[English] 日本語
Yorodumi
- PDB-6kac: Cryo-EM structure of the C2S2-type PSII-LHCII supercomplex from C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kac
TitleCryo-EM structure of the C2S2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii
Components
  • (Chlorophyll a-b binding protein, ...Light-harvesting complexes of green plants) x 4
  • (Cytochrome b559 subunit ...) x 2
  • (Oxygen-evolving enhancer protein ...) x 3
  • (Photosystem II ...) x 14
  • 10 kDa photosystem II polypeptide PsbR (potential)
  • 4.1 kDa photosystem II subunit
  • Chlorophyll a-b binding protein CP29
  • Predicted proteinProtein structure prediction
  • Unindentified Stromal Protein (USP)
KeywordsPHOTOSYNTHESIS / PhotosystemII / supercomplex
Function / homology
Function and homology information


thylakoid light-harvesting complex / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / photosystem II repair / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem II assembly / photosystem II stabilization ...thylakoid light-harvesting complex / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / photosystem II repair / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / response to herbicide / photosystem II / extrinsic component of membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / response to light stimulus / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / calcium ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II Pbs27 / Photosystem II Pbs27 superfamily / Photosystem II Pbs27 / PsbP, C-terminal / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 (PsbQ) ...Photosystem II Pbs27 / Photosystem II Pbs27 superfamily / Photosystem II Pbs27 / PsbP, C-terminal / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 (PsbQ) / Protein Transport Mog1p; Chain A / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbZ, reaction centre / Photosystem II reaction center protein H / photosystem ii from thermosynechococcus elongatus / Photosystem II cytochrome b559, alpha subunit / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / PsbQ-like domain superfamily / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Arc Repressor Mutant, subunit A / Roll / Up-down Bundle / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Chem-XAT / Uncharacterized protein / Uncharacterized protein / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II protein D1 / Photosystem II CP43 reaction center protein / Oxygen-evolving enhancer protein 2, chloroplastic / Oxygen-evolving enhancer protein 3, chloroplastic / Oxygen-evolving enhancer protein 1, chloroplastic / Photosystem II reaction center protein K / Photosystem II reaction center protein H / Photosystem II reaction center protein L / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein T / Cytochrome b559 subunit alpha / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II reaction center protein Z / Photosystem II reaction center protein M / Cytochrome b559 subunit beta / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein CP29 / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center W protein, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSheng, X. / Li, A.J. / Song, D.F. / Liu, Z.F.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFA0503702 China
Chinese Academy of SciencesXDB27020106 China
Chinese Academy of SciencesXDB08020302 China
Chinese Academy of SciencesQYZDB-SSW-SMC005 China
National Natural Science Foundation of China31670749 China
CitationJournal: Nat Plants / Year: 2019
Title: Structural insight into light harvesting for photosystem II in green algae.
Authors: Xin Sheng / Akimasa Watanabe / Anjie Li / Eunchul Kim / Chihong Song / Kazuyoshi Murata / Danfeng Song / Jun Minagawa / Zhenfeng Liu /
Abstract: Green algae and plants rely on light-harvesting complex II (LHCII) to collect photon energy for oxygenic photosynthesis. In Chlamydomonas reinhardtii, LHCII molecules associate with photosystem II ...Green algae and plants rely on light-harvesting complex II (LHCII) to collect photon energy for oxygenic photosynthesis. In Chlamydomonas reinhardtii, LHCII molecules associate with photosystem II (PSII) to form various supercomplexes, including the CSML type, which is the largest PSII-LHCII supercomplex in algae and plants that is presently known. Here, we report high-resolution cryo-electron microscopy (cryo-EM) maps and structural models of the CSML and CS supercomplexes from C. reinhardtii. The CS supercomplex contains an LhcbM1-LhcbM2/7-LhcbM3 heterotrimer in the strongly associated LHCII, and the LhcbM1 subunit assembles with CP43 through two interfacial galactolipid molecules. The loosely and moderately associated LHCII trimers interact closely with the minor antenna complex CP29 to form an intricate subcomplex bound to CP47 in the CSML supercomplex. A notable direct pathway is established for energy transfer from the loosely associated LHCII to the PSII reaction centre, as well as several indirect routes. Structure-based computational analysis on the excitation energy transfer within the two supercomplexes provides detailed mechanistic insights into the light-harvesting process in green algae.
History
DepositionJun 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9955
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Photosystem II protein D1
B: Photosystem II CP47 reaction center protein
V: Photosystem II reaction center protein Ycf12
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Oxygen-evolving enhancer protein 1, chloroplastic
P: Oxygen-evolving enhancer protein 2, chloroplastic
Q: Oxygen-evolving enhancer protein 3, chloroplastic
T: Photosystem II reaction center protein T
W: Photosystem II reaction center W protein, chloroplastic
X: 4.1 kDa photosystem II subunit
Z: Photosystem II reaction center protein Z
N: Chlorophyll a-b binding protein, chloroplastic
G: Chlorophyll a-b binding protein, chloroplastic
R: Chlorophyll a-b binding protein CP29
S: Chlorophyll a-b binding protein, chloroplastic
Y: Chlorophyll a-b binding protein, chloroplastic
U: Predicted protein
1: 10 kDa photosystem II polypeptide PsbR (potential)
4: Unindentified Stromal Protein (USP)
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
v: Photosystem II reaction center protein Ycf12
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Oxygen-evolving enhancer protein 1, chloroplastic
p: Oxygen-evolving enhancer protein 2, chloroplastic
q: Oxygen-evolving enhancer protein 3, chloroplastic
t: Photosystem II reaction center protein T
w: Photosystem II reaction center W protein, chloroplastic
x: 4.1 kDa photosystem II subunit
z: Photosystem II reaction center protein Z
n: Chlorophyll a-b binding protein, chloroplastic
g: Chlorophyll a-b binding protein, chloroplastic
r: Chlorophyll a-b binding protein CP29
s: Chlorophyll a-b binding protein, chloroplastic
y: Chlorophyll a-b binding protein, chloroplastic
u: Predicted protein
0: 10 kDa photosystem II polypeptide PsbR (potential)
3: Unindentified Stromal Protein (USP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,273,107374
Polymers1,020,94856
Non-polymers252,159318
Water10,719595
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Photosystem II ... , 14 types, 28 molecules AaBbVvCcDdHhIiJjKkLlMmTtWwZz

