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- PDB-9ifm: STRUCTURE OF UNSTACKED C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PIS... -

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Entry
Database: PDB / ID: 9ifm
TitleSTRUCTURE OF UNSTACKED C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PISUM SATIVUM
Components
  • (Chlorophyll a-b binding protein ...) x 2
  • (Chlorophyll a-b binding protein, ...) x 2
  • (Cytochrome b559 subunit ...) x 2
  • (Oxygen-evolving enhancer protein ...) x 3
  • (Photosystem II ...) x 14
  • Ultraviolet-B-repressible protein
KeywordsPHOTOSYNTHESIS / Plant / PSII / Pisum sativum / membrane protein / Cryo-EM
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I ...photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / photosystem II / extrinsic component of membrane / response to herbicide / : / photosynthetic electron transport in photosystem II / chlorophyll binding / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / mRNA binding / heme binding / calcium ion binding / metal ion binding
Similarity search - Function
Photosystem II 5kDa protein, chloroplastic / 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-like domain superfamily ...Photosystem II 5kDa protein, chloroplastic / 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-like domain superfamily / Photosystem II PsbJ / Photosystem II PsbX, type 1 subfamily / 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 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. / : / Chlorophyll A-B binding protein, plant and chromista / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / 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 / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Chem-XAT / Chlorophyll a-b binding protein, chloroplastic / PSII 6.1 kDa protein / Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center protein K / Photosystem II reaction center protein I / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 / Chlorophyll a-b binding protein AB80, chloroplastic / Cytochrome b559 subunit alpha / Photosystem II reaction center protein J / Oxygen-evolving enhancer protein 1, chloroplastic / Oxygen-evolving enhancer protein 2, chloroplastic / Chlorophyll a-b binding protein 8, chloroplastic / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Photosystem II reaction center protein M / Photosystem II reaction center protein Z / 16 kDa subunit of oxygen evolving system of photosystem II / Photosystem II reaction center protein T / Ultraviolet-B-repressible protein / Photosystem II reaction center protein H
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsKlaiman, D. / Fadeeva, M. / Kandiah, E. / Nelson, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation199/21 Israel
CitationJournal: To Be Published
Title: STRUCTURE OF UNSTACKED C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PISUM SATIVUM
Authors: Klaiman, D. / Fadeeva, M. / Nelson, N.
History
DepositionFeb 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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 8, 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 8, chloroplastic
O: Oxygen-evolving enhancer protein 1, chloroplastic
P: Oxygen-evolving enhancer protein 2, chloroplastic
Q: Oxygen-evolving enhancer protein 3
R: Chlorophyll a-b binding protein, chloroplastic
S: Chlorophyll a-b binding protein, chloroplastic
T: Photosystem II reaction center protein T
W: Photosystem II reaction center protein W
X: Ultraviolet-B-repressible protein
Y: Chlorophyll a-b binding protein AB80, chloroplastic
Z: Photosystem II reaction center protein Z
U: Photosystem II 5 kDa protein, chloroplastic
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 8, 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 8, chloroplastic
o: Oxygen-evolving enhancer protein 1, chloroplastic
p: Oxygen-evolving enhancer protein 2, chloroplastic
q: Oxygen-evolving enhancer protein 3
r: Chlorophyll a-b binding protein, chloroplastic
s: Chlorophyll a-b binding protein, chloroplastic
t: Photosystem II reaction center protein T
w: Photosystem II reaction center protein W
x: Ultraviolet-B-repressible protein
y: Chlorophyll a-b binding protein AB80, chloroplastic
z: Photosystem II reaction center protein Z
u: Photosystem II 5 kDa protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,119,366389
Polymers848,85850
Non-polymers270,507339
Water30,8241711
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Photosystem II ... , 14 types, 28 molecules AaBbCcDdHhIiJjKkLlMmTtWwZzUu

#1: Protein Photosystem II protein D1 / PSII D1 protein / 32 kDa thylakoid membrane protein / Photosystem II Q(B) protein


