ISDA

Deposition Date 2014-06-04

Release Date 2014-07-09

Last Version Date 2024-10-23

Entry Detail

PDB ID:

4TNH

Keywords:

ELECTRON TRANSPORT,PHOTOSYNTHESIS

Title:

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

Biological Source:

Source Organism:

Thermosynechococcus elongatus (Taxon ID: 197221)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

4.90 Å

R-Value Free:

0.29

R-Value Work:

0.28

R-Value Observed:

0.28

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem Q(B) protein 1
Gene (Uniprot):psbA1
Chain IDs:A, U (auth: a)
Chain Length:344
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:P0A444 Pfam ID:PF00124 EC:1.10.3.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II core light harvesting protein
Gene (Uniprot):psbB
Chain IDs:B, V (auth: b)
Chain Length:510
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DIQ1 Pfam ID:PF00421

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 protein
Gene (Uniprot):psbC
Chain IDs:C, W (auth: c)
Chain Length:461
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DIF8 Pfam ID:PF00421

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD1, psbD2
Chain IDs:D, X (auth: d)
Chain Length:352
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8CM25 Pfam ID:PF00124 EC:1.10.3.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
Chain IDs:E, Y (auth: e)
Chain Length:84
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DIP0 Pfam ID:PF00283, PF00284

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
Chain IDs:F, Z (auth: f)
Chain Length:45
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DIN9 Pfam ID:PF00283

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein H
Gene (Uniprot):psbH
Chain IDs:G (auth: H), AA (auth: h)
Chain Length:66
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DJ43 Pfam ID:PF00737

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein I
Gene (Uniprot):psbI
Chain IDs:H (auth: I), BA (auth: i)
Chain Length:38
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DJZ6 Pfam ID:PF02532

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein J
Gene (Uniprot):psbJ
Chain IDs:I (auth: J), CA (auth: j)
Chain Length:40
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:P59087 Pfam ID:PF01788

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein K
Gene (Uniprot):psbK
Chain IDs:J (auth: K), DA (auth: k)
Chain Length:46
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q9F1K9 Pfam ID:PF02533

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein L
Gene (Uniprot):psbL
Chain IDs:K (auth: L), EA (auth: l)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DIN8 Pfam ID:PF02419

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein M
Gene (Uniprot):psbM
Chain IDs:L (auth: M), FA (auth: m)
Chain Length:36
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DHA7 Pfam ID:PF05151

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II manganese-stabilizing polypeptide
Gene (Uniprot):psbO
Chain IDs:M (auth: O), GA (auth: o)
Chain Length:272
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:P0A431 Pfam ID:PF01716

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
Chain IDs:N (auth: T), HA (auth: t)
Chain Length:32
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DIQ0 Pfam ID:PF01405

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II 12 kDa extrinsic protein
Gene (Uniprot):psbU
Chain IDs:O (auth: U), IA (auth: u)
Chain Length:134
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q9F1L5 Pfam ID:PF06514

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c-550
Gene (Uniprot):psbV
Chain IDs:P (auth: V), JA (auth: v)
Chain Length:163
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:P0A386 Pfam ID:PF14495

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center X protein
Gene (Uniprot):psbX
Chain IDs:R (auth: X), LA (auth: x)
Chain Length:41
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q9F1R6 Pfam ID:PF06596

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Y
Chain IDs:S (auth: Y), MA (auth: G)
Chain Length:46
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
Chain IDs:T (auth: Z), NA (auth: z)
Chain Length:62
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DHJ2 Pfam ID:PF01737

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Ycf12
Gene (Uniprot):psb30
Chain IDs:Q (auth: y), KA (auth: g)
Chain Length:46
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DJI1 Pfam ID:PF05969

Ligand Molecules

BCR

BCT

CLA

DGD

FE2

HEM

LHG

LMG

LMT

OEX

PHO

PL9

SQD

Primary Citation

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, Afonine, P.V, Grosse-Kunstleve, R.W, Echols, N, Headd, J.J, Moriarty, N.W, Mustyakimov, M, Terwilliger, T.C, Urzhumtsev, A, Zwart, P.H, Adams, P.D, Adams, P.D, Afonine, P.V, Bunkoczi, G, Chen, V.B, Davis, I.W, Echols, N, Headd, J.J, Hung, L.W, Kapral, G.J, Grosse-Kunstleve, R.W, McCoy, A.J, Moriarty, N.W, Oeffner, R, Read, R.J, Richardson, D.C, Richardson, J.S, Terwilliger, T.C, Zwart, P.H.Show

Nat Commun 5 4371 4371 (2014)

PMID: 25006873 DOI: 10.1038/ncomms5371

Abstact

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.

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Primary Citation of related structures