#1: Protein Photosystem II protein D1 / / PSII D1 protein / 32 kDa thylakoid membrane protein / Photosystem II Q(B) protein


Mass: 39066.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P07753, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / / PSII 47 kDa protein / Protein CP-47


Mass: 56159.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P37255
#3: Protein/peptide Photosystem II reaction center protein Ycf12 /


Mass: 3333.058 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P50370*PLUS
#4: Protein Photosystem II CP43 reaction center protein / / PSII 43 kDa protein / Protein CP-43 / Protein P6


Mass: 50680.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P10898
#5: Protein Photosystem II D2 protein / / PSII D2 protein / Photosystem Q(A) protein


Mass: 39474.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P06007, photosystem II
#8: Protein Photosystem II reaction center protein H / / PSII-H / Photosystem II 8 kDa phosphoprotein


Mass: 9445.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P22666
#9: Protein/peptide Photosystem II reaction center protein I / / PSII-I / PSII 4.8 kDa protein


Mass: 4245.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P59763
#10: Protein/peptide Photosystem II reaction center protein J / / PSII-J


Mass: 4291.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: O19930
#11: Protein/peptide Photosystem II reaction center protein K / / PSII-K


Mass: 5062.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P18263
#12: Protein/peptide Photosystem II reaction center protein L / / PSII-L


Mass: 4431.229 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P32974
#13: Protein/peptide Photosystem II reaction center protein M / / PSII-M


Mass: 3762.433 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P92277
#17: Protein/peptide Photosystem II reaction center protein T / / PSII-T


Mass: 3639.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P37256
#18: Protein Photosystem II reaction center W protein, chloroplastic / / PSII 6.1 kDa protein


Mass: 12155.054 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q9SPI9
#20: Protein Photosystem II reaction center protein Z / / PSII-Z


Mass: 6565.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P92276

-
Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#6: Protein Cytochrome b559 subunit alpha / / PSII reaction center subunit V


Mass: 9312.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P48268
#7: Protein/peptide Cytochrome b559 subunit beta / / PSII reaction center subunit VI


Mass: 4986.013 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q08363

-
Oxygen-evolving enhancer protein ... , 3 types, 6 molecules OoPpQq

#14: Protein Oxygen-evolving enhancer protein 1, chloroplastic / OEE1


Mass: 30557.697 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12853
#15: Protein Oxygen-evolving enhancer protein 2, chloroplastic / OEE2


Mass: 25930.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P11471
#16: Protein Oxygen-evolving enhancer protein 3, chloroplastic / OEE3


Mass: 21860.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12852

-
Protein , 3 types, 6 molecules XxRrUu

#19: Protein 4.1 kDa photosystem II subunit /


Mass: 9894.716 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I846
#23: Protein Chlorophyll a-b binding protein CP29 / Lhcbm4


Mass: 29970.846 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q93WD2
#26: Protein Predicted protein / Protein structure prediction


Mass: 19116.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I5A0

-
Chlorophyll a-b binding protein, ... , 4 types, 8 molecules NnGgSsYy

#21: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 27405.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q93WL4
#22: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 26675.350 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q93WE0
#24: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 30742.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q9FEK6
#25: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 27591.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q93VE0

-
Protein/peptide , 2 types, 4 molecules 1043

#27: Protein/peptide 10 kDa photosystem II polypeptide PsbR (potential) /


Mass: 1738.856 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#28: Protein/peptide Unindentified Stromal Protein (USP)


Mass: 2380.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)

-
Sugars , 2 types, 16 molecules

#37: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C51H96O15
#42: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 17 types, 897 molecules

#29: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#30: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#31: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#32: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 148 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#34: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56
#35: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H78O12S
#36: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10
#38: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#39: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#40: Chemical ChemComp-PL9 / 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 / Plastoquinone


Mass: 749.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H80O2
#41: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#43: Chemical...
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#44: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL, LUTEIN / Lutein


Mass: 568.871 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C40H56O2
#45: Chemical
ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN / Violaxanthin


Mass: 600.870 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56O4
#46: Chemical
ChemComp-NEX / (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL, 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H56O4
#47: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: The C2S2-type PSII-LHCII supercomplex / Type: COMPLEX / Entity ID: #1-#28 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 6.5
SpecimenConc.: 3.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 1.875 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 32

-
Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
4RELION3CTF correction
7UCSF Chimera1.9model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
12RELION33D reconstruction
13PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 358312
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 258242 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more