4Y28

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

• PDB DOI: https://doi.org/10.2210/pdb4Y28/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Pisum sativum
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTM


• Deposited: 2015-02-09 Released: 2015-08-19 
• Deposition Author(s): Mazor, Y., Brovikov, A., Nelson, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.268 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

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

• PubMed: 26076232 
• DOI: https://doi.org/10.7554/eLife.07433
• Primary Citation of Related Structures:  
  4Y28


• 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 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.

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Organizational Affiliation: 

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

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 554.63 kDa 
• Atom Count: 35,653 
• Modelled Residue Count: 3,187 
• Deposited Residue Count: 3,492 
• Unique protein chains: 16

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A	758	Pisum sativum	Mutation(s): 4  EC: 1.97.1.12 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	733	Pisum sativum	Mutation(s): 7  EC: 1.97.1.12 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 reaction center subunit VIII	C [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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IX	D [auth J]	42	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D5MAL3 (Pisum sativum) Explore D5MAL3  Go to UniProtKB:  D5MAL3

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit III	E [auth F]	154	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A0M3KL12 (Pisum sativum) Explore A0A0M3KL12  Go to UniProtKB:  A0A0M3KL12

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
photosystem I reaction center	F [auth G]	97	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A0M3KL13 (Pisum sativum) Explore A0A0M3KL13  Go to UniProtKB:  A0A0M3KL13

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	G [auth L]	167	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for E1C9L1 (Pisum sativum) Explore E1C9L1  Go to UniProtKB:  E1C9L1

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I iron-sulfur center	H [auth C]	81	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: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit II, chloroplastic	I [auth D]	147	Pisum sativum	Mutation(s): 0
UniProt
Find proteins for E1C9K8 (Pisum sativum) Explore E1C9K8  Go to UniProtKB:  E1C9K8

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IV A, chloroplastic	J [auth E]	66	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for E1C9K6 (Pisum sativum) Explore E1C9K6  Go to UniProtKB:  E1C9K6

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit VI	K [auth H]	90	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A0M3KL10 (Pisum sativum) Explore A0A0M3KL10  Go to UniProtKB:  A0A0M3KL10

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit X psaK	L [auth K]	129	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A0M3KL11 (Pisum sativum) Explore A0A0M3KL11  Go to UniProtKB:  A0A0M3KL11

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II chlorophyll a/b binding protein from photosystem I	M [auth 2]	269	Pisum sativum	Mutation(s): 1
UniProt
Find proteins for Q41038 (Pisum sativum) Explore Q41038  Go to UniProtKB:  Q41038

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein P4, chloroplastic	N [auth 4]	252	Pisum sativum	Mutation(s): 1  Membrane Entity: Yes
UniProt
Find proteins for Q9SQL2 (Pisum sativum) Explore Q9SQL2  Go to UniProtKB:  Q9SQL2

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting complex I chlorophyll A/B-binding protein	O [auth 1]	202	Pisum sativum	Mutation(s): 0
UniProt
Find proteins for E1C9L2 (Pisum sativum) Explore E1C9L2  Go to UniProtKB:  E1C9L2

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein 3, chloroplastic	P [auth 3]	275	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q32904 (Pisum sativum) Explore Q32904  Go to UniProtKB:  Q32904

