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- PDB-7dkz: Structure of plant photosystem I-light harvesting complex I super... -

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Basic information

Entry
Database: PDB / ID: 7dkz
TitleStructure of plant photosystem I-light harvesting complex I supercomplex
Components
  • (Chlorophyll a-b binding protein ...Light-harvesting complexes of green plants) x 2
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 2
  • Chlorophyll a-b binding protein, chloroplastic
  • Lhca1
  • PSI-F
  • PSI-K
  • Photosystem I iron-sulfur center
  • PsaD
  • PsaE
  • PsaG
  • PsaH
  • PsaL
KeywordsPHOTOSYNTHESIS / PSI-LHCI high plants
Function / homology
Function and homology information


chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis ...chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily ...4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit IV / PSI-K / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein 3, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein P4, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.393 Å
AuthorsWang, J. / Yu, L.J. / Wang, W.
CitationJournal: J Integr Plant Biol / Year: 2021
Title: Structure of plant photosystem I-light harvesting complex I supercomplex at 2.4 angstrom resolution.
Authors: Wang, J. / Yu, L.J. / Wang, W. / Yan, Q. / Kuang, T. / Qin, X. / Shen, J.R.
History
DepositionNov 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 21, 2021Group: Data collection / Database references / Non-polymer description
Category: chem_comp / citation / pdbx_validate_chiral
Item: _chem_comp.formula / _citation.journal_volume ..._chem_comp.formula / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Lhca1
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein 3, chloroplastic
4: Chlorophyll a-b binding protein P4, chloroplastic
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: PsaD
E: PsaE
F: PSI-F
G: PsaG
H: PsaH
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: PsaL
K: PSI-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)543,371231
Polymers372,52716
Non-polymers170,844215
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)225.652, 168.952, 185.224
Angle α, β, γ (deg.)90.000, 121.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 10 types, 10 molecules 12CDEFGHLK

#1: Protein Lhca1


Mass: 21477.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Tissue: leaf / Production host: Pisum sativum (garden pea)
#2: Protein Chlorophyll a-b binding protein, chloroplastic / Lhca2


Mass: 28912.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: lhaB / Production host: Pisum sativum (garden pea) / References: UniProt: Q41038
#7: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8991.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psaC, frxA / Production host: Pisum sativum (garden pea) / References: UniProt: P10793, photosystem I
#8: Protein PsaD


Mass: 16041.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea)
#9: Protein PsaE


Mass: 7479.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea) / References: UniProt: E1C9K6
#10: Protein PSI-F


Mass: 17238.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea) / References: UniProt: A0A0M3KL12
#11: Protein PsaG


Mass: 10678.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea)
#12: Protein PsaH


Mass: 9491.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea)
#15: Protein PsaL


Mass: 16564.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea)
#16: Protein PSI-K / PsaK / Photosystem I subunit X


Mass: 7988.296 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea) / References: UniProt: E1C9L3

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Chlorophyll a-b binding protein ... , 2 types, 2 molecules 34

#3: Protein Chlorophyll a-b binding protein 3, chloroplastic / Lhca3 / LHCII type III CAB-3


Mass: 29634.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: lhca3 / Production host: Pisum sativum (garden pea) / References: UniProt: Q32904
#4: Protein Chlorophyll a-b binding protein P4, chloroplastic / Lhca4 / LHCI type III CAB-P4


Mass: 21994.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: lhcA-P4 / Production host: Pisum sativum (garden pea) / References: UniProt: Q9SQL2

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#5: Protein Photosystem I P700 chlorophyll a apoprotein A1 / / PSI-A / PsaA


Mass: 84279.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psaA / Production host: Pisum sativum (garden pea) / References: UniProt: A0A0F6NFW5, photosystem I
#6: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 82512.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psaB / Production host: Pisum sativum (garden pea) / References: UniProt: A0A0F6NGI2, photosystem I

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Photosystem I reaction center subunit ... , 2 types, 2 molecules IJ

#13: Protein/peptide Photosystem I reaction center subunit VIII / / PSI-I


Mass: 4474.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psaI / Production host: Pisum sativum (garden pea) / References: UniProt: P17227
#14: Protein/peptide Photosystem I reaction center subunit IX / / PSI-J


Mass: 4767.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psaJ / Production host: Pisum sativum (garden pea) / References: UniProt: D5MAL3

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Sugars , 3 types, 12 molecules

#23: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#25: Sugar
ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#26: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 10 types, 296 molecules

