5V2C

RE-REFINEMENT OF CRYSTAL STRUCTURE OF PHOTOSYSTEM II COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.092 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 3ARC - determined by Umena, Y., Kawakami, K., Shen, J.-R., Kamiya, N.  

Literature

Chlorophyll a with a farnesyl tail in thermophilic cyanobacteria.

Wiwczar, J.M.LaFountain, A.M.Wang, J.Frank, H.A.Brudvig, G.W.

(2017) Photosyn. Res. 134: 175-182

  • DOI: 10.1007/s11120-017-0425-4

  • PubMed Abstract: 
  • Photosystem II (PSII) of oxygenic photosynthetic organisms normally contains exclusively chlorophyll a (Chl a) as its major light-harvesting pigment. Chl a canonically consists of the chlorin headgroup with a 20-carbon, 4-isoprene unit, phytyl tail. ...

    Photosystem II (PSII) of oxygenic photosynthetic organisms normally contains exclusively chlorophyll a (Chl a) as its major light-harvesting pigment. Chl a canonically consists of the chlorin headgroup with a 20-carbon, 4-isoprene unit, phytyl tail. We have examined the 1.9 Å crystal structure of PSII from thermophilic cyanobacteria reported by Shen and coworkers in 2012 (PDB accession of 3ARC/3WU2). A newly refined electron density map from this structure, presented here, reveals that some assignments of the cofactors may be different from those modeled in the 3ARC/3WU2 structure, including a specific Chl a that appears to have a truncated tail by one isoprene unit. We provide experimental evidence using high-performance liquid chromatography and mass spectrometry for a small population of Chl a esterified to a 15-carbon farnesyl tail in PSII of thermophilic cyanobacteria.


    Related Citations: 
    • Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 A
      Umena, Y.,Kawakami, K.,Shen, J.-R.,Kamiya, N.
      (2011) Nature 473: 55


    Organizational Affiliation

    Department of Chemistry, University of Connecticut, Storrs, CT, 06269-3060, USA.,Department of Chemistry, Yale University, New Haven, CT, 06520-8107, USA. gary.brudvig@yale.edu.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520-8107, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II protein D1
A, a
344Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbA (psbA-1)
EC: 1.10.3.9
Find proteins for P51765 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P51765
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP47 reaction center protein
B, b
506Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbB
Find proteins for D0VWR1 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II CP43 reaction center protein
C, c
458Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbC
Find proteins for D0VWR7 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II D2 protein
D, d
342Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
Find proteins for D0VWR8 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit alpha
E, e
83Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbE
Find proteins for P12238 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12238
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 subunit beta
F, f
44Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbF
Find proteins for P12239 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12239
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein H
H, h
65Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbH
Find proteins for P19052 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P19052
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein I
I, i
38Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbI
Find proteins for P12240 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12240
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein J
J, j
40Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbJ
Find proteins for Q7DGD4 (Thermosynechococcus vulcanus)
Go to UniProtKB:  Q7DGD4
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein K
K, k
37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbK
Find proteins for P19054 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P19054
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein L
L, l
37Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbL
Find proteins for P12241 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12241
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein M
M, m
36Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbM
Find proteins for P12312 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12312
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II manganese-stabilizing polypeptide
O, o
245Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbO
Find proteins for D0VWR2 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR2
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein T
T, t
32Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbT
Find proteins for P12313 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P12313
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic protein
U, u
104Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbU
Find proteins for P56152 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P56152
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550
V, v
137Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbV
Find proteins for P0A387 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P0A387
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Ycf12
Y, y
30Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: ycf12 (psbY)
Find proteins for D0VWR3 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR3
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein X
X, x
41Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbX
Find proteins for D0VWR4 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR4
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein Z
Z, z
62Thermosynechococcus vulcanusMutation(s): 0 
Gene Names: psbZ
Find proteins for D0VWR5 (Thermosynechococcus vulcanus)
Go to UniProtKB:  D0VWR5
Small Molecules
Ligands 24 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQD
Query on SQD

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a, A, b, F, h, l, x
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
CLA
Query on CLA

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A, a, B, b, c, C, d, D
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PL9
Query on PL9

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a, A, D, d
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
PLASTOQUINONE 9
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
 Ligand Interaction
OEX
Query on OEX

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a, A
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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a, A, v, V
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, a, b, B, C, c, d, D, e, F, f, m, o, O, t, T, u, U, V, v, y
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HTG
Query on HTG

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a, B, b, c, C, h, H, O, o, V
HEPTYL 1-THIOHEXOPYRANOSIDE
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
CA
Query on CA

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b, B, c, h, o, O
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DGD
Query on DGD

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c, C, d, D, H, h
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
LMG
Query on LMG

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a, A, B, b, c, C, d, j, J, z
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
2PE
Query on 2PE

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i, V
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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a, A, B, C, c, D, d, E, e, H, I, i, J, O, o, V, X
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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A, a, b, B, C, c, D, d, e, E, h, H, I, i, J, j, K, l, U, V, x, X
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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a, A, m
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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f, F, j, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

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A, b, B, c, C, D, d, E, I, j, T
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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e, E, v, V
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PGE
Query on PGE

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a, A, B, b, C, c, D, E, f, h, H, i, I, j, J, O, o, T, t, V, x, Y
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
BCR
Query on BCR

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a, A, B, b, c, C, d, D, h, H, k, K, t, T
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PHO
Query on PHO

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A, a, d, D
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
FE2
Query on FE2

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A, a
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

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A, a, b, B, c, C, F, f, I, J, j, m, M, t, u, Y
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
LHG
Query on LHG

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A, a, B, D, d, e, E, l
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
1PE
Query on 1PE

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B, e, j, L, V, x
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
I, i, M, m, T, t
L-PEPTIDE LINKINGC6 H11 N O3 SMET
MHS
Query on MHS
D, d
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.092 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 122.190α = 90.00
b = 228.510β = 90.00
c = 286.400γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references