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- PDB-9lk5: The structure of Lhcb8-C2S2 PSII-LHCII supercomplex from Arabidop... -

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Basic information

Entry
Database: PDB / ID: 9lk5
TitleThe structure of Lhcb8-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


photosynthesis, light harvesting in photosystem II / response to desiccation / photoinhibition / cellular response to abscisic acid stimulus / cellular response to water deprivation / photosystem II antenna complex / response to red light / PSII associated light-harvesting complex II / nonphotochemical quenching / chloroplast stromal thylakoid ...photosynthesis, light harvesting in photosystem II / response to desiccation / photoinhibition / cellular response to abscisic acid stimulus / cellular response to water deprivation / photosystem II antenna complex / response to red light / PSII associated light-harvesting complex II / nonphotochemical quenching / chloroplast stromal thylakoid / plastid thylakoid membrane / thylakoid lumen / response to low light intensity stimulus / plastoglobule / regulation of stomatal closure / response to high light intensity / response to far red light / thylakoid membrane / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / vacuolar transport / thylakoid / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem II oxygen evolving complex / apoplast / photosystem II assembly / response to fructose / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / chloroplast envelope / plant-type vacuole / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / response to herbicide / photosystem II / poly(U) RNA binding / plastid / chloroplast stroma / chlorophyll binding / positive regulation of reactive oxygen species biosynthetic process / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / : / 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 / Golgi apparatus / mitochondrion / metal ion binding / nucleus / 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 / RRR-ALPHA-TOCOPHERYLQUINONE / 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 / 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 CP29.3, 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 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: To Be Published
Title: A stress-induced paralog of Lhcb4 controls the photosystem II functional architecture in Arabidopsis thaliana
Authors: Caferri, R. / Zhou, Q. / Dall'Osto, L. / Amelii, A. / Shan, J.Y. / Liu, Z.F. / Bassi, R.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 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
S: Chlorophyll a-b binding protein CP26, 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
o: Oxygen-evolving enhancer protein 1-1, chloroplastic
r: Chlorophyll a-b binding protein CP29.3, chloroplastic
s: Chlorophyll a-b binding protein CP26, 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
z: Photosystem II reaction center protein Z
n: Chlorophyll a-b binding protein 2, chloroplastic
y: Chlorophyll a-b binding protein 2.2, chloroplastic
R: Chlorophyll a-b binding protein CP29.3, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,190,931384
Polymers920,71046
Non-polymers270,221338
Water00
1


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

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Components

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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

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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

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

#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 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
#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 CP29.3, chloroplastic / LHCB4.3 / LHCII protein 4.3


Mass: 31297.531 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: LHCB4.3, At2g40100, F27I1.2 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9S7W1

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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

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Sugars , 2 types, 14 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15
#32: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 15 types, 324 molecules

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


Mass: 893.489 Da / Num. of mol.: 154 / 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.: 8 / Source method: obtained synthetically / Formula: C41H78O12S
#27: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#29: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#30: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C45H86O10
#31: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#33: 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
#34: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 907.472 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#36: 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
#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
#38: 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
#39: Chemical ChemComp-VTQ / RRR-ALPHA-TOCOPHERYLQUINONE


Mass: 446.706 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H50O3

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Details

Has ligand of interestY
Has protein modificationY

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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: Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana
Type: COMPLEX / Entity ID: #1-#22 / 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

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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)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104217 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00574562
ELECTRON MICROSCOPYf_angle_d1.225104148
ELECTRON MICROSCOPYf_dihedral_angle_d18.12213732
ELECTRON MICROSCOPYf_chiral_restr0.0929610
ELECTRON MICROSCOPYf_plane_restr0.00913456

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