4RKU

Crystal structure of plant Photosystem I at 3 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb4RKU/pdb

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


• Deposited: 2014-10-14 Released: 2015-02-04 
• Deposition Author(s): Mazor, Y., Borovikova, A., Greenberg, I., Nelson, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.293 
• R-Value Work: 0.258 
• R-Value Observed: 0.259 

Literature

Crystal structure of plant Photosystem I at 3.1 Angstrom resolution

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 17-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 17-mer - A3B2C1D1E1F1G1H1I1J1K1L1M1N1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 528.53 kDa 
• Atom Count: 34,540 
• Modelled Residue Count: 3,094 
• Deposited Residue Count: 3,288 
• Unique protein chains: 17

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A	721	Pisum sativum	Mutation(s): 0  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	731	Pisum sativum	Mutation(s): 0  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 iron-sulfur center	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
Photosystem I reaction center subunit II, chloroplastic	D	137	Pisum sativum	Mutation(s): 0
UniProt
Find proteins for E1C9K8 (Pisum sativum) Explore E1C9K8  Go to UniProtKB:  E1C9K8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IV B, chloroplastic	E	63	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	152	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A0H2UKZ4 (Pisum sativum) Explore A0A0H2UKZ4  Go to UniProtKB:  A0A0H2UKZ4

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit V, chloroplastic	G	84	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P20120 (Pisum sativum) Explore P20120  Go to UniProtKB:  P20120

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit VI, chloroplastic	H	82	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for E1C9K9 (Pisum sativum) Explore E1C9K9  Go to UniProtKB:  E1C9K9

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit VIII	I	26	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	40	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D5MAL3 (Pisum sativum) Explore D5MAL3  Go to UniProtKB:  D5MAL3

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit X psaK	K	72	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
Photosystem I reaction center subunit XI, chloroplastic	L	163	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
Photosystem I-N subunit	M [auth N]	85	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for E1C9K7 (Pisum sativum) Explore E1C9K7  Go to UniProtKB:  E1C9K7

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein 6A, chloroplastic	N [auth 1]	182	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for E1C9L2 (Pisum sativum) Explore E1C9L2  Go to UniProtKB:  E1C9L2

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II chlorophyll a/b binding protein from photosystem I	O [auth 2]	199	Pisum sativum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q41038 (Pisum sativum) Explore Q41038  Go to UniProtKB:  Q41038

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

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein P4, chloroplastic	Q [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 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	XB [auth B]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CL0	SB [auth A]	CHLOROPHYLL A ISOMER C55 H72 Mg N4 O5 VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA	AA [auth A], AB [auth A], AD [auth B], AE [auth G], AF [auth 1], AG [auth 3], AH [auth 4], BA [auth A], BB [auth A], BD [auth B], BE [auth G], BF [auth 1], BG [auth 3], BH [auth 4], CA [auth A], CB [auth A], CD [auth B], CF [auth 1], CG [auth 3], CH [auth 4], DA [auth A], DB [auth A], DD [auth B], DF [auth 1], DG [auth 3], DH [auth 4], EA [auth A], EB [auth A], EC [auth B], ED [auth B], EE [auth H], EF [auth 1], EG [auth 3], EH [auth 4], FA [auth A], FB [auth A], FC [auth B], FD [auth B], FF [auth 1], FG [auth 3], GA [auth A], GB [auth A], GC [auth B], GD [auth B], GF [auth 1], GG [auth 3], HA [auth A], HB [auth A], HC [auth B], HD [auth B], HF [auth 1], HG [auth 3], IA [auth A], IB [auth A], IC [auth B], ID [auth B], IG [auth 3], JA [auth A], JB [auth A], JC [auth B], JD [auth B], JF [auth 2], JG [auth 3], KA [auth A], KB [auth A], KC [auth B], KD [auth B], KE [auth J], KF [auth 2], KG [auth 3], LA [auth A], LB [auth A], LC [auth B], LD [auth B], LE [auth J], LF [auth 2], LG [auth 3], MA [auth A], MB [auth A], MC [auth B], MD [auth B], ME [auth J], MF [auth 2], MG [auth 3], NA [auth A], NB [auth A], NC [auth B], ND [auth B], NF [auth 2], NG [auth 3], OA [auth A], OB [auth A], OC [auth B], OD [auth B], OF [auth 2], OG [auth 3], PA [auth A], PB [auth A], PC [auth B], PD [auth B], PE [auth L], PF [auth 2], PG [auth 3], QA [auth A], QB [auth A], QC [auth B], QD [auth B], QE [auth L], QF [auth 2], QG [auth 4], RA [auth A], RC [auth B], RD [auth B], RE [auth L], RF [auth 2], RG [auth 4], SA [auth A], SC [auth B], SD [auth B], SF [auth 2], SG [auth 4], TA [auth A], TB [auth A], TC [auth B], TF [auth 2], TG [auth 4], UA [auth A], UB [auth A], UC [auth B], UE [auth 1], UF [auth 2], UG [auth 4], VA [auth A], VC [auth B], VE [auth 1], VF [auth 2], VG [auth 4], WA [auth A], WC [auth B], WE [auth 1], WF [auth 2], WG [auth 4], XA [auth A], XC [auth B], XD [auth F], XE [auth 1], XG [auth 4], YA [auth A], YC [auth B], YD [auth F], YE [auth 1], YG [auth 4], ZA [auth A], ZC [auth B], ZD [auth F], ZE [auth 1], ZG [auth 4]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG	DE [auth G], JE [auth J]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
LHG	IF [auth 1], WB [auth B], Y [auth A], Z [auth A], ZF [auth 2]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX	HH [auth 4]	(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL C40 H56 O4 PGYAYSRVSAJXTE-OQASCVKESA-N
LUT	FH [auth 4], GH [auth 4], SE [auth 1], TE [auth 1], XF [auth 2], YF [auth 2]	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C40 H56 O2 KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR	AC [auth B], BC [auth B], CC [auth B], CE [auth G], DC [auth B], FE [auth I], GE [auth I], HE [auth J], IE [auth J], NE [auth L], OE [auth L], S [auth A], T [auth A], U [auth A], V [auth A], VD [auth F], W [auth A], WD [auth F], X [auth A], YB [auth B], ZB [auth B]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
PQN	R [auth A], VB [auth B]	PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4	RB [auth A], TD [auth C], UD [auth C]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
G3P	IH [auth 4]	SN-GLYCEROL-3-PHOSPHATE C3 H9 O6 P AWUCVROLDVIAJX-GSVOUGTGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.293 
• R-Value Work: 0.258 
• R-Value Observed: 0.259 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.631	α = 90
b = 189.168	β = 91.11
c = 129.667	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-04 
Deposition Author(s): Mazor, Y., Borovikova, A., Greenberg, I., Nelson, N.

Revision History  

• Version 1.0: 2015-02-04
  Type: Initial release
  
• Version 2.0: 2024-11-06
  Changes: Advisory, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary