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- PDB-3jcu: Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angst... -

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Entry
Database: PDB / ID: 3jcu
TitleCryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom resolution
Components
  • (Chlorophyll A-B Binding protein ...Light-harvesting complexes of green plants) x 2
  • (Cytochrome b559 subunit ...) x 2
  • (Oxygen-evolving enhancer protein ...) x 3
  • (Photosystem II ...) x 13
  • (Protein Photosystem II reaction center protein ...) x 2
  • Chlorophyll a-b binding protein, chloroplastic
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


chloroplast photosystem II / plastoglobule / photosynthesis, light harvesting in photosystem I / : / photosynthesis, light harvesting / photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II ...chloroplast photosystem II / plastoglobule / photosynthesis, light harvesting in photosystem I / : / photosynthesis, light harvesting / photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / chloroplast envelope / : / ion binding / 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 / phosphoprotein binding / electron transfer activity / membrane => GO:0016020 / protein stabilization / iron ion binding / calcium ion binding / heme binding / metal ion binding
Similarity search - Function
PsbP, C-terminal / Photosystem II 5kDa protein, chloroplastic / Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle / Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / PsbP, C-terminal / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / : / Photosystem II PsbW, class 2 ...PsbP, C-terminal / Photosystem II 5kDa protein, chloroplastic / Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle / Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / 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) / photosynthetic oxygen evolving center fold / photosynthetic oxygen evolving center domain / Protein Transport Mog1p; Chain A / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II, cytochrome c-550 precursor / 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 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 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 / Porin / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Arc Repressor Mutant, subunit A / Roll / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / 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 / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem II 5 kDa 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 reaction center protein K / Oxygen-evolving enhancer protein 3, chloroplastic / Oxygen-evolving enhancer protein 2, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Oxygen-evolving enhancer protein 1, 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 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: 3.2 Å
AuthorsWei, X.P. / Zhang, X.Z. / Su, X.D. / Cao, P. / Liu, X.Y. / Li, M. / Chang, W.R. / Liu, Z.F.
CitationJournal: Nature / Year: 2016
Title: Structure of spinach photosystem II-LHCII supercomplex at 3.2 Å resolution.
Authors: Xuepeng Wei / Xiaodong Su / Peng Cao / Xiuying Liu / Wenrui Chang / Mei Li / Xinzheng Zhang / Zhenfeng Liu /
Abstract: During photosynthesis, the plant photosystem II core complex receives excitation energy from the peripheral light-harvesting complex II (LHCII). The pathways along which excitation energy is ...During photosynthesis, the plant photosystem II core complex receives excitation energy from the peripheral light-harvesting complex II (LHCII). The pathways along which excitation energy is transferred between them, and their assembly mechanisms, remain to be deciphered through high-resolution structural studies. Here we report the structure of a 1.1-megadalton spinach photosystem II-LHCII supercomplex solved at 3.2 Å resolution through single-particle cryo-electron microscopy. The structure reveals a homodimeric supramolecular system in which each monomer contains 25 protein subunits, 105 chlorophylls, 28 carotenoids and other cofactors. Three extrinsic subunits (PsbO, PsbP and PsbQ), which are essential for optimal oxygen-evolving activity of photosystem II, form a triangular crown that shields the Mn4CaO5-binding domains of CP43 and D1. One major trimeric and two minor monomeric LHCIIs associate with each core-complex monomer, and the antenna-core interactions are reinforced by three small intrinsic subunits (PsbW, PsbH and PsbZ). By analysing the closely connected interfacial chlorophylls, we have obtained detailed insights into the energy-transfer pathways between the antenna and core complexes.
History
DepositionMar 10, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Structure summary
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3May 1, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: cell / database_2 ...cell / database_2 / database_PDB_caveat / em_image_scans / em_software / pdbx_validate_chiral / pdbx_validate_close_contact
Item: _cell.Z_PDB / _cell.length_a ..._cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _em_software.name / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2
Revision 1.4Dec 18, 2019Group: Data collection / Category: em_software / Item: _em_software.image_processing_id

