[English] 日本語
Yorodumi
- PDB-8z9d: cryo-EM structure of PSII-LHCII megacomplex from spinach -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8z9d
Titlecryo-EM structure of PSII-LHCII megacomplex from spinach
Components
  • (Chlorophyll a-b binding protein, ...) x 5
  • (Cytochrome b559 subunit ...) x 2
  • (Oxygen-evolving enhancer protein ...) x 3
  • (Photosystem II ...) x 17
  • Chlorophyll a-b binding protein CP24, chloroplastic
KeywordsPHOTOSYNTHESIS / PSII / LHCII / megacomplex
Function / homology
Function and homology information


chloroplast photosystem II / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor ...chloroplast photosystem II / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / photosystem II / response to herbicide / extrinsic component of membrane / chlorophyll binding / photosynthetic electron transport in photosystem II / : / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / response to light stimulus / photosynthesis / cell redox homeostasis / chloroplast / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / mRNA binding / heme binding / calcium ion binding / metal ion binding
Similarity search - Function
Photosystem II PsbR / Photosystem II PsbY, plant / Photosystem II 10 kDa polypeptide PsbR / Photosystem II 5kDa protein, chloroplastic / PsbP, C-terminal / : / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) ...Photosystem II PsbR / Photosystem II PsbY, plant / Photosystem II 10 kDa polypeptide PsbR / Photosystem II 5kDa protein, chloroplastic / 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-like domain superfamily / Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / 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 reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / 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 cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / 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.
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 / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II 10 kDa polypeptide, chloroplastic / Photosystem II reaction center protein K / Oxygen-evolving enhancer protein 3, chloroplastic / Oxygen-evolving enhancer protein 2, chloroplastic / Oxygen-evolving enhancer protein 1, chloroplastic / Chlorophyll a-b binding protein CP24, chloroplastic / Cytochrome b559 subunit beta / Photosystem II reaction center protein L / Photosystem II reaction center protein T / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Cytochrome b559 subunit alpha / Photosystem II protein D1 / Photosystem II reaction center proteins PsbY, chloroplastic / Photosystem II reaction center W protein, chloroplastic / Photosystem II reaction center protein J / Photosystem II reaction center protein Z
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsShan, J.Y. / Liu, Z.F.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Sci Adv / Year: 2024
Title: Architecture and functional regulation of a plant PSII-LHCII megacomplex.
Authors: Jianyu Shan / Dariusz M Niedzwiedzki / Rupal S Tomar / Zhenfeng Liu / Haijun Liu /
Abstract: Photosystem II (PSII) splits water in oxygenic photosynthesis on Earth. The structure and function of the CSM-type PSII-LHCII (light-harvesting complex II) megacomplexes from the wild-type and PsbR- ...Photosystem II (PSII) splits water in oxygenic photosynthesis on Earth. The structure and function of the CSM-type PSII-LHCII (light-harvesting complex II) megacomplexes from the wild-type and PsbR-deletion mutant plants are studied through electron microscopy (EM), structural mass spectrometry, and ultrafast fluorescence spectroscopy [time-resolved fluorescence (TRF)]. The cryo-EM structure of a type I CSM megacomplex demonstrates that the three domains of PsbR bind to the stromal side of D1, D2, and CP43; associate with the single transmembrane helix of the redox active Cyt ; and stabilize the luminal extrinsic PsbP, respectively. This megacomplex, with PsbR and PsbY centered around the narrow interface between two dimeric PSII cores, provides the supramolecular structural basis that regulates the plastoquinone occupancy in Q site, excitation energy transfer, and oxygen evolution. PSII-LHCII megacomplexes (types I and II) and LHC aggregation levels in mutant were also interrogated and compared to wild-type plants through EM and picosecond TRF.
History
DepositionApr 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.0Nov 13, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 13, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 13, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 13, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 13, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 13, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 13, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.2Feb 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1Feb 26, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Photosystem II protein D1