Small Molecules

Ligands 13 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	XC [auth B]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL	AG [auth 4], DF [auth 2], EF [auth 2], GF [auth 2], IH [auth 3], QG [auth 1], RG [auth 1], XF [auth 4], YF [auth 4]	CHLOROPHYLL B C55 H70 Mg N4 O6 MWVCRINOIIOUAU-UYSPMESUSA-M
CLA	AB [auth A], AD [auth B], AF [auth 2], AH [auth 3], BB [auth A], BD [auth B], BE [auth F], BF [auth 2], BG [auth 4], BH [auth 3], CB [auth A], CD [auth B], CE [auth F], CF [auth 2], CG [auth 4], CH [auth 3], DA [auth A], DB [auth A], DD [auth B], DH [auth 3], EA [auth A], EB [auth A], ED [auth B], EH [auth 3], FA [auth A], FB [auth A], FD [auth B], FF [auth 2], FH [auth 3], GA [auth A], GB [auth A], GD [auth B], GE [auth G], GH [auth 3], HA [auth A], HB [auth A], HC [auth B], HD [auth B], HE [auth G], HF [auth 2], HH [auth 3], IA [auth A], IB [auth A], IC [auth B], ID [auth B], IE [auth G], IG [auth 1], JA [auth A], JB [auth A], JC [auth B], JD [auth B], JG [auth 1], JH [auth 3], KA [auth A], KB [auth A], KC [auth B], KD [auth B], KG [auth 1], KH [auth 3], LA [auth A], LB [auth A], LC [auth B], LD [auth B], LG [auth 1], LH [auth 3], MA [auth A], MB [auth A], MC [auth B], MD [auth B], ME [auth L], MF [auth 2], MG [auth 1], MH [auth 3], NA [auth A], NB [auth A], NC [auth B], ND [auth B], NE [auth L], NF [auth 2], NG [auth 1], OA [auth A], OB [auth A], OC [auth B], OD [auth B], OE [auth L], OF [auth 4], OG [auth 1], PA [auth A], PC [auth B], PD [auth B], PF [auth 4], PG [auth 1], QA [auth A], QB [auth A], QC [auth B], QD [auth B], QF [auth 4], QH [auth 3], R [auth A], RA [auth A], RB [auth A], RC [auth B], RD [auth B], RF [auth 4], S [auth A], SA [auth A], SB [auth A], SC [auth B], SE [auth H], SF [auth 4], SG [auth 1], T [auth A], TA [auth A], TB [auth B], TC [auth B], TF [auth 4], TG [auth 1], UA [auth A], UB [auth B], UC [auth B], UE [auth K], UF [auth 4], UG [auth 1], VA [auth A], VB [auth B], VE [auth 2], VF [auth 4], VG [auth 1], WA [auth A], WB [auth B], WD [auth J], WE [auth 2], WF [auth 4], XA [auth A], XB [auth B], XE [auth 2], YA [auth A], YB [auth B], YC [auth B], YE [auth 2], ZA [auth A], ZB [auth B], ZC [auth B], ZE [auth 2], ZF [auth 4], ZG [auth 3]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0	Q [auth A]	CHLOROPHYLL A ISOMER C55 H72 Mg N4 O5 VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG	AE [auth F], CC [auth B], DE [auth F], GG [auth 4], KE [auth G], LF [auth 2], XD [auth J]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
LHG	BC [auth B], CA [auth A], KF [auth 2], W [auth A], YG [auth 1]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
ZEX	HG [auth 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
LUT	DG [auth 4], EG [auth 4], FG [auth 4], IF [auth 2], JF [auth 2], NH [auth 3], OH [auth 3], UD [auth I], WG [auth 1], XG [auth 1]	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C40 H56 O2 KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR	AA [auth A], BA [auth A], EC [auth B], EE [auth F], FC [auth B], FE [auth F], GC [auth B], JE [auth G], LE [auth L], PB [auth A], PE [auth L], PH [auth 3], TE [auth K], VC [auth B], VD [auth I], WC [auth B], X [auth A], Y [auth A], YD [auth J], Z [auth A], ZD [auth J]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMU	SD [auth B], TD [auth B]	DODECYL-ALPHA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN	AC [auth B], V [auth A]	PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4	QE [auth C], RE [auth C], U [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
CA	DC [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.268 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189	α = 90
b = 201.9	β = 90
c = 213.2	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-19 
Deposition Author(s): Mazor, Y., Brovikov, A., Nelson, N.

Revision History  

• Version 1.0: 2015-08-19
  Type: Initial release
  
• Version 1.1: 2015-08-26
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Advisory, Derived calculations, Structure summary
• Version 1.3: 2018-09-19
  Changes: Data collection
• Version 1.4: 2019-04-24
  Changes: Advisory, Data collection, Source and taxonomy
• Version 2.0: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary