[English] 日本語
Yorodumi
- PDB-9lk4: Cryo-EM structure of Lhcb4.1-C2S2 PSII-LHCII supercomplex from Ar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lk4
TitleCryo-EM structure of Lhcb4.1-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana
Components
  • (Chlorophyll a-b binding protein ...) x 4
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 14
  • (thale cress) hypothetical protein
  • Oxygen-evolving enhancer protein 1-1, chloroplastic
KeywordsPHOTOSYNTHESIS / Photosystem II / light harvesting / photoacclimation / stress-induced antennae / cryo-EM
Function / homology
Function and homology information


response to desiccation / photoinhibition / photosynthesis, light harvesting in photosystem II / photosystem II antenna complex / cellular response to abscisic acid stimulus / PSII associated light-harvesting complex II / cellular response to water deprivation / response to red light / nonphotochemical quenching / plastid thylakoid membrane ...response to desiccation / photoinhibition / photosynthesis, light harvesting in photosystem II / photosystem II antenna complex / cellular response to abscisic acid stimulus / PSII associated light-harvesting complex II / cellular response to water deprivation / response to red light / nonphotochemical quenching / plastid thylakoid membrane / response to low light intensity stimulus / chloroplast stromal thylakoid / thylakoid lumen / plastoglobule / regulation of stomatal closure / response to high light intensity / thylakoid membrane / response to far red light / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / thylakoid / vacuolar transport / chloroplast thylakoid lumen / apoplast / photosynthesis, light harvesting / photosystem II oxygen evolving complex / response to fructose / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / chloroplast envelope / photosystem II reaction center / photosystem II / plant-type vacuole / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / photosystem II / response to herbicide / poly(U) RNA binding / plastid / chloroplast stroma / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / positive regulation of reactive oxygen species biosynthetic process / : / response to light stimulus / photosynthesis / response to cold / chloroplast / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / heme binding / mitochondrion / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Photosystem II 5kDa protein, chloroplastic / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Snf7 family / Snf7 / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide ...Photosystem II 5kDa protein, chloroplastic / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Snf7 family / Snf7 / 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 / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Chem-XAT / (thale cress) hypothetical protein / Chlorophyll a-b binding protein 2, chloroplastic / Oxygen-evolving enhancer protein 1-1, chloroplastic / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein H / Photosystem II reaction center protein J / Photosystem II reaction center protein K / Photosystem II reaction center protein Z / Photosystem II reaction center protein L / Photosystem II reaction center protein T / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Photosystem II protein D1 / Chlorophyll a-b binding protein CP29.1, chloroplastic / Photosystem II reaction center W protein, chloroplastic / Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein 2.2, chloroplastic / Chlorophyll a-b binding protein CP26, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhou, Q. / Caferri, R. / Shan, J.Y. / Amelii, A. / Bassi, R. / Liu, Z.F.
Funding supportEuropean Union, China, 3items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
National Natural Science Foundation of China (NSFC) China
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2025
Title: A stress-induced paralog of Lhcb4 controls the photosystem II functional architecture in Arabidopsis thaliana.
Authors: Roberto Caferri / Qian Zhou / Luca Dall'Osto / Antonello Amelii / Jianyu Shan / Zhenfeng Liu / Roberto Bassi /
Abstract: Photosystem II (PSII) is the pigment-protein complex catalysing light-induced water oxidation. In Arabidopsis thaliana, it includes three Lhcb4-6 proteins linking the core complex to peripheral ...Photosystem II (PSII) is the pigment-protein complex catalysing light-induced water oxidation. In Arabidopsis thaliana, it includes three Lhcb4-6 proteins linking the core complex to peripheral trimeric antennae. While Lhcb5 and Lhcb6 are encoded by single genes, Lhcb4 is encoded by three isoforms: Lhcb4.1 and Lhcb4.2, constitutively expressed, and Lhcb4.3 (Lhcb8), which accumulates under prolonged abiotic stress. Lhcb8 substitutes for Lhcb4, preventing Lhcb6 accumulation and resulting in a smaller PSII with high quantum yield. Cryo-electron microscopy reveals that Lhcb8 has a shorter carboxy-terminal domain, lacks two chlorophylls, and interacts more tightly with the PSII core, inducing structural changes in the PSII antenna system, ultimately inhibiting the formation of PSII arrays and favouring plastoquinone diffusion. We suggest that dynamic Lhcb4 vs Lhcb8 expression allows for PSII acclimation to contrasting light conditions, offering the potential for engineering crops with improved light use efficiency.
History
DepositionJan 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 6, 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.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.2Aug 13, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
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 2, 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 2, chloroplastic
O: Oxygen-evolving enhancer protein 1-1, chloroplastic
R: Chlorophyll a-b binding protein CP29.1, chloroplastic
T: Photosystem II reaction center protein T
U: Photosystem II 5 kDa protein, chloroplastic
W: Photosystem II reaction center W protein, chloroplastic
X: (thale cress) hypothetical protein
Y: Chlorophyll a-b binding protein 2.2, 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 2, 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 2, chloroplastic
o: Oxygen-evolving enhancer protein 1-1, chloroplastic
r: Chlorophyll a-b binding protein CP29.1, chloroplastic
t: Photosystem II reaction center protein T
u: Photosystem II 5 kDa protein, chloroplastic
w: Photosystem II reaction center W protein, chloroplastic
x: (thale cress) hypothetical protein
y: Chlorophyll a-b binding protein 2.2, chloroplastic
z: Photosystem II reaction center protein Z
S: Chlorophyll a-b binding protein CP26, chloroplastic
s: Chlorophyll a-b binding protein CP26, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,182,946368
Polymers922,57046
Non-polymers260,377322
Water00
1


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

-
Components

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

#1: Protein Photosystem II protein D1 / PSII D1 protein / Photosystem II Q(B) protein


Mass: 38961.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P83755, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56091.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56777
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 51915.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56778
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39575.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56761, photosystem II
#8: Protein Photosystem II reaction center protein H / PSII-H / Photosystem II 10 kDa phosphoprotein


Mass: 7706.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56780
#9: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 4170.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62100
#10: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 4117.832 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56781
#11: Protein Photosystem II reaction center protein K / PSII-K


Mass: 6977.381 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56782
#12: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4471.075 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P60129
#13: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3783.538 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62109
#16: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3825.642 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P61839
#17: Protein Photosystem II 5 kDa protein, chloroplastic / PSII-T / Nuclear encoded psbT / PsbTn


Mass: 11042.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q39195
#18: Protein Photosystem II reaction center W protein, chloroplastic / PSII 6.1 kDa protein


Mass: 13685.823 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q39194
#21: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6569.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56790

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

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


Mass: 9393.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56779
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4428.228 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62095

-
Chlorophyll a-b binding protein ... , 4 types, 10 molecules GNgnRrYySs

#7: Protein
Chlorophyll a-b binding protein 2, chloroplastic / Chlorophyll a-b protein 165 / CAB-165 / LHCII type I CAB-2


Mass: 28250.984 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P0CJ48
#15: Protein Chlorophyll a-b binding protein CP29.1, chloroplastic / LHCB4.1 / LHCII protein 4.1


Mass: 32227.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A 4*glycine followed by a 6*HisTAG was added to the C-terminal of the protein
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHCB4.1, At5g01530, F7A7_50 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q07473
#20: Protein Chlorophyll a-b binding protein 2.2, chloroplastic / Photosystem II light harvesting complex gene 2.2 / Protein LIGHT-HARVESTING CHLOROPHYLL B-BINDING 2.2


Mass: 28644.432 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S7J7
#22: Protein Chlorophyll a-b binding protein CP26, chloroplastic / LHCB5 / LHCIIc / Light-harvesting complex II protein 5


Mass: 30187.576 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9XF89

-
Protein , 2 types, 4 molecules OoXx

#14: Protein Oxygen-evolving enhancer protein 1-1, 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 / Manganese-stabilizing protein 1 / MSP-1 / OEC 33 kDa subunit


Mass: 35180.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P23321
#19: Protein (thale cress) hypothetical protein


Mass: 11826.013 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A7G2E9B1

-
Sugars , 1 types, 6 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C51H96O15

-
Non-polymers , 14 types, 316 molecules

#23: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 156 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical
ChemComp-PHO / PHEOPHYTIN A


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


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56
#26: 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.: 6 / Source method: obtained synthetically / Formula: C41H78O12S
#27: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C45H86O10
#29: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#30: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#31: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#32: 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.: 2 / Source method: obtained synthetically / Formula: C53H80O2
#33: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 907.472 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#35: 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.: 18 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#36: 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 / Feature type: SUBJECT OF INVESTIGATION
#37: 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.: 8 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION

-
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: Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana
Type: COMPLEX / Entity ID: #1-#21 / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.5
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: TFS 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: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67864 / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00773724
ELECTRON MICROSCOPYf_angle_d1.428103196
ELECTRON MICROSCOPYf_dihedral_angle_d18.84912818
ELECTRON MICROSCOPYf_chiral_restr0.0989446
ELECTRON MICROSCOPYf_plane_restr0.0113460

+
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