Oo: Oxygen-evolving enhancer protein 1, chloroplastic
Rr: Chlorophyll a-b binding protein, chloroplastic
Ss: Chlorophyll a-b binding protein, chloroplastic
Tt: Photosystem II reaction center protein T
Uu: Photosystem II 5 kDa protein, chloroplastic
Ww: Photosystem II reaction center W protein, chloroplastic
Xx: Photosystem II reaction center X protein, chloroplastic
Yy: Chlorophyll a-b binding protein, chloroplastic
Zz: Photosystem II reaction center protein Z
44: Chlorophyll a-b binding protein CP24, chloroplastic
Pp: Oxygen-evolving enhancer protein 2, chloroplastic
Qq: Oxygen-evolving enhancer protein 3, chloroplastic
p: Oxygen-evolving enhancer protein 2, chloroplastic
q: Oxygen-evolving enhancer protein 3, chloroplastic
11: Chlorophyll a-b binding protein, chloroplastic
22: Chlorophyll a-b binding protein, chloroplastic
33: Chlorophyll a-b binding protein, chloroplastic
1: Chlorophyll a-b binding protein, chloroplastic
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
0: Photosystem II 10 kDa polypeptide, chloroplastic
5: Photosystem II reaction center proteins PsbY, chloroplastic
00: Photosystem II 10 kDa polypeptide, chloroplastic
55: Photosystem II reaction center proteins PsbY, chloroplastic
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
G: Chlorophyll a-b binding protein, chloroplastic
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
N: Chlorophyll a-b binding protein, chloroplastic
O: Oxygen-evolving enhancer protein 1, chloroplastic
P: Oxygen-evolving enhancer protein 2, chloroplastic
Q: Oxygen-evolving enhancer protein 3, chloroplastic
R: Chlorophyll a-b binding protein, chloroplastic
S: Chlorophyll a-b binding protein, chloroplastic
T: Photosystem II reaction center protein T
U: Photosystem II 5 kDa protein, chloroplastic
W: Photosystem II reaction center W protein, chloroplastic
X: Photosystem II reaction center X protein, chloroplastic
Y: Chlorophyll a-b binding protein, chloroplastic
Z: Photosystem II reaction center protein Z
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
g: Chlorophyll a-b binding protein, chloroplastic
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
n: Chlorophyll a-b binding protein, chloroplastic
o: Oxygen-evolving enhancer protein 1, chloroplastic
r: Chlorophyll a-b binding protein, chloroplastic
s: Chlorophyll a-b binding protein, chloroplastic
t: Photosystem II reaction center protein T
u: Photosystem II 5 kDa protein, chloroplastic
w: Photosystem II reaction center W protein, chloroplastic
x: Photosystem II reaction center X protein, chloroplastic
y: Chlorophyll a-b binding protein, chloroplastic
z: Photosystem II reaction center protein Z
4: Chlorophyll a-b binding protein CP24, chloroplastic
AA: Photosystem II protein D1
BB: Photosystem II CP47 reaction center protein
CC: Photosystem II CP43 reaction center protein
DD: Photosystem II D2 protein
B: Photosystem II CP47 reaction center protein
EE: Cytochrome b559 subunit alpha
FF: Cytochrome b559 subunit beta
GG: Chlorophyll a-b binding protein, chloroplastic
HH: Photosystem II reaction center protein H
II: Photosystem II reaction center protein I
JJ: Photosystem II reaction center protein J
KK: Photosystem II reaction center protein K
LL: Photosystem II reaction center protein L
MM: Photosystem II reaction center protein M
NN: Chlorophyll a-b binding protein, chloroplastic
OO: Oxygen-evolving enhancer protein 1, chloroplastic
PP: Oxygen-evolving enhancer protein 2, chloroplastic
QQ: Oxygen-evolving enhancer protein 3, chloroplastic
RR: Chlorophyll a-b binding protein, chloroplastic
SS: Chlorophyll a-b binding protein, chloroplastic
TT: Photosystem II reaction center protein T
UU: Photosystem II 5 kDa protein, chloroplastic
WW: Photosystem II reaction center W protein, chloroplastic
XX: Photosystem II reaction center X protein, chloroplastic
YY: Chlorophyll a-b binding protein, chloroplastic
ZZ: Photosystem II reaction center protein Z
Aa: Photosystem II protein D1
Bb: Photosystem II CP47 reaction center protein
Cc: Photosystem II CP43 reaction center protein
Dd: Photosystem II D2 protein
Ee: Cytochrome b559 subunit alpha
Ff: Cytochrome b559 subunit beta
Gg: Chlorophyll a-b binding protein, chloroplastic
Hh: Photosystem II reaction center protein H
Ii: Photosystem II reaction center protein I
Jj: Photosystem II reaction center protein J
Kk: Photosystem II reaction center protein K
Ll: Photosystem II reaction center protein L
Mm: Photosystem II reaction center protein M
Nn: Chlorophyll a-b binding protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,986,188893
Polymers2,355,228112
Non-polymers630,960781
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Photosystem II ... , 17 types, 64 molecules AaAAAaTtTtTTUuUuUUWwWwWWXxXxXXZzZzZZ000555Cc...