#17: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 140 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#18: Chemical
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#19: 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.: 4 / Source method: obtained synthetically / Formula: C40H56O2
#20: 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
#21: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C40H56
#22: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#24: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#28: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#29: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 4.05 Å3/Da / Density % sol: 69.59 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: sodium chlotide, magnesium chloride, PEG 400 / PH range: 8.0-9.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→44.41 Å / Num. obs: 230250 / % possible obs: 98.84 % / Redundancy: 6.8 % / Biso Wilson estimate: 65.37 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.04 / Rrim(I) all: 0.11 / Net I/σ(I): 17.8
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 6.2 % / Num. unique obs: 21565 / CC1/2: 0.708 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XK8

4xk8


Resolution: 2.393→44.405 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 11603 5.04 %
Rwork0.189 218420 -
obs0.1909 230023 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 307.68 Å2 / Biso mean: 101.2191 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.393→44.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25009 0 10991 93 36093
Biso mean--102.45 77.66 -
Num. residues----3200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00838062
X-RAY DIFFRACTIONf_angle_d1.67654040
X-RAY DIFFRACTIONf_chiral_restr0.0764657
X-RAY DIFFRACTIONf_plane_restr0.0086697
X-RAY DIFFRACTIONf_dihedral_angle_d17.81218206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3932-2.42040.3383300.3065574279
2.4204-2.44890.33713640.31477383100
2.4489-2.47870.36544030.30517318100
2.4787-2.51010.31983810.2877730299
2.5101-2.54310.30874030.27967263100
2.5431-2.5780.29644050.26337364100
2.578-2.61480.30054070.2557322100
2.6148-2.65380.284150.24287303100
2.6538-2.69530.28033960.23547308100
2.6953-2.73950.29594080.23447273100
2.7395-2.78670.25623880.21947378100
2.7867-2.83740.25094240.2127309100
2.8374-2.89190.26383980.2047349100
2.8919-2.95090.25633570.20257370100
2.9509-3.01510.24613840.20567345100
3.0151-3.08520.28773920.21417325100
3.0852-3.16230.25673720.20397313100
3.1623-3.24780.24763850.19777364100
3.2478-3.34340.24333510.19737418100
3.3434-3.45120.2623820.20197331100
3.4512-3.57450.243730.18527326100
3.5745-3.71760.21013800.17937350100
3.7176-3.88670.20793920.17537336100
3.8867-4.09150.19983810.16937366100
4.0915-4.34760.19293780.1681732699
4.3476-4.68290.19063820.1667731099
4.6829-5.15360.20423930.168732999
5.1536-5.89780.22434400.1802732899
5.8978-7.4250.20543630.1705731798
7.425-44.4050.21723760.1853735298
Refinement TLS params.Method: refined / Origin x: 33.6643 Å / Origin y: 66.1507 Å / Origin z: 28.6623 Å
111213212223313233
T0.4627 Å20.0825 Å20.0257 Å2-0.5926 Å2-0.0416 Å2--0.4984 Å2
L0.7951 °2-0.0942 °20.1091 °2-0.4892 °20.0325 °2--0.394 °2
S-0.0477 Å °-0.3699 Å °-0.0704 Å °0.1592 Å °0.1478 Å °0.0545 Å °0.0252 Å °0.0825 Å °0.0133 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1all135 - 229
2X-RAY DIFFRACTION1all1301 - 404
3X-RAY DIFFRACTION1all252 - 255
4X-RAY DIFFRACTION1all2601 - 704
5X-RAY DIFFRACTION1all350 - 265
6X-RAY DIFFRACTION1all3301 - 403
7X-RAY DIFFRACTION1all453 - 709
8X-RAY DIFFRACTION1allA17 - 758
9X-RAY DIFFRACTION1allA801 - 933
10X-RAY DIFFRACTION1allB2 - 734
11X-RAY DIFFRACTION1allB801 - 954
12X-RAY DIFFRACTION1allC2 - 81
13X-RAY DIFFRACTION1allC101 - 103
14X-RAY DIFFRACTION1allD71 - 210
15X-RAY DIFFRACTION1allE1 - 63
16X-RAY DIFFRACTION1allF77 - 406
17X-RAY DIFFRACTION1allG2 - 96
18X-RAY DIFFRACTION1allG101 - 105
19X-RAY DIFFRACTION1allH56 - 143
20X-RAY DIFFRACTION1allI2 - 31
21X-RAY DIFFRACTION1allI101
22X-RAY DIFFRACTION1allJ1 - 39
23X-RAY DIFFRACTION1allJ3001 - 3004
24X-RAY DIFFRACTION1allL6 - 156
25X-RAY DIFFRACTION1allL201 - 301
26X-RAY DIFFRACTION1allK47 - 125
27X-RAY DIFFRACTION1allK201 - 205

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