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- PDB-8asl: RCII/PSI complex, class 2 -

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Basic information

Entry
Database: PDB / ID: 8asl
TitleRCII/PSI complex, class 2
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • (Photosystem II ...) x 4
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / photosystem / assembly factor / membrane protein
Function / homology
Function and homology information


plasma membrane-derived thylakoid photosystem II / plasma membrane-derived photosystem I / thylakoid lumen / photosystem II assembly / oxygen evolving activity / photosystem II / photosystem II reaction center / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I ...plasma membrane-derived thylakoid photosystem II / plasma membrane-derived photosystem I / thylakoid lumen / photosystem II assembly / oxygen evolving activity / photosystem II / photosystem II reaction center / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / heme binding / magnesium ion binding / identical protein binding / metal ion binding
Similarity search - Function
Photosynthesis system II assembly factor Ycf48/Hcf136 / Photosynthesis system II assembly factor Ycf48/Hcf136-like domain / Photosynthesis system II assembly factor YCF48 / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. ...Photosynthesis system II assembly factor Ycf48/Hcf136 / Photosynthesis system II assembly factor Ycf48/Hcf136-like domain / Photosynthesis system II assembly factor YCF48 / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem II PsbI / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem II PsbI superfamily / Photosystem I reaction centre subunit III / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / 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 I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
beta,beta-carotene-4,4'-dione / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / beta,beta-caroten-4-one / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE ...beta,beta-carotene-4,4'-dione / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / beta,beta-caroten-4-one / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-ZEX / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II D2 protein / Photosystem I reaction center subunit IV / Photosystem II protein D1 2 / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII / Photosystem II assembly lipoprotein Ycf48 / Photosystem II reaction center protein I / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VIII
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsZhao, Z. / Vercellino, I. / Knoppova, J. / Sobotka, R. / Murray, J.W. / Nixon, P.J. / Sazanov, L.A. / Komenda, J.
Funding support United Kingdom, European Union, Czech Republic, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L003260/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P00931X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P00931X/1 United Kingdom
European Research Council (ERC)854126European Union
Czech Science Foundation19-29225X Czech Republic
CitationJournal: Nat Commun / Year: 2023
Title: The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis.
Authors: Ziyu Zhao / Irene Vercellino / Jana Knoppová / Roman Sobotka / James W Murray / Peter J Nixon / Leonid A Sazanov / Josef Komenda /
Abstract: Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly ...Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising MnCaO cluster, thereby preventing the premature binding of Mn and Ca ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the MnCaO cluster.
History
DepositionAug 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: 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 I P700 chlorophyll a apoprotein A1
b: Photosystem I P700 chlorophyll a apoprotein A2
c: Photosystem I iron-sulfur center
d: Photosystem I reaction center subunit II
e: Photosystem I reaction center subunit IV
f: Photosystem I reaction center subunit III
i: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
k: Photosystem I reaction center subunit PsaK 1
l: Photosystem I reaction center subunit XI
m: Photosystem I reaction center subunit XII
A: Photosystem II protein D1 2
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
I: Photosystem II reaction center protein I
S: Photosystem II assembly lipoprotein Ycf48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)500,876162
Polymers385,06017
Non-polymers115,816145
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area244180 Å2
ΔGint-1875 kcal/mol
Surface area99630 Å2
MethodPISA

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules ab

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / / PsaA


Mass: 83036.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PsaA / Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaA, slr1834 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P29254, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PsaB


Mass: 81369.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PsaB / Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaB, slr1835 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P29255, photosystem I

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Photosystem I reaction center subunit ... , 8 types, 8 molecules defijklm

#4: Protein Photosystem I reaction center subunit II / / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15663.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaD, slr0737 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P19569
#5: Protein Photosystem I reaction center subunit IV / / Photosystem I 8.1 kDa protein / p30 protein


Mass: 8154.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaE, ssr2831 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P12975
#6: Protein Photosystem I reaction center subunit III / / PSI-F


Mass: 18267.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaF, sll0819 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P29256
#7: Protein/peptide Photosystem I reaction center subunit VIII /


Mass: 4414.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaI, smr0004 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: Q55330
#8: Protein/peptide Photosystem I reaction center subunit IX /


