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- PDB-6j40: Structure of C2S2M2-type PSII-FCPII supercomplex from diatom -

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Basic information

Entry
Database: PDB / ID: 6j40
TitleStructure of C2S2M2-type PSII-FCPII supercomplex from diatom
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Extrinsic protein in photosystem ...) x 3
  • (Fucoxanthin chlorophyll a/c-binding protein monomer ...) x 3
  • (Photosystem II chlorophyll protein ...) x 2
  • (Photosystem II reaction center protein ...) x 12
  • (Unknown protein ...) x 3
  • Cytochrome c-550
  • Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
  • Photosystem II reaction center X protein
KeywordsELECTRON TRANSPORT / Photosystem
Function / homology
Function and homology information


thylakoid / photosystem II assembly / photosystem II stabilization / photosystem II / extrinsic component of membrane / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / photosynthesis / respiratory electron transport chain ...thylakoid / photosystem II assembly / photosystem II stabilization / photosystem II / extrinsic component of membrane / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding
Similarity search - Function
PsbQ-like domain superfamily / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II PsbX, type 1 subfamily ...PsbQ-like domain superfamily / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Chem-A86 / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER ...Chem-A86 / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Extrinsic protein in photosystem II / Extrinsic protein in photosystem II / Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein X / Photosystem II extrinsic protein V / Photosystem II reaction center protein H
Similarity search - Component
Biological speciesChaetoceros gracilis (Diatom)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsNagao, R. / Kato, K. / Shen, J.R. / Miyazaki, N. / Akita, F.
CitationJournal: Nat Plants / Year: 2019
Title: Structural basis for energy harvesting and dissipation in a diatom PSII-FCPII supercomplex.
Authors: Ryo Nagao / Koji Kato / Takehiro Suzuki / Kentaro Ifuku / Ikuo Uchiyama / Yasuhiro Kashino / Naoshi Dohmae / Seiji Akimoto / Jian-Ren Shen / Naoyuki Miyazaki / Fusamichi Akita /
Abstract: Light-harvesting antenna systems in photosynthetic organisms harvest solar energy and transfer it to the photosynthetic reaction centres to initiate charge-separation and electron-transfer reactions. ...Light-harvesting antenna systems in photosynthetic organisms harvest solar energy and transfer it to the photosynthetic reaction centres to initiate charge-separation and electron-transfer reactions. Diatoms are one of the important groups of oxyphototrophs and possess fucoxanthin chlorophyll a/c-binding proteins (FCPs) as light harvesters. The organization and association pattern of FCP with the photosystem II (PSII) core are unknown. Here we solved the structure of PSII-FCPII supercomplexes isolated from a diatom, Chaetoceros gracilis, by single-particle cryoelectron microscopy. The PSII-FCPII forms a homodimer. In each monomer, two FCP homotetramers and three FCP monomers are associated with one PSII core. The structure reveals a highly complicated protein-pigment network that is different from the green-type light-harvesting apparatus. Comparing these two systems allows the identification of energy transfer and quenching pathways. These findings provide structural insights into not only excitation-energy transfer mechanisms in the diatom PSII-FCPII, but also changes of light harvesters between the red- and green-lineage oxyphototrophs during evolution.
History
DepositionJan 7, 2019Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

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Assembly

Deposited unit
A: Photosystem II reaction center protein D1
B: Photosystem II chlorophyll protein CP47
C: Photosystem II chlorophyll protein CP43
D: Photosystem II reaction center protein D2
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Extrinsic protein in photosystem II
T: Photosystem II reaction center protein T
U: Extrinsic protein in photosystem II
V: Cytochrome c-550
Y: Photosystem II reaction center protein Ycf12
X: Photosystem II reaction center X protein
Z: Photosystem II reaction center protein Z
Q: Extrinsic protein in photosystem II
W: Photosystem II reaction center protein W
0: Unknown protein 0
1: Unknown protein 1
2: Unknown protein 2
a: Photosystem II reaction center protein D1
b: Photosystem II chlorophyll protein CP47
c: Photosystem II chlorophyll protein CP43
d: Photosystem II reaction center protein D2
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Extrinsic protein in photosystem II
t: Photosystem II reaction center protein T
u: Extrinsic protein in photosystem II
v: Cytochrome c-550
y: Photosystem II reaction center protein Ycf12
x: Photosystem II reaction center X protein
z: Photosystem II reaction center protein Z
q: Extrinsic protein in photosystem II
w: Photosystem II reaction center protein W
5: Unknown protein 0
6: Unknown protein 1
7: Unknown protein 2
11: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
12: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
13: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
14: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
15: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
16: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
17: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
18: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
19: Fucoxanthin chlorophyll a/c-binding protein monomer 1
20: Fucoxanthin chlorophyll a/c-binding protein monomer 2
21: Fucoxanthin chlorophyll a/c-binding protein monomer 3
31: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
32: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
33: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
34: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
35: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
36: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
37: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
38: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
39: Fucoxanthin chlorophyll a/c-binding protein monomer 1
40: Fucoxanthin chlorophyll a/c-binding protein monomer 2
41: Fucoxanthin chlorophyll a/c-binding protein monomer 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,510,991558
Polymers1,121,19270
Non-polymers389,799488
Water00
1


