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Entry
Database: PDB / ID: 2o01
TitleThe Structure of a plant photosystem I supercomplex at 3.4 Angstrom resolution
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 9
  • AT3g54890
  • PSI light-harvesting antenna chlorophyll a/b-binding protein
  • PSI type III chlorophyll a/b-binding protein
  • Photosystem I iron-sulfur center
  • Photosystem I-N subunit
  • Type II chlorophyll a/b binding protein from photosystem I
KeywordsPHOTOSYNTHESIS / Membranal Super Complex
Function / homology
Function and homology information


chloroplast photosystem I / response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / thylakoid / chloroplast thylakoid lumen / photosynthesis, light harvesting / chloroplast envelope ...chloroplast photosystem I / response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / thylakoid / chloroplast thylakoid lumen / photosynthesis, light harvesting / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / response to cold / chloroplast / phosphoprotein binding / 4 iron, 4 sulfur cluster binding / molecular adaptor activity / electron transfer activity / oxidoreductase activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding / nucleus / plasma membrane
Similarity search - Function
Chlorophyll a-b binding protein like / Single helix bin / Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / 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; ...Chlorophyll a-b binding protein like / Single helix bin / Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / 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 / GTP Cyclohydrolase I; Chain A, domain 1 / Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / Single helix bin / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / SH3 type barrels. - #50 / 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 / Alpha-Beta Plaits - #20 / 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 PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / 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 / Helicase, Ruva Protein; domain 3 / 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 / 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 A / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic ...BETA-CAROTENE / CHLOROPHYLL A / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VI, chloroplastic / Chlorophyll a-b binding protein 6, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit N, chloroplastic / Photosystem I reaction center subunit IV A, chloroplastic / Chlorophyll a-b binding protein P4, chloroplastic / Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
Spinacia oleracea (spinach)
Arabidopsis thaliana (thale cress)
Phaseolus vulgaris (common bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsAmunts, A. / Drory, O. / Nelson, N.
CitationJournal: Nature / Year: 2007
Title: The structure of a plant photosystem I supercomplex at 3.4 A resolution.
Authors: Amunts, A. / Drory, O. / Nelson, N.
History
DepositionNov 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2012Group: Non-polymer description
Revision 2.0Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _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_atom_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Structure summary
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z
Remark 650HELIX determination method: author determined
Remark 700SHEET determination method: author determined
Remark 750TURN determination method: author determined
Remark 999SEQUENCE Sequence for Chain K was modeled as ALA due to poor electron density, therefore alignment ...SEQUENCE Sequence for Chain K was modeled as ALA due to poor electron density, therefore alignment is unclear and residues in coordinates were labeled as UNK. Proper sequence is LGAKCDFIGSSTNLIMVTSTTLMLFAGRFGLAPSANRKATAGLRLEARDSGLQ TGDPAGFTLADTLACGTVGHIIGVGVVLGLKNIGAI

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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
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II, chloroplast
E: Photosystem I reaction center subunit IV A, chloroplast
F: Photosystem I reaction center subunit III, chloroplast
G: Photosystem I reaction center subunit V, chloroplast
H: Photosystem I reaction center subunit VI, chloroplast
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit psaK, chloroplast
L: Photosystem I reaction center subunit XI, chloroplast
N: Photosystem I-N subunit
1: AT3g54890
2: Type II chlorophyll a/b binding protein from photosystem I
3: PSI type III chlorophyll a/b-binding protein
4: PSI light-harvesting antenna chlorophyll a/b-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)504,246195
Polymers349,49917
Non-polymers154,747178
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.054, 188.784, 127.518
Angle α, β, γ (deg.)90.00, 95.19, 90.00
Int Tables number4
Space group name H-MP1211

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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 / PsaA / PSI-A


Mass: 83669.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Strain: alaska / References: UniProt: P05310
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB / PSI-B


Mass: 82226.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P05311

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Protein , 6 types, 6 molecules CN1234

#3: Protein Photosystem I iron-sulfur center / Photosystem I subunit VII / 9 kDa polypeptide / PSI-C / PsaC


Mass: 8860.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P10793
#13: Protein Photosystem I-N subunit


Mass: 9767.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (common bean) / References: UniProt: Q84U30
#14: Protein AT3g54890 / Chlorophyll A/B-binding protein / At3g54890/F28P10_130


Mass: 20415.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q01667
#15: Protein Type II chlorophyll a/b binding protein from photosystem I


Mass: 20580.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q41038
#16: Protein PSI type III chlorophyll a/b-binding protein


Mass: 17929.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SY97
#17: Protein PSI light-harvesting antenna chlorophyll a/b-binding protein


Mass: 18561.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9SQL2

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Photosystem I reaction center subunit ... , 9 types, 9 molecules DEFGHIJKL

#4: Protein Photosystem I reaction center subunit II, chloroplast / Photosystem I 20 kDa subunit / PSI-D


Mass: 15553.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12353
#5: Protein Photosystem I reaction center subunit IV A, chloroplast / PSI-E A


Mass: 7127.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S831
#6: Protein Photosystem I reaction center subunit III, chloroplast / Light-harvesting complex I 17 kDa protein / PSI-F


Mass: 17299.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12355
#7: Protein Photosystem I reaction center subunit V, chloroplast / PSI-G / Photosystem I 9 kDa protein


Mass: 10518.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12357
#8: Protein Photosystem I reaction center subunit VI, chloroplast / PSI- H / Light-harvesting complex I 11 kDa protein


Mass: 8143.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P22179
#9: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3270.042 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P17227
#10: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4845.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P17230
#11: Protein/peptide Photosystem I reaction center subunit psaK, chloroplast


Mass: 3252.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#12: Protein Photosystem I reaction center subunit XI, chloroplast / PSI- L / PSI subunit V


Mass: 17479.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q41385

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Non-polymers , 4 types, 178 molecules

#18: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 168 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#19: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#20: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H56
#21: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.33 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.875 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.875 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 70551 / % possible obs: 91.1 % / Observed criterion σ(F): 3.4 / Observed criterion σ(I): 3.4 / Redundancy: 3.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.41
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.4 / Num. unique all: 6034 / % possible all: 78.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 1QZV

1qzv


Resolution: 3.4→40 Å / Cor.coef. Fo:Fc: 0.778 / Cor.coef. Fo:Fc free: 0.707 / SU B: 34.519 / SU ML: 0.625 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.975 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.409 3516 5 %RANDOM
Rwork0.348 ---
obs0.351 70551 90.85 %-
all-69817 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å22.78 Å2
2--0.74 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 3.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23599 0 6247 0 29846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02131845
X-RAY DIFFRACTIONr_angle_refined_deg4.1012.22245477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.28453024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.94623.2851032
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.622153623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.58815103
X-RAY DIFFRACTIONr_chiral_restr0.2160.23853
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0231360
X-RAY DIFFRACTIONr_nbd_refined0.3880.224775
X-RAY DIFFRACTIONr_nbtor_refined0.3340.219001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3370.21577
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4110.2238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.212
X-RAY DIFFRACTIONr_mcbond_it0.5631.515464
X-RAY DIFFRACTIONr_mcangle_it0.878224032
X-RAY DIFFRACTIONr_scbond_it1.334352416
X-RAY DIFFRACTIONr_scangle_it1.6974.521073
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 190 -
Rwork0.292 4106 -
obs-4296 75.93 %

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