4Y28

The structure of plant photosystem I super-complex at 2.8 angstrom resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of plant photosystem I super-complex at 2.8 angstrom resolution.

Mazor, Y.Borovikova, A.Nelson, N.

(2015) Elife 4: e07433-e07433

  • DOI: 10.7554/eLife.07433

  • PubMed Abstract: 
  • Most life forms on Earth are supported by solar energy harnessed by oxygenic photosynthesis. In eukaryotes, photosynthesis is achieved by large membrane-embedded super-complexes, containing reaction centers and connected antennae. Here, we report the ...

    Most life forms on Earth are supported by solar energy harnessed by oxygenic photosynthesis. In eukaryotes, photosynthesis is achieved by large membrane-embedded super-complexes, containing reaction centers and connected antennae. Here, we report the structure of the higher plant PSI-LHCI super-complex determined at 2.8 Å resolution. The structure includes 16 subunits and more than 200 prosthetic groups, which are mostly light harvesting pigments. The complete structures of the four LhcA subunits of LHCI include 52 chlorophyll a and 9 chlorophyll b molecules, as well as 10 carotenoids and 4 lipids. The structure of PSI-LHCI includes detailed protein pigments and pigment-pigment interactions, essential for the mechanism of excitation energy transfer and its modulation in one of nature's most efficient photochemical machines.


    Organizational Affiliation

    Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A1
A
758Pisum sativumMutation(s): 4 
Gene Names: psaA (psaA1)
EC: 1.97.1.12
Find proteins for P05310 (Pisum sativum)
Go to UniProtKB:  P05310
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A2
B
733Pisum sativumMutation(s): 7 
Gene Names: psaB (psaA2)
EC: 1.97.1.12
Find proteins for P05311 (Pisum sativum)
Go to UniProtKB:  P05311
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit VIII
I
30Pisum sativumMutation(s): 0 
Gene Names: psaI
Find proteins for P17227 (Pisum sativum)
Go to UniProtKB:  P17227
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit IX
J
42Pisum sativumMutation(s): 0 
Gene Names: psaJ
Find proteins for D5MAL3 (Pisum sativum)
Go to UniProtKB:  D5MAL3
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit III
F
154Pisum sativumMutation(s): 0 
Find proteins for A0A0M3KL12 (Pisum sativum)
Go to UniProtKB:  A0A0M3KL12
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
photosystem I reaction center
G
97Pisum sativumMutation(s): 0 
Find proteins for A0A0M3KL13 (Pisum sativum)
Go to UniProtKB:  A0A0M3KL13
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
L
167Pisum sativumMutation(s): 0 
Find proteins for E1C9L1 (Pisum sativum)
Go to UniProtKB:  E1C9L1
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem I iron-sulfur center
C
81Pisum sativumMutation(s): 0 
Gene Names: psaC (frxA)
EC: 1.97.1.12
Find proteins for P10793 (Pisum sativum)
Go to UniProtKB:  P10793
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit II, chloroplastic
D
147Pisum sativumMutation(s): 0 
Find proteins for E1C9K8 (Pisum sativum)
Go to UniProtKB:  E1C9K8
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit IV A, chloroplastic
E
66Pisum sativumMutation(s): 0 
Find proteins for E1C9K6 (Pisum sativum)
Go to UniProtKB:  E1C9K6
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit VI
H
90Pisum sativumMutation(s): 0 
Find proteins for A0A0M3KL10 (Pisum sativum)
Go to UniProtKB:  A0A0M3KL10
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit X psaK
K
129Pisum sativumMutation(s): 0 
Find proteins for A0A0M3KL11 (Pisum sativum)
Go to UniProtKB:  A0A0M3KL11
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Type II chlorophyll a/b binding protein from photosystem I
2
269Pisum sativumMutation(s): 1 
Gene Names: lhaB
Find proteins for Q41038 (Pisum sativum)
Go to UniProtKB:  Q41038
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Chlorophyll a-b binding protein P4, chloroplastic
4
252Pisum sativumMutation(s): 1 
Gene Names: lhcA-P4
Find proteins for Q9SQL2 (Pisum sativum)
Go to UniProtKB:  Q9SQL2
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Light-harvesting complex I chlorophyll A/B-binding protein
1
202Pisum sativumMutation(s): 0 
Find proteins for E1C9L2 (Pisum sativum)
Go to UniProtKB:  E1C9L2
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Chlorophyll a-b binding protein 3, chloroplastic
3
275Pisum sativumMutation(s): 0 
Gene Names: lhca3
Find proteins for Q32904 (Pisum sativum)
Go to UniProtKB:  Q32904
Small Molecules
Ligands 13 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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A, C
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PQN
Query on PQN

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A, B
PHYLLOQUINONE
VITAMIN K1; 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
LUT
Query on LUT

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1, 2, 3, 4, I
(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
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
 Ligand Interaction
CLA
Query on CLA

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1, 2, 3, 4, A, B, F, G, H, J, K, L
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
CL0
Query on CL0

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A
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
 Ligand Interaction
ZEX
Query on ZEX

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4
(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
C40 H56 O2
YRMDXLDAZBQLBK-WIHRHFSMSA-N
 Ligand Interaction
CA
Query on CA

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B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DGD
Query on DGD

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B
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
LMG
Query on LMG

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2, 4, B, F, G, J
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCR
Query on BCR

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Download CCD File 
3, A, B, F, G, I, J, K, L
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
CHL
Query on CHL

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1, 2, 3, 4
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-YFMFQLGVDX
 Ligand Interaction
LHG
Query on LHG

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Download CCD File 
1, 2, A, B
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
LMU
Query on LMU

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Download CCD File 
B
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.259 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 189.000α = 90.00
b = 201.900β = 90.00
c = 213.200γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-08-26
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Advisory, Derived calculations, Structure summary
  • Version 1.3: 2018-09-19
    Type: Data collection