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


Mass: 38804.152 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P69560, photosystem II
#5: Protein/peptide
Photosystem II reaction center protein T / PSII-T


Mass: 3825.642 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P61840
#6: Protein
Photosystem II 5 kDa protein, chloroplastic


Mass: 10676.572 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0J8H2
#7: Protein
Photosystem II reaction center W protein, chloroplastic / PSII 6.1 kDa protein


Mass: 14186.097 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q41387
#8: Protein
Photosystem II reaction center X protein, chloroplastic


Mass: 11958.141 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JQ89
#10: Protein
Photosystem II reaction center protein Z / PSII-Z


Mass: 6541.715 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3M6
#16: Protein Photosystem II 10 kDa polypeptide, chloroplastic


Mass: 14409.401 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P10690
#17: Protein Photosystem II reaction center proteins PsbY, chloroplastic / L-arginine-metabolizing enzyme / L-AME


Mass: 20678.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P80470
#18: Protein
Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Photosystem II 44 kDa chlorophyll apoprotein / Protein CP-43


Mass: 51880.559 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06003
#19: Protein
Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39422.016 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06005, photosystem II
#22: Protein
Photosystem II reaction center protein H / PSII-H / Photosystem II 10 kDa phosphoprotein


Mass: 7735.004 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P05146
#23: Protein/peptide
Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 4170.891 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P62103
#24: Protein/peptide
Photosystem II reaction center protein J / PSII-J


Mass: 4117.832 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3L2
#25: Protein
Photosystem II reaction center protein K / PSII-K


Mass: 6751.023 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12163
#26: Protein/peptide
Photosystem II reaction center protein L / PSII-L


Mass: 4498.100 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P60150
#27: Protein/peptide
Photosystem II reaction center protein M / PSII-M


Mass: 3783.538 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P62112
#28: Protein
Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56207.852 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P04160

-
Oxygen-evolving enhancer protein ... , 3 types, 12 molecules OoOoOOPppPPPQqqQQQ

#2: Protein
Oxygen-evolving enhancer protein 1, chloroplastic / OEE1 / 33 kDa subunit of oxygen evolving system of photosystem II / 33 kDa thylakoid membrane ...OEE1 / 33 kDa subunit of oxygen evolving system of photosystem II / 33 kDa thylakoid membrane protein / OEC 33 kDa subunit


Mass: 35207.383 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12359
#12: Protein
Oxygen-evolving enhancer protein 2, chloroplastic / OEE2 / 23 kDa subunit of oxygen evolving system of photosystem II / 23 kDa thylakoid membrane ...OEE2 / 23 kDa subunit of oxygen evolving system of photosystem II / 23 kDa thylakoid membrane protein / OEC 23 kDa subunit


Mass: 28495.918 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12302
#13: Protein
Oxygen-evolving enhancer protein 3, chloroplastic / OEE3 / 16 kDa subunit of oxygen evolving system of photosystem II / OEC 16 kDa subunit


Mass: 24884.426 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12301

-
Chlorophyll a-b binding protein, ... , 5 types, 26 molecules RrRrRRSsSsSSYyGNYgnyGGNNYYGgNn112212333

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


Mass: 31046.254 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0HRF2
#4: Protein
Chlorophyll a-b binding protein, chloroplastic


Mass: 31341.840 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0IJF3
#9: Protein
Chlorophyll a-b binding protein, chloroplastic


Mass: 28433.391 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JBE4
#14: Protein
Chlorophyll a-b binding protein, chloroplastic


Mass: 28429.234 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A4F3R4
#15: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 28512.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: NCBI Reference Sequence: XP_021861951.1 / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0J656

-
Protein , 1 types, 2 molecules 444

#11: Protein Chlorophyll a-b binding protein CP24, chloroplastic


Mass: 27693.525 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P36494

-
Cytochrome b559 subunit ... , 2 types, 8 molecules EeEEEeFfFFFf

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


Mass: 9393.501 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P69383
#21: Protein/peptide
Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4502.351 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P60128

-
Sugars , 2 types, 24 molecules

#43: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#44: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C51H96O15

-
Non-polymers , 16 types, 757 molecules

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


Mass: 339.827 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CaMn4O5
#30: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#31: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#32: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 374 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#33: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C55H74N4O5
#34: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C40H56
#35: 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


Mass: 749.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C53H80O2 / Feature type: SUBJECT OF INVESTIGATION
#36: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#37: 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.: 14 / Source method: obtained synthetically / Formula: C41H78O12S
#38: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C45H86O10
#39: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 140 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#40: 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


Mass: 568.871 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C40H56O2
#41: 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


Mass: 600.870 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H56O4
#42: 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.: 14 / Source method: obtained synthetically / Formula: C40H56O4
#45: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHO3
#46: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: PSII-LHCII megacomplex / Type: COMPLEX
Entity ID: #16, #14-#15, #11, #17, #1, #28, #18-#21, #9, #22-#27, #2, #12-#13, #3-#8, #10
Source: NATURAL
Source (natural)Organism: Spinacia oleracea (spinach)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93684 / Symmetry type: POINT

+
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