4XK8

Crystal structure of plant photosystem I-LHCI super-complex at 2.8 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb4XK8/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Pisum sativum
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2015-01-10 Released: 2015-06-10 
• Deposition Author(s): Suga, M., Qin, X., Kuang, T., Shen, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Literature

Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex

Qin, X., Suga, M., Kuang, T., Shen, J.R.

(2015) Science 348: 989-995

• PubMed: 26023133 
• DOI: https://doi.org/10.1126/science.aab0214
• Primary Citation of Related Structures:  
  4XK8


• PubMed Abstract: 
  

  Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by a large light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core with extremely high efficiency. We report the structure of PSI-LHCI, a 600-kilodalton membrane protein supercomplex, from Pisum sativum (pea) at a resolution of 2.8 angstroms. The structure reveals the detailed arrangement of pigments and other cofactors—especially within LHCI—as well as numerous specific interactions between the PSI core and LHCI. These results provide a firm structural basis for our understanding on the energy transfer and photoprotection mechanisms within the PSI-LHCI supercomplex.

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Organizational Affiliation: 

Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China. Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, Tsushima Naka 3-1-1, Okayama 700-8530, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 16-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 16-mer - A4B2C1D1E1F1G1H1I1J1K1L1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 16-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 16-mer - A4B2C1D1E1F1G1H1I1J1K1L1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1,046.38 kDa 
• Atom Count: 71,157 
• Modelled Residue Count: 6,350 
• Deposited Residue Count: 6,434 
• Unique protein chains: 16

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A, Q [auth a]	742	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P05310 (Pisum sativum) Explore P05310  Go to UniProtKB:  P05310

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A2	B, R [auth b]	733	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P05311 (Pisum sativum) Explore P05311  Go to UniProtKB:  P05311

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I iron-sulfur center	C, S [auth c]	80	Pisum sativum	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P10793 (Pisum sativum) Explore P10793  Go to UniProtKB:  P10793

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	D, T [auth d]	141	Pisum sativum	Mutation(s): 0
UniProt
Find proteins for A5Z2K3 (Glycine max) Explore A5Z2K3  Go to UniProtKB:  A5Z2K3

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	E, U [auth e]	64	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for E1C9K6 (Pisum sativum) Explore E1C9K6  Go to UniProtKB:  E1C9K6

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit III, chloroplastic	F, V [auth f]	151	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12355 (Spinacia oleracea) Explore P12355  Go to UniProtKB:  P12355

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit V, chloroplastic	G, W [auth g]	95	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12357 (Spinacia oleracea) Explore P12357  Go to UniProtKB:  P12357

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	H, X [auth h]	90	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for C6T221 (Glycine max) Explore C6T221  Go to UniProtKB:  C6T221

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit VIII	I, Y [auth i]	30	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P17227 (Pisum sativum) Explore P17227  Go to UniProtKB:  P17227

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IX	J, Z [auth j]	39	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A4GGC6 (Phaseolus vulgaris) Explore A4GGC6  Go to UniProtKB:  A4GGC6

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit X psaK	AA [auth k], K	84	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for E1C9L3 (Pisum sativum) Explore E1C9L3  Go to UniProtKB:  E1C9L3

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	BA [auth l], L	153	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for E1C9L1 (Pisum sativum) Explore E1C9L1  Go to UniProtKB:  E1C9L1

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein 6, chloroplastic	CA [auth 6], M [auth 1]	195	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q01667 (Arabidopsis thaliana) Explore Q01667  Go to UniProtKB:  Q01667

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II chlorophyll a/b binding protein from photosystem I	DA [auth 7], N [auth 2]	206	Pisum sativum	Mutation(s): 0
UniProt
Find proteins for Q41038 (Pisum sativum) Explore Q41038  Go to UniProtKB:  Q41038

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein 3, chloroplastic	EA [auth 8], O [auth 3]	218	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q32904 (Pisum sativum) Explore Q32904  Go to UniProtKB:  Q32904

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein P4, chloroplastic	FA [auth 9], P [auth 4]	196	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q9SQL2 (Pisum sativum) Explore Q9SQL2  Go to UniProtKB:  Q9SQL2

