5L8R

The structure of plant photosystem I super-complex at 2.6 angstrom resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6ZXS


Literature

Structure of the plant photosystem I supercomplex at 2.6 angstrom resolution.

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

(2017) Nat Plants 3: 17014-17014

  • DOI: 10.1038/nplants.2017.14
  • Primary Citation of Related Structures:  
    5L8R

  • PubMed Abstract: 
  • Four elaborate membrane complexes carry out the light reaction of oxygenic photosynthesis. Photosystem I (PSI) is one of two large reaction centres responsible for converting light photons into the chemical energy needed to sustain life. In the thylakoid membranes of plants, PSI is found together with its integral light-harvesting antenna, light-harvesting complex I (LHCI), in a membrane supercomplex containing hundreds of light-harvesting pigments ...

    Four elaborate membrane complexes carry out the light reaction of oxygenic photosynthesis. Photosystem I (PSI) is one of two large reaction centres responsible for converting light photons into the chemical energy needed to sustain life. In the thylakoid membranes of plants, PSI is found together with its integral light-harvesting antenna, light-harvesting complex I (LHCI), in a membrane supercomplex containing hundreds of light-harvesting pigments. Here, we report the crystal structure of plant PSI-LHCI at 2.6 Å resolution. The structure reveals the configuration of PsaK, a core subunit important for state transitions in plants, a conserved network of water molecules surrounding the electron transfer centres and an elaborate structure of lipids bridging PSI and its LHCI antenna. We discuss the implications of the structure for energy transfer and the evolution of PSI.


    Organizational Affiliation

    Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lhca1A [auth 1]193Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L2 (Pisum sativum)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticB [auth 2]269Pisum sativumMutation(s): 0 
Gene Names: lhaB
Membrane Entity: Yes 
UniProt
Find proteins for Q41038 (Pisum sativum)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticC [auth 3]275Pisum sativumMutation(s): 0 
Gene Names: lhca3
Membrane Entity: Yes 
UniProt
Find proteins for Q32904 (Pisum sativum)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticD [auth 4]198Pisum sativumMutation(s): 0 
Gene Names: lhcA-P4
Membrane Entity: Yes 
UniProt
Find proteins for Q9SQL2 (Pisum sativum)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth A]758Pisum sativumMutation(s): 0 
Gene Names: psaApsaA1
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P05310 (Pisum sativum)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]734Pisum sativumMutation(s): 0 
Gene Names: psaB
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A0F6NGI2 (Pisum sativum)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerG [auth C]81Pisum sativumMutation(s): 0 
Gene Names: psaCfrxA
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P10793 (Pisum sativum)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
PsaDH [auth D]143Pisum sativumMutation(s): 0 
UniProt
Find proteins for E1C9K8 (Pisum sativum)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized proteinI [auth E]66Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K6 (Pisum sativum)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIJ [auth F]154Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL12 (Pisum sativum)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
PsaGK [auth G]97Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9S7N7 (Arabidopsis thaliana)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIL [auth H]88Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL10 (Pisum sativum)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth I]40Pisum sativumMutation(s): 0 
Gene Names: psaI
Membrane Entity: Yes 
UniProt
Find proteins for P17227 (Pisum sativum)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXN [auth J]42Pisum sativumMutation(s): 0 
Gene Names: psaJ
Membrane Entity: Yes 
UniProt
Find proteins for D5MAL3 (Pisum sativum)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaKO [auth K]80Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized proteinP [auth L]157Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L1 (Pisum sativum)
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  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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EF [auth B], FH [auth B], II [auth J], WC [auth 4], WH [auth G]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CHL (Subject of Investigation/LOI)
Query on CHL

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AB [auth 2] , BA [auth 1] , DA [auth 1] , KA [auth 1] , KB [auth 2] , QC [auth 4] , RC [auth 4] , TC [auth 4] , 
AB [auth 2], BA [auth 1], DA [auth 1], KA [auth 1], KB [auth 2], QC [auth 4], RC [auth 4], TC [auth 4], UC [auth 4], WA [auth 2], XA [auth 2], YB [auth 3], ZA [auth 2]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
 Ligand Interaction
CL0 (Subject of Investigation/LOI)
Query on CL0

