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- PDB-4y28: The structure of plant photosystem I super-complex at 2.8 angstro... -

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Basic information

Entry
Database: PDB / ID: 4y28
TitleThe structure of plant photosystem I super-complex at 2.8 angstrom resolution.
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 7
  • Light-harvesting complex I chlorophyll A/B-binding protein
  • Photosystem I iron-sulfur center
  • Putative uncharacterized protein
  • Type II chlorophyll a/b binding protein from photosystem I
  • photosystem I reaction center
KeywordsPHOTOSYNTHESIS / light harvesting / antenna / reaction center
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 / membrane => GO:0016020 / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Single helix bin / 4Fe-4S dicluster domain / Photosystem I PsaH, reaction centre subunit VI ...Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Single helix bin / 4Fe-4S dicluster domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / SH3 type barrels. - #50 / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / 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 PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / 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 / Alpha-Beta Plaits - #20 / 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. / Helicase, Ruva Protein; domain 3 / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-ZEX / Photosystem I reaction center subunit VI / PSI-K / Photosystem I reaction center subunit III / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II, chloroplastic / PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / 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 / SAD / Resolution: 2.8 Å
AuthorsMazor, Y. / Brovikov, A. / Nelson, N.
CitationJournal: Elife / Year: 2015
Title: The structure of plant photosystem I super-complex at 2.8 angstrom resolution.
Authors: Mazor, Y. / Borovikova, A. / Nelson, N.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Derived calculations / Structure summary
Category: database_PDB_caveat / entity ...database_PDB_caveat / entity / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description
Revision 1.3Sep 19, 2018Group: Data collection
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source
Revision 1.4Apr 24, 2019Group: Advisory / Data collection / Source and taxonomy
Category: database_PDB_caveat / entity_src_nat ...database_PDB_caveat / entity_src_nat / pdbx_seq_map_depositor_info / pdbx_validate_chiral
Item: _entity_src_nat.pdbx_ncbi_taxonomy_id / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
F: Photosystem I reaction center subunit III
G: photosystem I reaction center
L: Putative uncharacterized protein
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II, chloroplastic
E: Photosystem I reaction center subunit IV A, chloroplastic
H: Photosystem I reaction center subunit VI
K: Photosystem I reaction center subunit X psaK
2: Type II chlorophyll a/b binding protein from photosystem I
4: Chlorophyll a-b binding protein P4, chloroplastic
1: Light-harvesting complex I chlorophyll A/B-binding protein
3: Chlorophyll a-b binding protein 3, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)554,633225
Polymers384,49916
Non-polymers170,134209
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90030 Å2
ΔGint-658 kcal/mol
Surface area172670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.000, 201.900, 213.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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

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


Mass: 84328.562 Da / Num. of mol.: 1 / Fragment: UNP residues 17-758 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P05310, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 82503.039 Da / Num. of mol.: 1 / Fragment: UNP residues 2-733 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P05311, photosystem I

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Photosystem I reaction center subunit ... , 7 types, 7 molecules IJFDEHK

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


Mass: 3296.041 Da / Num. of mol.: 1 / Fragment: UNP residues 3-32 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P17227
#4: Protein/peptide Photosystem I reaction center subunit IX / / PSI-J


Mass: 4733.593 Da / Num. of mol.: 1 / Fragment: UNP residues 2-42 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: D5MAL3
#5: Protein Photosystem I reaction center subunit III / / Uncharacterized protein


Mass: 17256.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0M3KL12*PLUS
#9: Protein Photosystem I reaction center subunit II, chloroplastic / / Photosystem I 20 kDa subunit / PSI-D


Mass: 16419.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K8*PLUS
#10: Protein Photosystem I reaction center subunit IV A, chloroplastic / / PSI-E A


Mass: 7509.449 Da / Num. of mol.: 1 / Fragment: UNP residues 1-64 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K6*PLUS
#11: Protein Photosystem I reaction center subunit VI / / Uncharacterized protein


Mass: 9692.042 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0M3KL10*PLUS
#12: Protein Photosystem I reaction center subunit X psaK /


Mass: 13320.767 Da / Num. of mol.: 1 / Fragment: UNP residues 2-80 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0M3KL11*PLUS

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Protein , 5 types, 5 molecules GLC21

#6: Protein photosystem I reaction center /


Mass: 10439.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0M3KL13*PLUS
#7: Protein Putative uncharacterized protein


