4TNH | pdb_00004tnh

RT XFEL structure of Photosystem II in the dark state at 4.9 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.90 Å
  • R-Value Free: 
    0.292 (Depositor), 0.297 (DCC) 
  • R-Value Work: 
    0.281 (Depositor), 0.287 (DCC) 
  • R-Value Observed: 
    0.281 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 762.72 kDa 
  • Atom Count: 50,244 
  • Modeled Residue Count: 5,270 
  • Deposited Residue Count: 5,674 
  • Unique protein chains: 20

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 
UniProt
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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence
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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 
UniProt
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Reference Sequence

Small Molecules

Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
BC [auth B]
HG [auth c]
ID [auth D]
IG [auth c]
JG [auth c]
BC [auth B],
HG [auth c],
ID [auth D],
IG [auth c],
JG [auth c],
NE [auth a],
PF [auth b],
SE [auth b],
TC [auth C],
UC [auth C],
VA [auth A],
VC [auth C],
WB [auth B],
XG [auth d]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AF [auth b]
AG [auth c]
BF [auth b]
BG [auth c]
CF [auth b]
AF [auth b],
AG [auth c],
BF [auth b],
BG [auth c],
CF [auth b],
CG [auth c],
DB [auth B],
DD [auth D],
DF [auth b],
DG [auth c],
EB [auth B],
ED [auth D],
EF [auth b],
EG [auth c],
EH [auth h],
FB [auth B],
FC [auth C],
FF [auth b],
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],
JF [auth b],
KB [auth B],
KC [auth C],
KE [auth a],
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],
QC [auth C],
RA [auth A],
RB [auth B],
SA [auth A],
SG [auth d],
TF [auth c],
TG [auth d],
UF [auth c],
VF [auth c],
WE [auth b],
WF [auth c],
XE [auth b],
XF [auth c],
YC [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



Download:Ideal Coordinates CCD File
AD [auth D],
BD [auth D],
JE [auth a],
PG [auth d]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD



Download:Ideal Coordinates CCD File
AB [auth A]
BB [auth A]
CC [auth B]
DE [auth a]
DH [auth f]
AB [auth A],
BB [auth A],
CC [auth B],
DE [auth a],
DH [auth f],
OD [auth F],
QG [auth d],
RE [auth a],
TE [auth b],
YB [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

Query on LMG



Download:Ideal Coordinates CCD File
AH [auth e]
CB [auth A]
EE [auth a]
FH [auth i]
GD [auth D]
AH [auth e],
CB [auth A],
EE [auth a],
FH [auth i],
GD [auth D],
HD [auth D],
KD [auth D],
KG [auth c],
KH [auth l],
LD [auth E],
LH [auth m],
OG [auth c],
QF [auth b],
RD [auth I],
VG [auth d],
WC [auth C],
WG [auth d],
XA [auth A],
XB [auth B],
XD [auth M],
ZC [auth C],
ZG [auth d]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9



Download:Ideal Coordinates CCD File
FD [auth D]
HH [auth j]
LE [auth a]
TA [auth A]
TD [auth J]
FD [auth D],
HH [auth j],
LE [auth a],
TA [auth A],
TD [auth J],
UG [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



Download:Ideal Coordinates CCD File
LG [auth c],
OE [auth a],
WA [auth A],
XC [auth C]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
BE [auth V],
BH [auth f],
MD [auth F],
NH [auth v]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR

Query on BCR



Download:Ideal Coordinates CCD File
CE [auth y]
CH [auth f]
FG [auth c]
GG [auth c]
IH [auth j]
CE [auth y],
CH [auth f],
FG [auth c],
GG [auth c],
IH [auth j],
LF [auth b],
ME [auth a],
MF [auth b],
ND [auth F],
NF [auth b],
NG [auth c],
OF [auth b],
OH [auth g],
PH [auth x],
QD [auth H],
RC [auth C],
SB [auth B],
SC [auth C],
TB [auth B],
UA [auth A],
UB [auth B],
UD [auth J],
VB [auth B],
WD [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
AC [auth B]
DC [auth B]
EC [auth B]
GH [auth i]
JD [auth D]
AC [auth B],
DC [auth B],
EC [auth B],
GH [auth i],
JD [auth D],
RF [auth b],
SD [auth I],
SF [auth b],
UE [auth b],
VE [auth b],
YD [auth M],
YG [auth d],
ZB [auth B],
ZD [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX

Query on OEX



Download:Ideal Coordinates CCD File
QE [auth a],
ZA [auth A]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
CD [auth D],
RG [auth d]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2



Download:Ideal Coordinates CCD File
FE [auth a],
OA [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AE [auth O],
JH [auth k],
MH [auth o],
VD [auth K]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
PE [auth a],
YA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.90 Å
  • R-Value Free:  0.292 (Depositor), 0.297 (DCC) 
  • R-Value Work:  0.281 (Depositor), 0.287 (DCC) 
  • R-Value Observed: 0.281 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.885α = 90
b = 229.033β = 90
c = 307.715γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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

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: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
  • Version 2.1: 2024-10-23
    Changes: Structure summary