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AD [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
 Ligand Interaction
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth 1] , AC [auth 3] , AE [auth A] , AG [auth B] , AI [auth H] , BC [auth 3] , BD [auth A] , BE [auth A] , 
AA [auth 1], AC [auth 3], AE [auth A], AG [auth B], AI [auth H], BC [auth 3], BD [auth A], BE [auth A], BF [auth A], BG [auth B], CA [auth 1], CD [auth A], CE [auth A], CF [auth A], CG [auth B], DD [auth A], DE [auth A], DG [auth B], DI [auth J], EA [auth 1], ED [auth A], EE [auth A], EG [auth B], EI [auth J], FA [auth 1], FD [auth A], FE [auth A], FG [auth B], GD [auth A], GE [auth A], GF [auth B], GG [auth B], HC [auth 4], HD [auth A], HE [auth A], HF [auth B], HG [auth B], HI [auth J], IC [auth 4], ID [auth A], IE [auth A], IF [auth B], IG [auth B], JC [auth 4], JD [auth A], JE [auth A], JF [auth B], JG [auth B], KC [auth 4], KD [auth A], KE [auth A], KF [auth B], KG [auth B], LC [auth 4], LD [auth A], LE [auth A], LF [auth B], LG [auth B], LH [auth F], MC [auth 4], MD [auth A], ME [auth A], MF [auth B], MG [auth B], MH [auth F], MI [auth K], NC [auth 4], ND [auth A], NE [auth A], NF [auth B], NG [auth B], NI [auth K], OA [auth 2], OC [auth 4], OD [auth A], OE [auth A], OF [auth B], OG [auth B], OI [auth K], PA [auth 2], PB [auth 3], PC [auth 4], PD [auth A], PE [auth A], PF [auth B], PG [auth B], PI [auth K], QA [auth 2], QB [auth 3], QD [auth A], QF [auth B], QG [auth B], QH [auth G], RA [auth 2], RB [auth 3], RD [auth A], RF [auth B], RG [auth B], RH [auth G], RI [auth L], SA [auth 2], SB [auth 3], SC [auth 4], SD [auth A], SF [auth B], SH [auth G], T [auth 1], TA [auth 2], TB [auth 3], TD [auth A], TF [auth B], TH [auth G], TI [auth L], U [auth 1], UA [auth 2], UB [auth 3], UD [auth A], UF [auth B], UI [auth L], V [auth 1], VA [auth 2], VB [auth 3], VC [auth 4], VD [auth A], VF [auth B], VI [auth L], W [auth 1], WB [auth 3], WD [auth A], WF [auth B], X [auth 1], XB [auth 3], XD [auth A], XF [auth B], Y [auth 1], YA [auth 2], YD [auth A], YF [auth B], Z [auth 1], ZB [auth 3], ZD [auth A], ZF [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
LMG (Subject of Investigation/LOI)
Query on LMG

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CB [auth 2] , DB [auth 2] , EB [auth 2] , FB [auth 2] , FI [auth J] , GB [auth 2] , GI [auth J] , HA [auth 1] , 
CB [auth 2], DB [auth 2], EB [auth 2], FB [auth 2], FI [auth J], GB [auth 2], GI [auth J], HA [auth 1], IA [auth 1], IB [auth 2], JB [auth 2], NH [auth F], OH [auth F], UE [auth A], VG [auth B], VH [auth G], WG [auth B], YC [auth 4], ZC [auth 4], ZH [auth G]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
LHG (Subject of Investigation/LOI)
Query on LHG

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AF [auth A], BB [auth 2], GA [auth 1], JA [auth 1], SE [auth A], TG [auth B], UG [auth B]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
XAT (Subject of Investigation/LOI)
Query on XAT

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GC [auth 4], MA [auth 2](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
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
 Ligand Interaction
ZEX (Subject of Investigation/LOI)
Query on ZEX

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KH [auth F](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
LUT (Subject of Investigation/LOI)
Query on LUT

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FC [auth 4], LA [auth 2], LB [auth 3], LI [auth J], MB [auth 3], Q [auth 1], R [auth 1](3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
 Ligand Interaction
BCR (Subject of Investigation/LOI)
Query on BCR

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AH [auth B] , BH [auth B] , BI [auth I] , CH [auth B] , CI [auth I] , DF [auth A] , DH [auth B] , EC [auth 4] , 
AH [auth B], BH [auth B], BI [auth I], CH [auth B], CI [auth I], DF [auth A], DH [auth B], EC [auth 4], EH [auth B], FF [auth B], HH [auth B], KI [auth J], NA [auth 2], NB [auth 3], OB [auth 3], PH [auth F], QI [auth K], S [auth 1], SI [auth L], UH [auth G], VE [auth A], WE [auth A], WI [auth L], XE [auth A], XI [auth L], YE [auth A], ZE [auth A]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT (Subject of Investigation/LOI)
Query on LMT

Download Ideal Coordinates CCD File 
CC [auth 3] , GH [auth B] , HB [auth 2] , JI [auth J] , TE [auth A] , XC [auth 4] , XG [auth B] , XH [auth G] , 
CC [auth 3], GH [auth B], HB [auth 2], JI [auth J], TE [auth A], XC [auth 4], XG [auth B], XH [auth G], YG [auth B], YH [auth G]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
PQN (Subject of Investigation/LOI)
Query on PQN

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RE [auth A], SG [auth B]PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
SF4
Query on SF4

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IH [auth C], JH [auth C], QE [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
DC [auth 3], ZG [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.611α = 90
b = 200.994β = 90
c = 212.943γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilIsrael293579
ISFIsrael71/14
I-COREIsrael1775/12

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Structure summary
  • Version 1.2: 2017-11-29
    Changes: Database references
  • Version 1.3: 2019-04-24
    Changes: Advisory, Author supporting evidence, Data collection