Mass: 17781.295 Da / Num. of mol.: 1 / Fragment: UNP residues 3-161 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L1*PLUS
#8: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8991.474 Da / Num. of mol.: 1 / Fragment: UNP residues 2-81 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P10793, photosystem I
#13: Protein Type II chlorophyll a/b binding protein from photosystem I


Mass: 28911.773 Da / Num. of mol.: 1 / Fragment: UNP residues 59-264 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q41038
#15: Protein Light-harvesting complex I chlorophyll A/B-binding protein / Uncharacterized protein


Mass: 22383.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L2*PLUS

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Chlorophyll a-b binding protein ... , 2 types, 2 molecules 43

#14: Protein Chlorophyll a-b binding protein P4, chloroplastic / LHCI type III CAB-P4


Mass: 27297.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9SQL2
#16: Protein Chlorophyll a-b binding protein 3, chloroplastic / LHCII type III CAB-3


Mass: 29634.801 Da / Num. of mol.: 1 / Fragment: UNP residues 58-272 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q32904

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Sugars , 2 types, 3 molecules

#25: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15
#26: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 11 types, 206 molecules

#17: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#18: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 146 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#19: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#20: 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
#21: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#22: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C40H56
#23: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C45H86O10
#24: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#27: 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.: 10 / Source method: obtained synthetically / Formula: C40H56O2
#28: Chemical
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#29: Chemical ChemComp-ZEX / (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O2

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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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.75
Details: 30mM Tris-Hcl pH8.75, 50mM KH2PO4, 0.03% Octyl Glucose Neopentyl Glycol, 14% PEG400, 2mM glutathione
PH range: 8-8.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.74 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 2.8→74.1 Å / Num. all: 200218 / Num. obs: 200218 / % possible obs: 99.99 % / Redundancy: 74.1 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 13.4
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 33.4 % / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 1.4 / % possible all: 98.4

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→48.646 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 32.33 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 3929 1.98 %random
Rwork0.2588 194047 --
obs0.259 197976 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 584.44 Å2 / Biso mean: 98.1935 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.8→48.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24722 0 10847 0 35569
Biso mean--97.36 --
Num. residues----3173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00437623
X-RAY DIFFRACTIONf_angle_d2.00653597
X-RAY DIFFRACTIONf_chiral_restr0.144653
X-RAY DIFFRACTIONf_plane_restr0.0116385
X-RAY DIFFRACTIONf_dihedral_angle_d25.90314774
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8-2.83420.46591490.424268547003
2.8342-2.870.42111550.405969007055
2.87-2.90780.43361210.39768466967
2.9078-2.94760.37531320.376268887020
2.9476-2.98970.3441530.366668557008
2.9897-3.03430.3821440.358168416985
3.0343-3.08170.34061270.346969037030
3.0817-3.13230.36961460.332868787024
3.1323-3.18630.31681570.318368537010
3.1863-3.24420.30861230.312868967019
3.2442-3.30660.31071420.304668887030
3.3066-3.3740.33071340.297168947028
3.374-3.44740.3271200.287169057025
3.4474-3.52760.26191370.270468937030
3.5276-3.61580.28211320.258969227054
3.6158-3.71350.26731450.261468797024
3.7135-3.82270.23941360.252969207056
3.8227-3.9460.26211400.245669487088
3.946-4.0870.28011310.237969127043
4.087-4.25060.2871310.23169217052
4.2506-4.44390.24031290.223169637092
4.4439-4.6780.20581350.216869537088
4.678-4.97080.24971420.217969667108
4.9708-5.35420.22541450.22369717116
5.3542-5.89220.26541320.242570287160
5.8922-6.74290.24561920.236369717163
6.7429-8.48790.21971390.216370957234
8.4879-48.65330.23041600.255373047464
Refinement TLS params.Method: refined / Origin x: 14.9211 Å / Origin y: 7.8237 Å / Origin z: 64.3676 Å
111213212223313233
T0.5384 Å20.0947 Å2-0.1488 Å2-0.4526 Å20.0541 Å2--0.5249 Å2
L0.7307 °2-0.0096 °20.0138 °2-1.3439 °2-0.0386 °2--0.9482 °2
S-0.0394 Å °-0.1202 Å °0.1239 Å °-0.0382 Å °0.0628 Å °0.2445 Å °-0.067 Å °0.0067 Å °0.1233 Å °
Refinement TLS groupSelection details: ALL and not water

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