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	HE [auth B], IM [auth b]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL	AH [auth 3], AP [auth 8], BI [auth 4], CG [auth 2], DO [auth 7], GG [auth 2], HG [auth 2], HO [auth 7], IG [auth 2], IO [auth 7], JF [auth 1], JO [auth 7], KN [auth 6], OF [auth 1], PG [auth 2], PN [auth 6], PP [auth 9], QO [auth 7], QP [auth 9], RH [auth 4], RP [auth 9], SH [auth 4], TH [auth 4], ZP [auth 9]	CHLOROPHYLL B C55 H70 Mg N4 O6 MWVCRINOIIOUAU-UYSPMESUSA-M
CLA	AB [auth A], AD [auth B], AF [auth K], AI [auth 4], AJ [auth a], AK [auth a], AL [auth b], AM [auth b], AN [auth k], BB [auth A], BD [auth B], BH [auth 3], BJ [auth a], BL [auth b], BP [auth 8], CB [auth A], CD [auth B], CH [auth 3], CJ [auth a], CL [auth b], CP [auth 8], DB [auth A], DD [auth B], DF [auth L], DG [auth 2], DH [auth 3], DJ [auth a], DL [auth b], DN [auth l], DP [auth 8], EB [auth A], ED [auth B], EF [auth L], EG [auth 2], EH [auth 3], EJ [auth a], EL [auth b], EN [auth l], EO [auth 7], EP [auth 8], FB [auth A], FD [auth B], FF [auth L], FG [auth 2], FH [auth 3], FJ [auth a], FL [auth b], FN [auth l], FO [auth 7], FP [auth 8], GA [auth A], GB [auth A], GD [auth B], GH [auth 3], GJ [auth a], GL [auth b], GO [auth 7], GP [auth 8], HA [auth A], HB [auth A], HC [auth A], HD [auth B], HH [auth 3], HI [auth a], HJ [auth a], HL [auth b], HP [auth 8], IA [auth A], IB [auth A], ID [auth B], IH [auth 3], II [auth a], IJ [auth a], IL [auth b], JA [auth A], JB [auth A], JD [auth B], JG [auth 2], JI [auth a], JJ [auth a], JL [auth b], KA [auth A], KB [auth A], KD [auth B], KE [auth F], KF [auth 1], KG [auth 2], KI [auth a], KJ [auth a], KK [auth a], KL [auth b], KO [auth 7], LA [auth A], LB [auth A], LC [auth B], LD [auth B], LF [auth 1], LG [auth 2], LI [auth a], LJ [auth a], LL [auth b], LN [auth 6], LO [auth 7], LP [auth 9], MA [auth A], MB [auth A], MC [auth B], MD [auth B], ME [auth F], MF [auth 1], MG [auth 2], MI [auth a], MJ [auth a], ML [auth b], MM [auth f], MN [auth 6], MO [auth 7], MP [auth 9], NA [auth A], NB [auth A], NC [auth B], ND [auth B], NE [auth F], NF [auth 1], NG [auth 2], NH [auth 4], NI [auth a], NJ [auth a], NK [auth b], NL [auth b], NM [auth f], NN [auth 6], NO [auth 7], NP [auth 9], OA [auth A], OB [auth A], OC [auth B], OD [auth B], OG [auth 2], OH [auth 4], OI [auth a], OJ [auth a], OK [auth b], OL [auth b], ON [auth 6], OO [auth 7], OP [auth 9], PA [auth A], PB [auth A], PC [auth B], PD [auth B], PE [auth G], PF [auth 1], PH [auth 4], PI [auth a], PJ [auth a], PK [auth b], PL [auth b], PM [auth g], PO [auth 7], QA [auth A], QB [auth A], QC [auth B], QD [auth B], QF [auth 1], QH [auth 4], QI [auth a], QJ [auth a], QK [auth b], QL [auth b], QM [auth g], QN [auth 6], RA [auth A], RB [auth A], RC [auth B], RD [auth B], RE [auth G], RF [auth 1], RI [auth a], RJ [auth a], RK [auth b], RL [auth b], RM [auth g], RN [auth 6], SA [auth A], SB [auth A], SC [auth B], SD [auth B], SE [auth G], SF [auth 1], SI [auth a], SJ [auth a], SK [auth b], SL [auth b], SN [auth 6], SP [auth 9], TA [auth A], TB [auth A], TC [auth B], TD [auth B], TF [auth 1], TI [auth a], TJ [auth a], TK [auth b], TL [auth b], TN [auth 6], TP [auth 9], UA [auth A], UB [auth A], UC [auth B], UD [auth B], UF [auth 1], UG [auth 3], UH [auth 4], UI [auth a], UJ [auth a], UK [auth b], UL [auth b], UN [auth 6], UP [auth 9], VA [auth A], VB [auth A], VC [auth B], VD [auth B], VF [auth 1], VG [auth 3], VH [auth 4], VI [auth a], VJ [auth a], VK [auth b], VL [auth b], VM [auth j], VN [auth 6], VO [auth 8], VP [auth 9], WA [auth A], WB [auth A], WC [auth B], WD [auth B], WE [auth J], WF [auth 1], WG [auth 3], WH [auth 4], WI [auth a], WJ [auth a], WK [auth b], WL [auth b], WN [auth 6], WO [auth 8], WP [auth 9], XA [auth A], XC [auth B], XD [auth B], XG [auth 3], XH [auth 4], XI [auth a], XJ [auth a], XK [auth b], XL [auth b], XN [auth 6], XO [auth 8], XP [auth 9], YA [auth A], YB [auth A], YC [auth B], YD [auth B], YG [auth 3], YH [auth 4], YI [auth a], YJ [auth a], YK [auth b], YL [auth b], YM [auth k], YO [auth 8], YP [auth 9], ZA [auth A], ZC [auth B], ZE [auth K], ZG [auth 3], ZH [auth 4], ZI [auth a], ZK [auth b], ZL [auth b], ZM [auth k], ZO [auth 8]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG	DQ [auth 9], FI [auth 4], GI [auth 4], JN [auth 6], QE [auth G]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
LHG	AC [auth A], AG [auth 1], BK [auth a], BO [auth 6], CK [auth a], IF [auth 1], IN [auth 6], MH [auth 3], TG [auth 2], UO [auth 7], ZB [auth A]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT	BQ [auth 9], DI [auth 4], JP [auth 8], KH [auth 3], RG [auth 2], SO [auth 7], YF [auth 1], ZN [auth 6]	(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
LUT	AQ [auth 9], BG [auth 1], CI [auth 4], CO [auth 6], IP [auth 8], JH [auth 3], QG [auth 2], RO [auth 7], XF [auth 1], YN [auth 6]	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C40 H56 O2 KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR	AE [auth B], AO [auth 6], BC [auth A], BE [auth B], BF [auth K], BN [auth k], CC [auth A], CE [auth B], CF [auth L], CM [auth b], CN [auth l], CQ [auth 9], DC [auth A], DE [auth B], DK [auth a], DM [auth b], EC [auth A], EE [auth B], EI [auth 4], EK [auth a], EM [auth b], FC [auth A], FE [auth B], FK [auth a], FM [auth b], GF [auth L], GK [auth a], GM [auth b], GN [auth l], HF [auth L], HK [auth a], HM [auth b], HN [auth l], IK [auth a], JC [auth A], KC [auth B], KP [auth 8], LH [auth 3], MK [auth b], OE [auth F], OM [auth f], SG [auth 2], SM [auth g], TE [auth G], TM [auth i], TO [auth 7], UE [auth I], WM [auth j], XE [auth J], XM [auth j], YE [auth K], ZF [auth 1]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	GE [auth B]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN	BM [auth b], XB [auth A], ZD [auth B], ZJ [auth a]	PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4	GC [auth A], IE [auth C], JE [auth C], JK [auth a], JM [auth c], KM [auth c]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
HTG	IC [auth A], LE [auth F], LK [auth a], LM [auth f], UM [auth j], VE [auth J]	heptyl 1-thio-beta-D-glucopyranoside C13 H26 O5 S HPEGNLMTTNTJSP-LBELIVKGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.624	α = 90
b = 192.22	β = 91.41
c = 175.089	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-10 
Deposition Author(s): Suga, M., Qin, X., Kuang, T., Shen, J.R.

Revision History  

• Version 1.0: 2015-06-10
  Type: Initial release
  
• Version 1.1: 2015-07-08
  Changes: Derived calculations
• Version 1.2: 2019-05-01
  Changes: Advisory, Data collection, Derived calculations, Source and taxonomy
• Version 1.3: 2020-03-04
  Changes: Source and taxonomy, Structure summary
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary