4TNI

RT XFEL structure of Photosystem II 500 ms after the third illumination at 4.6 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 

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This is version 2.1 of the entry. See complete history. 


Literature

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.

Kern, J., Tran, R., Alonso-Mori, R., Koroidov, S., Echols, N., Hattne, J., Ibrahim, M., Gul, S., Laksmono, H., Sierra, R.G., Gildea, R.J., Han, G., Hellmich, J., Lassalle-Kaiser, B., Chatterjee, R., Brewster, A.S., Stan, C.A., Glockner, C., Lampe, A., DiFiore, D., Milathianaki, D., Fry, A.R., Seibert, M.M., Koglin, J.E., Gallo, E., Uhlig, J., Sokaras, D., Weng, T.C., Zwart, P.H., Skinner, D.E., Bogan, M.J., Messerschmidt, M., Glatzel, P., Williams, G.J., Boutet, S., Adams, P.D., Zouni, A., Messinger, J., Sauter, N.K., Bergmann, U., Yano, J., Yachandra, V.K.

(2014) Nat Commun 5: 4371-4371

  • DOI: https://doi.org/10.1038/ncomms5371
  • Primary Citation of Related Structures:  
    4TNH, 4TNI, 4TNJ, 4TNK, 4TNL

  • PubMed Abstract: 

    The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 μs after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 Å. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.

    • Organizational Affiliation: 

    1] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2] LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem Q(B) protein 1A,
U [auth a]		344Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II core light harvesting proteinB,
V [auth b]		510Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 proteinC,
W [auth c]		461Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [auth d]		352Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Y [auth e]		84Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]		45Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAA [auth h],
G [auth H]		66Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IBA [auth i],
H [auth I]		38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JCA [auth j],
I [auth J]		40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KDA [auth k],
J [auth K]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LEA [auth l],
K [auth L]		37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MFA [auth m],
L [auth M]		36Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideGA [auth o],
M [auth O]		272Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein THA [auth t],
N [auth T]		32Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinIA [auth u],
O [auth U]		134Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550JA [auth v],
P [auth V]		163Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12KA [auth g],
Q [auth y]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinLA [auth x],
R [auth X]		41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein YMA [auth G],
S [auth Y]		28Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZNA [auth z],
T [auth Z]		62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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AC [auth B]
HG [auth c]
ID [auth D]
IG [auth c]
JG [auth c]
AC [auth B],
HG [auth c],
ID [auth D],
IG [auth c],
JG [auth c],
ME [auth a],
PF [auth b],
SC [auth C],
SE [auth b],
TC [auth C],
UC [auth C],
VA [auth A],
VB [auth B],
YG [auth d]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA
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AF [auth b]
AG [auth c]
BF [auth b]
BG [auth c]
CB [auth B]
AF [auth b],
AG [auth c],
BF [auth b],
BG [auth c],
CB [auth B],
CF [auth b],
CG [auth c],
DB [auth B],
DD [auth D],
DF [auth b],
DG [auth c],
EB [auth B],
EC [auth C],
ED [auth D],
EF [auth b],
EG [auth c],
FB [auth B],
FC [auth C],
FF [auth b],
FH [auth h],
GB [auth B],
GC [auth C],
GE [auth a],
GF [auth b],
HB [auth B],
HC [auth C],
HE [auth a],
HF [auth b],
IB [auth B],
IC [auth C],
IE [auth a],
IF [auth b],
JB [auth B],
JC [auth C],
JE [auth a],
JF [auth b],
KB [auth B],
KC [auth C],
KF [auth b],
LB [auth B],
LC [auth C],
MB [auth B],
MC [auth C],
MG [auth c],
NB [auth B],
NC [auth C],
OB [auth B],
OC [auth C],
PA [auth A],
PB [auth B],
PC [auth C],
PD [auth H],
QA [auth A],
QB [auth B],
RA [auth A],
SA [auth A],
TF [auth c],
TG [auth d],
UF [auth c],
UG [auth d],
VF [auth c],
WE [auth b],
WF [auth c],
XC [auth C],
XE [auth b],
XF [auth c],
YE [auth b],
YF [auth c],
ZE [auth b],
ZF [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO
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AD [auth D],
PG [auth d],
QG [auth d],
ZC [auth D]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD
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AB [auth A]
BC [auth B]
DE [auth a]
EH [auth f]
OD [auth F]
AB [auth A],
BC [auth B],
DE [auth a],
EH [auth f],
OD [auth F],
RE [auth a],
RG [auth d],
TE [auth b],
XB [auth B],
ZA [auth A]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG
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AH [auth d]
BB [auth A]
BH [auth e]
EE [auth a]
GD [auth D]
AH [auth d],
BB [auth A],
BH [auth e],
EE [auth a],
GD [auth D],
GH [auth i],
HD [auth D],
KD [auth D],
KG [auth c],
LD [auth E],
LH [auth m],
OE [auth a],
OG [auth c],
QF [auth b],
RD [auth I],
VC [auth C],
WB [auth B],
WG [auth d],
XA [auth A],
XD [auth M],
XG [auth d],
YC [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9
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FD [auth D]
IH [auth j]
KE [auth a]
TA [auth A]
TD [auth J]
FD [auth D],
IH [auth j],
KE [auth a],
TA [auth A],
TD [auth J],
VG [auth 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
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
Query on LHG
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LG [auth c],
NE [auth a],
WA [auth A],
WC [auth C]		1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM
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BE [auth V],
CH [auth f],
MD [auth F],
NH [auth v]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR
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CE [auth y]
DH [auth f]
FG [auth c]
GG [auth c]
JH [auth j]
CE [auth y],
DH [auth f],
FG [auth c],
GG [auth c],
JH [auth j],
LE [auth a],
LF [auth b],
MF [auth b],
ND [auth F],
NF [auth b],
NG [auth c],
OF [auth b],
OH [auth g],
PH [auth x],
QC [auth C],
QD [auth H],
RB [auth B],
RC [auth C],
SB [auth B],
TB [auth B],
UA [auth A],
UB [auth B],
UD [auth J],
WD [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT
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CC [auth B]
DC [auth B]
HH [auth i]
JD [auth D]
RF [auth b]
CC [auth B],
DC [auth B],
HH [auth i],
JD [auth D],
RF [auth b],
SD [auth I],
SF [auth b],
UE [auth b],
VE [auth b],
YB [auth B],
YD [auth M],
ZB [auth B],
ZD [auth M],
ZG [auth d]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX
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QE [auth a],
YA [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT
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CD [auth D],
SG [auth d]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
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FE [auth a],
OA [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA
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AE [auth O],
KH [auth k],
MH [auth o],
VD [auth K]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
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BD [auth D],
PE [auth a]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.433α = 90
b = 228.809β = 90
c = 307.918γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM055302
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM095887
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102520

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 1.2: 2015-10-07
    Changes: Other
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 2.0: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Non-polymer description
  • Version 2.1: 2024-11-06
    Changes: Structure summary