Mass: 4535.415 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaJ, sml0008 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: Q55329
#9: Protein Photosystem I reaction center subunit PsaK 1 / / Photosystem I subunit X 1


Mass: 8649.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaK1, psaK, ssr0390 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P72712
#10: Protein Photosystem I reaction center subunit XI / / PSI subunit V / PSI-L


Mass: 16631.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaL, slr1655 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P37277
#11: Protein/peptide Photosystem I reaction center subunit XII / / PSI-M


Mass: 3382.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaM, smr0005 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P72986

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Photosystem II ... , 4 types, 4 molecules ADIS

#12: Protein Photosystem II protein D1 2 / / PSII D1 protein 2 / Photosystem II Q(B) protein 2


Mass: 38280.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psbA2, psbA-2, slr1311, psbA3, psbA-3, sll1867 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P16033, photosystem II
#13: Protein Photosystem II D2 protein / / PSII D2 protein / Photosystem Q(A) protein


Mass: 37816.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psbD, sll0849 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P09192, photosystem II
#16: Protein/peptide Photosystem II reaction center protein I / / PSII-I / PSII 4.4 kDa protein


Mass: 4310.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psbI, sml0001 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: Q54697
#17: Protein Photosystem II assembly lipoprotein Ycf48 /


Mass: 37321.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: ycf48, slr2034 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P73069

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Cytochrome b559 subunit ... , 2 types, 2 molecules EF

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


Mass: 9454.577 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psbE, ssr3451 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P09190
#15: Protein/peptide Cytochrome b559 subunit beta / / PSII reaction center subunit VI


Mass: 4935.784 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psbF, smr0006 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P09191

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Protein / Sugars , 2 types, 2 molecules c

#29: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8837.261 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: psaC, ssl0563 / Production host: Synechocystis sp. PCC 6803 (bacteria) / Strain (production host): His-D2/DeltaCP47 / References: UniProt: P32422, photosystem I

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Non-polymers , 14 types, 144 molecules

#18: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#19: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 101 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#21: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H56
#22: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#23: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10
#24: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin / Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H52O2
#25: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#26: Chemical ChemComp-ECH / beta,beta-caroten-4-one / echinenone / Echinenone


Mass: 550.856 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H54O
#27: Chemical ChemComp-EQ3 / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / 3'-Hydroxyechinenone / 3'-OH-Echinenone / 3'-Hydroxyechinenone


Mass: 566.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54O2
#28: Chemical ChemComp-ZEX / (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O2
#30: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#31: Chemical ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O5
#32: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Details

Has ligand of interestY

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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: RCII/PSI complex class 2 / Type: COMPLEX / Entity ID: #4-#5, #14, #16-#17 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: His-D2/DeltaCP47
Source (recombinant)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: His-D2/DeltaCP47
Buffer solutionpH: 6.5
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 90.9 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2853

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4CTFFIND4CTF correction
7PHENIX1.19model fittingphenix.dock_in_map
9PHENIX1.19model refinementphenix.real_space_refine
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1250000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178513 / Algorithm: FOURIER SPACE / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Correlation coefficient
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-ID
16WJ6

6wj6

A6WJ6A
26WJ6

6wj6

D6WJ6D
36WJ6

6wj6

E6WJ6E
46WJ6

6wj6

F6WJ6F
56WJ6

6wj6

I6WJ6I
65OY0

5oy0

a5OY0a
75OY0

5oy0

b5OY0b
85OY0

5oy0

c5OY0c
95OY0

5oy0

d5OY0d
105OY0

5oy0

e5OY0e
115OY0

5oy0

f5OY0f
125OY0

5oy0

j5OY0j
135OY0

5oy0

k5OY0k
145OY0

5oy0

l5OY0l
155OY0

5oy0

l5OY0l
162XBG

2xbg

S2XBGS
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00434388
ELECTRON MICROSCOPYf_angle_d0.57948284
ELECTRON MICROSCOPYf_dihedral_angle_d17.2555767
ELECTRON MICROSCOPYf_chiral_restr0.0414332
ELECTRON MICROSCOPYf_plane_restr0.0046081

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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

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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

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