4IL6

Structure of Sr-substituted photosystem II

• PDB DOI: https://doi.org/10.2210/pdb4IL6/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Thermostichus vulcanus, Thermosynechococcus vestitus BP-1
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2012-12-29 Released: 2013-03-06 
• Deposition Author(s): Koua, F.H.M., Umena, Y., Kawakami, K., Kamiya, N., Shen, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structure of Sr-substituted photosystem II at 2.1 A resolution and its implications in the mechanism of water oxidation

Koua, F.H., Umena, Y., Kawakami, K., Shen, J.R.

(2013) Proc Natl Acad Sci U S A 110: 3889-3894

• PubMed: 23426624 
• DOI: https://doi.org/10.1073/pnas.1219922110
• Primary Citation of Related Structures:  
  4IL6


• PubMed Abstract: 
  

  Oxygen-evolving complex of photosystem II (PSII) is a tetra-manganese calcium penta-oxygenic cluster (Mn4CaO5) catalyzing light-induced water oxidation through several intermediate states (S-states) by a mechanism that is not fully understood. To elucidate the roles of Ca(2+) in this cluster and the possible location of water substrates in this process, we crystallized Sr(2+)-substituted PSII from Thermosynechococcus vulcanus, analyzed its crystal structure at a resolution of 2.1 Å, and compared it with the 1.9 Å structure of native PSII. Our analysis showed that the position of Sr was moved toward the outside of the cubane structure of the Mn4CaO5-cluster relative to that of Ca(2+), resulting in a general elongation of the bond distances between Sr and its surrounding atoms compared with the corresponding distances in the Ca-containing cluster. In particular, we identified an apparent elongation in the bond distance between Sr and one of the two terminal water ligands of Ca(2+), W3, whereas that of the Sr-W4 distance was not much changed. This result may contribute to the decrease of oxygen evolution upon Sr(2+)-substitution, and suggests a weak binding and rather mobile nature of this particular water molecule (W3), which in turn implies the possible involvement of this water molecule as a substrate in the O-O bond formation. In addition, the PsbY subunit, which was absent in the 1.9 Å structure of native PSII, was found in the Sr-PSII structure.

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Organizational Affiliation: 

Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science, Okayama University, Okayama 700-8530, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 39-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 39-mer - A12B4C2D2E2F2G2H2I2J2K2L2M2N1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 38-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 38-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 719.09 kDa 
• Atom Count: 53,568 
• Modelled Residue Count: 5,288 
• Deposited Residue Count: 5,296 
• Unique protein chains: 20

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem Q(B) protein	A, U [auth a]	334	Thermostichus vulcanus	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for P51765 (Thermostichus vulcanus) Explore P51765  Go to UniProtKB:  P51765

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II core light harvesting protein	B, V [auth b]	505	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR1 (Thermostichus vulcanus) Explore D0VWR1  Go to UniProtKB:  D0VWR1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 protein	C, W [auth c]	451	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR7 (Thermostichus vulcanus) Explore D0VWR7  Go to UniProtKB:  D0VWR7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	D, X [auth d]	342	Thermostichus vulcanus	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for D0VWR8 (Thermostichus vulcanus) Explore D0VWR8  Go to UniProtKB:  D0VWR8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	E, Y [auth e]	80	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12238 (Thermostichus vulcanus) Explore P12238  Go to UniProtKB:  P12238

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	F, Z [auth f]	34	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12239 (Thermostichus vulcanus) Explore P12239  Go to UniProtKB:  P12239

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	AA [auth h], G [auth H]	63	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P19052 (Thermostichus vulcanus) Explore P19052  Go to UniProtKB:  P19052

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	BA [auth i], H [auth I]	36	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12240 (Thermostichus vulcanus) Explore P12240  Go to UniProtKB:  P12240

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein J	CA [auth j], I [auth J]	37	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q7DGD4 (Thermostichus vulcanus) Explore Q7DGD4  Go to UniProtKB:  Q7DGD4

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	DA [auth k], J [auth K]	37	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P19054 (Thermostichus vulcanus) Explore P19054  Go to UniProtKB:  P19054

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	EA [auth l], K [auth L]	37	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12241 (Thermostichus vulcanus) Explore P12241  Go to UniProtKB:  P12241

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	FA [auth m], L [auth M]	34	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12312 (Thermostichus vulcanus) Explore P12312  Go to UniProtKB:  P12312

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II manganese-stabilizing polypeptide	GA [auth o], M [auth O]	244	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR2 (Thermostichus vulcanus) Explore D0VWR2  Go to UniProtKB:  D0VWR2

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	HA [auth t], N [auth T]	31	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12313 (Thermostichus vulcanus) Explore P12313  Go to UniProtKB:  P12313

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II 12 kDa extrinsic protein	IA [auth u], O [auth U]	97	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P56152 (Thermostichus vulcanus) Explore P56152  Go to UniProtKB:  P56152

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-550	JA [auth v], P [auth V]	137	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0A387 (Thermostichus vulcanus) Explore P0A387  Go to UniProtKB:  P0A387

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein ycf12	KA [auth y], Q [auth Y]	30	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR3 (Thermostichus vulcanus) Explore D0VWR3  Go to UniProtKB:  D0VWR3

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein X	LA [auth x], R [auth X]	40	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR4 (Thermostichus vulcanus) Explore D0VWR4  Go to UniProtKB:  D0VWR4

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	MA [auth z], S [auth Z]	62	Thermostichus vulcanus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D0VWR5 (Thermostichus vulcanus) Explore D0VWR5  Go to UniProtKB:  D0VWR5