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

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Components

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Photosystem II reaction center protein ... , 12 types, 24 molecules AaDdHhIiJjKkLlMmTtYyZzWw

#1: Protein Photosystem II reaction center protein D1


Mass: 38183.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#4: Protein Photosystem II reaction center protein D2


Mass: 39069.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#7: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7418.827 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B7XBY7
#8: Protein/peptide Photosystem II reaction center protein I


Mass: 4427.212 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#9: Protein/peptide Photosystem II reaction center protein J


Mass: 4093.833 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#10: Protein/peptide Photosystem II reaction center protein K


Mass: 4978.028 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#11: Protein/peptide Photosystem II reaction center protein L


Mass: 4367.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#12: Protein Photosystem II reaction center protein M


Mass: 14180.403 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#14: Protein/peptide Photosystem II reaction center protein T


Mass: 3711.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#17: Protein/peptide Photosystem II reaction center protein Ycf12


Mass: 3609.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#19: Protein Photosystem II reaction center protein Z


Mass: 6528.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#21: Protein Photosystem II reaction center protein W


Mass: 7848.743 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Photosystem II chlorophyll protein ... , 2 types, 4 molecules BbCc

#2: Protein Photosystem II chlorophyll protein CP47


Mass: 56475.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#3: Protein Photosystem II chlorophyll protein CP43


Mass: 51947.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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

#5: Protein Cytochrome b559 subunit alpha


Mass: 9507.667 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#6: Protein/peptide Cytochrome b559 subunit beta


Mass: 4912.796 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Extrinsic protein in photosystem ... , 3 types, 6 molecules OoUuQq

#13: Protein Extrinsic protein in photosystem II / Extrinsic protein O of oxygen-evolving complex


Mass: 26762.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHE8
#15: Protein Extrinsic protein in photosystem II / Extrinsic protein U of oxygen-evolving complex


Mass: 10137.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF0
#20: Protein Extrinsic protein in photosystem II / Extrinsic protein Q of oxygen-evolving complex


Mass: 17088.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHE9

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Protein , 2 types, 18 molecules Vv11121314151617183132333435363738

#16: Protein Cytochrome c-550 / Extrinsic protein V of oxygen-evolving complex


Mass: 14893.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF4
#25: Protein
Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1


Mass: 22098.182 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Protein/peptide , 1 types, 2 molecules Xx

#18: Protein/peptide Photosystem II reaction center X protein / Photosystem II reaction center protein X


Mass: 3859.647 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF2

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Unknown protein ... , 3 types, 6 molecules 051627

#22: Protein/peptide Unknown protein 0


Mass: 2656.265 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#23: Protein/peptide Unknown protein 1


Mass: 2571.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#24: Protein/peptide Unknown protein 2


Mass: 869.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Fucoxanthin chlorophyll a/c-binding protein monomer ... , 3 types, 6 molecules 193920402141

#26: Protein Fucoxanthin chlorophyll a/c-binding protein monomer 1


Mass: 18315.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#27: Protein Fucoxanthin chlorophyll a/c-binding protein monomer 2


Mass: 12188.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#28: Protein Fucoxanthin chlorophyll a/c-binding protein monomer 3


Mass: 13209.274 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Sugars , 2 types, 10 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15
#42: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 12 types, 478 molecules

#29: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#30: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 290 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#31: Chemical
ChemComp-PHO / PHEOPHYTIN A


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


Mass: 536.873 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H56
#33: 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
#34: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#35: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#36: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C45H86O10
#37: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#39: 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.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#40: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#41: Chemical...
ChemComp-A86 / (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate / Fucoxanthin


Mass: 658.906 Da / Num. of mol.: 118 / Source method: obtained synthetically / Formula: C42H58O6

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Details

Has protein modificationY
Sequence detailsUnknown protein 0/1/2 are supposed to be new components of photosystem II. Fucoxanthin chlorophyll ...Unknown protein 0/1/2 are supposed to be new components of photosystem II. Fucoxanthin chlorophyll a/c-binding protein monomer 1/2/3 are obviously Fucoxanthin chlorophyll a/c-binding protein which are different from Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1. Sequence of above entities could not be assigned.

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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: C2S2M2-type PSII-FCPII supercomplex / Type: COMPLEX / Entity ID: #1-#28 / Source: NATURAL
Molecular weightValue: 1.15 MDa / Experimental value: NO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Buffer solutionpH: 6.5
Buffer component
IDConc.FormulaBuffer-ID
120 mMMES-NaOH1
20.02 %DDM1
SpecimenConc.: 0.256 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: (1.14_3260: phenix.real_space_refine) / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
7UCSF Chimera1.12model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.13_2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98936 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13WU2

3wu2

13WU21PDBexperimental model
23JCU

3jcu

13JCU2PDBexperimental model

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