Mass: 36972.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P06585, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 55534.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: D5MAL6
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Photosystem II 44 kDa chlorophyll apoprotein / Protein CP-43


Mass: 49275.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P06004
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39426.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P06006, photosystem II
#8: Protein Photosystem II reaction center protein H / PSII-H / Photosystem II 10 kDa phosphoprotein / Photosystem II 9 kDa phosphoprotein


Mass: 6455.607 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9XQR3
#9: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 3926.691 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: D5MAJ9
#10: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 3598.264 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P13555
#11: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4287.155 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: D5MAJ8
#12: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4265.800 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P60147
#13: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3641.425 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P69529
#19: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3563.292 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q8HS25
#20: Protein Photosystem II reaction center protein W / Photosystem II reaction center protein W / PSBW


Mass: 5914.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A2D0TCJ2
#23: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6468.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q32902
#24: Protein/peptide Photosystem II 5 kDa protein, chloroplastic


Mass: 3080.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A9D4VSA9

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

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


Mass: 8624.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P13554
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 3396.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P62096

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Chlorophyll a-b binding protein ... , 2 types, 6 molecules GNgnYy

#7: Protein
Chlorophyll a-b binding protein 8, chloroplastic / LHCII type I CAB-8


Mass: 23320.176 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P27490
#22: Protein Chlorophyll a-b binding protein AB80, chloroplastic / LHCII type I CAB-AB80 / LHCP


Mass: 23557.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P07371

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

#14: Protein Oxygen-evolving enhancer protein 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 / OEC 33 kDa subunit


Mass: 26554.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P14226
#15: Protein Oxygen-evolving enhancer protein 2, chloroplastic / OEE2 / 23 kDa subunit of oxygen evolving system of photosystem II / 23 kDa thylakoid membrane ...OEE2 / 23 kDa subunit of oxygen evolving system of photosystem II / 23 kDa thylakoid membrane protein / OEC 23 kDa subunit


Mass: 20287.494 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P16059
#16: Protein Oxygen-evolving enhancer protein 3


Mass: 16398.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q7Y1T5

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Chlorophyll a-b binding protein, ... , 2 types, 4 molecules RrSs

#17: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24791.123 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A2D0TCJ0
#18: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23839.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A9D5GXR9

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Protein/peptide / Sugars , 2 types, 12 molecules Xx

#21: Protein/peptide Ultraviolet-B-repressible protein


Mass: 3929.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q8VYY1
#36: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 17 types, 2040 molecules

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


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


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


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


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


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


Mass: 536.873 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: C40H56
#31: 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
#32: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C45H86O10
#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.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#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.: 28 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#37: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 907.472 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#39: 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
#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.: 9 / Source method: obtained synthetically / Formula: C40H56O4
#41: 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.: 4 / Source method: obtained synthetically / Formula: C40H56O4
#42: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1711 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: C2S2-TYPE PSII-LHCII SUPERCOMPLEX FROM PISUM SATIVUM / Type: COMPLEX / Entity ID: #1-#24 / Source: NATURAL
Molecular weightValue: 1.2 MDa / Experimental value: YES
Source (natural)Organism: Pisum sativum (garden pea)
Buffer solutionpH: 6
SpecimenEmbedding 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: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 288 K

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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 magnification: 105000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 900 nm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 29624

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Processing

EM software
IDNameVersionCategory
1RELION4.0.0particle selection
4CTFFIND4.1CTF correction
10RELION4.0.0initial Euler assignment
11RELION4.0.0final Euler assignment
12RELION4.0.0classification
13RELION4.0.03D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 5998672
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200827 / Algorithm: FOURIER SPACE / Num. of class averages: 3 / Symmetry type: POINT
RefinementHighest resolution: 2.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00881222
ELECTRON MICROSCOPYf_angle_d1.784112437
ELECTRON MICROSCOPYf_dihedral_angle_d21.732341
ELECTRON MICROSCOPYf_chiral_restr0.09710610
ELECTRON MICROSCOPYf_plane_restr0.01615585

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  • 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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