2019YFA0906300 China
Chinese Academy of Sciences2021YFA1300403 China
Chinese Academy of SciencesXDA26050402 China
Chinese Academy of SciencesXDB17000000 China
Chinese Academy of Sciences2020081 China
Chinese Academy of SciencesJCTD-2020-06 China
Chinese Academy of SciencesYSBR-004 China
Chinese Academy of Sciences31970260 China
Chinese Academy of Sciences32222007 China
CitationJournal: Structure / Year: 2023
Title: Structural and functional properties of different types of siphonous LHCII trimers from an intertidal green alga Bryopsis corticulans.
Authors: Zhenhua Li / Cuicui Zhou / Songhao Zhao / Jinyang Zhang / Xueyang Liu / Min Sang / Xiaochun Qin / Yanyan Yang / Guangye Han / Tingyun Kuang / Jian-Ren Shen / Wenda Wang /
Abstract: Light-harvesting complexes of photosystem II (LHCIIs) in green algae and plants are vital antenna apparatus for light harvesting, energy transfer, and photoprotection. Here we determined the ...Light-harvesting complexes of photosystem II (LHCIIs) in green algae and plants are vital antenna apparatus for light harvesting, energy transfer, and photoprotection. Here we determined the structure of a siphonous-type LHCII trimer from the intertidal green alga Bryopsis corticulans by X-ray crystallography and cryo-electron microscopy (cryo-EM), and analyzed its functional properties by spectral analysis. The Bryopsis LHCII (Bry-LHCII) structures in both homotrimeric and heterotrimeric form show that green light-absorbing siphonaxanthin and siphonein occupied the sites of lutein and violaxanthin in plant LHCII, and two extra chlorophylls (Chls) b replaced Chls a. Binding of these pigments expands the blue-green light absorption of B. corticulans in the tidal zone. We observed differences between the Bry-LHCII homotrimer crystal and cryo-EM structures, and also between Bry-LHCII homotrimer and heterotrimer cryo-EM structures. These conformational changes may reflect the flexibility of Bry-LHCII, which may be required to adapt to light fluctuations from tidal rhythms.
History
DepositionDec 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
B: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
C: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
D: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
E: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
F: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,922135
Polymers160,1776
Non-polymers101,746129
Water73941
1
A: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
B: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
C: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,21971
Polymers80,0883
Non-polymers52,13168
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area74680 Å2
ΔGint-591 kcal/mol
Surface area27200 Å2
MethodPISA
2
D: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
E: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
F: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,70364
Polymers80,0883
Non-polymers49,61561
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area72830 Å2
ΔGint-587 kcal/mol
Surface area26880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.720, 91.610, 169.220
Angle α, β, γ (deg.)90.00, 103.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 11 molecules ABCDEF

#1: Protein
siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1


Mass: 26696.133 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#4: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 10 types, 165 molecules

#2: Chemical
ChemComp-0IE / Siphonaxanthin


Mass: 600.870 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#3: 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.: 6 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-0UR / Siphonein


Mass: 781.157 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C52H76O5 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-BET / TRIMETHYL GLYCINE / Trimethylglycine


Mass: 118.154 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12NO2
#11: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.16 Å3/Da / Density % sol: 76.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: HEPES, PEG 1000, magnesium chloride,betaine, Cymal3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 68491 / % possible obs: 94.29 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Net I/σ(I): 13.84
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.062 / Num. unique obs: 1284

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Processing

Software
NameVersionClassification
PHENIX(1.18_3861: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→39.9 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 1954 2.94 %
Rwork0.2071 --
obs0.2083 66574 66.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10051 0 6388 41 16480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02117474
X-RAY DIFFRACTIONf_angle_d1.23323553
X-RAY DIFFRACTIONf_dihedral_angle_d20.5595893
X-RAY DIFFRACTIONf_chiral_restr0.0531874
X-RAY DIFFRACTIONf_plane_restr0.0053062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.5349260.3972842X-RAY DIFFRACTION12
2.67-2.740.35330.30371104X-RAY DIFFRACTION16
2.74-2.820.3601430.2961415X-RAY DIFFRACTION20
2.82-2.910.4493570.30581882X-RAY DIFFRACTION27
2.91-3.010.3144710.2822385X-RAY DIFFRACTION34
3.01-3.130.28581000.2673264X-RAY DIFFRACTION47
3.13-3.280.29861580.25695223X-RAY DIFFRACTION75
3.28-3.450.29842040.22026772X-RAY DIFFRACTION98
3.45-3.660.2622090.20286918X-RAY DIFFRACTION99
3.66-3.950.21852080.17856874X-RAY DIFFRACTION99
3.95-4.340.21892100.16476939X-RAY DIFFRACTION99
4.34-4.970.22232090.17346938X-RAY DIFFRACTION99
4.97-6.260.24362110.21976976X-RAY DIFFRACTION99
6.26-39.90.25492150.22737088X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 52.5265 Å / Origin y: 58.2831 Å / Origin z: 123.0319 Å
111213212223313233
T0.5083 Å20.3034 Å20.0404 Å2-0.1464 Å20.0762 Å2--0.3251 Å2
L6.0911 °2-0.2568 °2-0.2629 °2-0.5791 °20.0438 °2--0.8551 °2
S-0.0215 Å °-0.0832 Å °0.3012 Å °0.192 Å °0.0483 Å °-0.0237 Å °0.0678 Å °0.051 Å °-0.02 Å °
Refinement TLS groupSelection details: all

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