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein Y	T [auth R]	34	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8DKM3 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DKM3  Go to UniProtKB:  Q8DKM3

Small Molecules

Ligands 19 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	CD [auth C], DD [auth C], DI [auth c], ED [auth C], EI [auth c], FI [auth c], LE [auth H], OJ [auth h]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AD [auth C], AI [auth c], BI [auth c], GB [auth B], HB [auth B], IB [auth B], JB [auth B], JG [auth b], KB [auth B], KG [auth b], LB [auth B], LG [auth b], MB [auth B], MG [auth b], NB [auth B], NG [auth b], OB [auth B], OC [auth C], OG [auth b], PB [auth B], PC [auth C], PG [auth b], PH [auth c], QB [auth B], QC [auth C], QD [auth D], QG [auth b], QH [auth c], RA [auth A], RB [auth B], RC [auth C], RD [auth D], RG [auth b], RH [auth c], SA [auth A], SB [auth B], SC [auth C], SF [auth a], SG [auth b], SH [auth c], TB [auth B], TC [auth C], TD [auth D], TF [auth a], TG [auth b], TH [auth c], TI [auth d], UA [auth A], UB [auth B], UC [auth C], UF [auth a], UG [auth b], UH [auth c], UI [auth d], VB [auth B], VC [auth C], VG [auth b], VH [auth c], WC [auth C], WG [auth b], WH [auth c], XC [auth C], XF [auth a], XG [auth b], XH [auth c], YC [auth C], YG [auth b], YH [auth c], ZC [auth C], ZH [auth c]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	SD [auth D], TA [auth A], VF [auth a], WF [auth a]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	CB [auth A], CH [auth b], GI [auth c], LJ [auth f], MF [auth a], WD [auth D], XA [auth A], ZB [auth B]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	AE [auth D], AG [auth a], AJ [auth d], BC [auth B], FD [auth C], GD [auth C], HI [auth c], II [auth c], JI [auth c], LF [auth Z], YA [auth A], YJ [auth m]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9	VD [auth D], WA [auth A], WI [auth d], ZF [auth a]	2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE C53 H80 O2 FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG	AC [auth B], DH [auth b], IE [auth E], JJ [auth e], XD [auth D], XI [auth d], YD [auth D], YI [auth d], ZD [auth D], ZI [auth d]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM	CF [auth V], FK [auth v], JE [auth F], KJ [auth f]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BCR	AF [auth T], AH [auth b], BD [auth C], BH [auth b], BK [auth t], CI [auth c], JK [auth y], KE [auth H], NJ [auth h], OE [auth J], RE [auth K], SE [auth K], TJ [auth k], UD [auth D], UJ [auth k], VA [auth A], VI [auth d], WB [auth B], XB [auth B], YB [auth B], YF [auth a], ZG [auth b]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	BG [auth a], CC [auth B], DB [auth A], DK [auth t], EB [auth A], EH [auth b], HD [auth C], KH [auth b], MJ [auth f], NF [auth a], QJ [auth i], WE [auth M], XE [auth M], XJ [auth m], ZJ [auth m]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
OER	NA [auth A], OF [auth a]	SR-MN4-O5 CLUSTER Mn4 O5 Sr CSESTIVEXPKVIG-UHFFFAOYSA-N
HTG	AK [auth o], BE [auth D], BJ [auth d], DC [auth B], DF [auth V], FH [auth b], GG [auth b], HC [auth B], HE [auth D], HG [auth b], HJ [auth d], IC [auth B], ID [auth C], JD [auth C], JH [auth b], KI [auth c], NI [auth c]	heptyl 1-thio-beta-D-glucopyranoside C13 H26 O5 S HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL	FB [auth A], FF [auth V], FG [auth a], GE [auth D], GJ [auth d], HF [auth V], HK [auth v], IF [auth V], IJ [auth d], IK [auth v], KC [auth B], LH [auth b]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	AB [auth A], BF [auth U], CG [auth a], DG [auth a], EE [auth D], EF [auth V], EJ [auth d], EK [auth u], FC [auth B], FE [auth D], FJ [auth d], GC [auth B], GF [auth V], GK [auth v], HH [auth b], IH [auth b], KD [auth C], LC [auth B], LD [auth C], MC [auth B], MD [auth C], MH [auth b], MI [auth c], NC [auth B], ND [auth C], NH [auth b], OD [auth C], OH [auth b], OI [auth c], PI [auth c], QI [auth c], RI [auth c], YE [auth O], ZA [auth A], ZE [auth O]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
BCT	PD [auth D], SI [auth d]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	OA [auth A], PF [auth a]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CL	PA [auth A], QA [auth A], QF [auth a], RF [auth a]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	QE [auth J], SJ [auth j], UE [auth K], VJ [auth k]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL	BB [auth A], CE [auth D], CJ [auth d], CK [auth t], DE [auth D], DJ [auth d], EC [auth B], EG [auth a], GH [auth b], IG [auth b], JC [auth B], JF [auth Y], KF [auth X], KK [auth y], LI [auth c], LK [auth x], ME [auth I], NE [auth I], PE [auth J], PJ [auth i], RJ [auth j], TE [auth K], VE [auth L], WJ [auth l]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	BA [auth i], H [auth I]	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.86	α = 90
b = 228.79	β = 90
c = 285.76	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Koua, F.H.M., Umena, Y., Kawakami, K., Kamiya, N., Shen, J.R.

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• Version 1.1: 2013-03-20
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 2.0: 2023-11-08
  Changes: Data collection, Database references, Non-polymer description, Refinement description, Structure summary
• Version 2.1: 2024-11-20
  Changes: Structure summary