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Structure visualization

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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, chloroplastic
H: Photosystem II reaction center protein H
I: Protein Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Protein 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 29 kD (CP29)
S: Chlorophyll A-B Binding protein 26 kD (CP26)
T: Photosystem II Reaction Center protein Tc
U: Photosystem II Reaction Center Tn protein
W: Photosystem II reaction center W protein, chloroplastic
X: Photosystem II Reaction Center X protein
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: Protein Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Protein 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 29 kD (CP29)
s: Chlorophyll A-B Binding protein 26 kD (CP26)
t: Photosystem II Reaction Center protein Tc
u: Photosystem II Reaction Center Tn protein
w: Photosystem II reaction center W protein, chloroplastic
x: Photosystem II Reaction Center X protein
y: Chlorophyll a-b binding protein, chloroplastic
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,276,895372
Polymers1,019,82350
Non-polymers257,072322
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Photosystem II ... , 13 types, 26 molecules AaBbCcDdHhJjKkMmTtUuWwXxZz

#1: Protein Photosystem II protein D1 /


Mass: 38134.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P69560
#2: Protein Photosystem II CP47 reaction center protein /


Mass: 56207.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P04160
#3: Protein Photosystem II CP43 reaction center protein /


Mass: 51880.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06003
#4: Protein Photosystem II D2 protein /


Mass: 39535.172 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06005
#8: Protein Photosystem II reaction center protein H /


Mass: 7735.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P05146
#10: Protein/peptide Photosystem II reaction center protein J /


Mass: 4117.832 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3L2
#11: Protein Photosystem II reaction center protein K /


Mass: 6751.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12163
#13: Protein/peptide Photosystem II reaction center protein M /


Mass: 3783.538 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P62112
#19: Protein/peptide Photosystem II Reaction Center protein Tc /


Mass: 3825.642 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P61840
#20: Protein Photosystem II Reaction Center Tn protein /


Mass: 10676.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RHP1
#21: Protein Photosystem II reaction center W protein, chloroplastic /


Mass: 14186.097 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q41387
#22: Protein Photosystem II Reaction Center X protein /


Mass: 11958.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RTU3, UniProt: A0A0K9RHP1*PLUS
#23: Protein Photosystem II reaction center protein Z /


Mass: 6541.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3M6

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

#5: Protein Cytochrome b559 subunit alpha /


Mass: 9393.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P69383
#6: Protein/peptide Cytochrome b559 subunit beta /


Mass: 4502.351 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P60128

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Protein Photosystem II reaction center protein ... , 2 types, 4 molecules IiLl

#9: Protein/peptide Protein Photosystem II reaction center protein I /


Mass: 4170.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P62103
#12: Protein/peptide Protein Photosystem II reaction center protein L /


Mass: 4498.100 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P60150

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

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


Mass: 35207.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12359
#15: Protein Oxygen-evolving enhancer protein 2, chloroplastic


Mass: 28495.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12302
#16: Protein Oxygen-evolving enhancer protein 3, chloroplastic


Mass: 24884.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12301

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Chlorophyll A-B Binding protein ... , 2 types, 4 molecules RrSs

#17: Protein Chlorophyll A-B Binding protein 29 kD (CP29)


Mass: 26735.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: F2Z293, UniProt: A0A0K9QLX6*PLUS
#18: Protein Chlorophyll A-B Binding protein 26 kD (CP26)


Mass: 31341.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QUQ7

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Protein / Sugars , 2 types, 14 molecules GNYgny

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


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15
#7: Protein
Chlorophyll a-b binding protein, chloroplastic


Mass: 28449.391 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12333

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Non-polymers , 16 types, 314 molecules

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


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


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


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


Mass: 893.489 Da / Num. of mol.: 156 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#28: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


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


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56
#30: 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
#31: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10
#33: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#34: 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
#35: 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
#36: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 907.472 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#38: 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.: 18 / Source method: obtained synthetically / Formula: C40H56O2
#39: 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
#40: 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

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Membrane protein / Type: COMPLEX / Details: dimer
Molecular weightValue: 1.1 MDa / Experimental value: NO
Buffer solutionName: HEPES / pH: 7.5 / Details: HEPES
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh copper grid
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 100 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Nov 20, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 50 e/Å2 / Film or detector model: OTHER

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Processing

EM software
IDNameCategory
1EMAN3D reconstruction
2RELION3D reconstruction
CTF correctionDetails: Each micrograph
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionMethod: maximum likelihood / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109042 / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms59354 0 16640 0 75994

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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

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