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- PDB-9hyu: Cryo-EM structure of the Chromera velia PSI supercomplex at 1.84 ... -

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Basic information

Entry
Database: PDB / ID: 9hyu
TitleCryo-EM structure of the Chromera velia PSI supercomplex at 1.84 Angstrom resolution
Components
  • (Photosystem I ...) x 11
  • (Plastid light harvesting ...) x 4
  • (Superoxide dismutase ...) x 2
  • Chlorophyll a-b binding protein, chloroplastic
  • photosystem I
KeywordsPHOTOSYNTHESIS / Photosystem I / PSI-FCP complex / Chrome velia / Cryo-EM.
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / superoxide dismutase / chlorophyll binding / superoxide dismutase activity / chloroplast thylakoid membrane ...thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / superoxide dismutase / chlorophyll binding / superoxide dismutase activity / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding / membrane
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / 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 / Chlorophyll A-B binding protein, plant and chromista ...Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / 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 / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / 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 / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / : / Lauryl Maltose Neopentyl Glycol / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE ...: / : / Lauryl Maltose Neopentyl Glycol / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Chem-XAT / Superoxide dismutase [Fe] / Uncharacterized protein / Uncharacterized protein / PSI subunit V / Photosystem I reaction center subunit III / Uncharacterized protein / Photosystem I reaction center subunit II / Uncharacterized protein / Superoxide dismutase [Fe] / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / Plastid light harvesting protein / Photosystem I iron-sulfur center / photosystem I / photosystem I
Similarity search - Component
Biological speciesChromera velia (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.84 Å
AuthorsYuan, X. / Qian, P. / Sobotka, R. / Naschberger, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)Synergy Award 854126European Union
CitationJournal: To Be Published
Title: Cryo-EM structure of PSI super complex from Chromera. velia
Authors: Yuan, X. / Qian, P. / Sobotka, R. / Naschberger, A.
History
DepositionJan 10, 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: 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
1: Superoxide dismutase [Fe]
2: Superoxide dismutase [Fe]
A: photosystem I
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 protein (PsaI)
L: Photosystem I reaction center subunit V
M: Photosystem I protein (PsaM)
R: Photosystem I protein (PsaR)
b: Plastid light harvesting protein
c: Plastid light harvesting protein
d: Plastid light harvesting protein
e: Plastid light harvesting protein
f: Chlorophyll a-b binding protein, chloroplastic
u: Photosystem I protein (PsaV)
a: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I protein (PsaB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)826,449267
Polymers647,09119
Non-polymers179,358248
Water28,0671558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Its 3d structure was reconstructed from cryo-EM single particles.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Superoxide dismutase ... , 2 types, 2 molecules 12

#1: Protein Superoxide dismutase [Fe] / SOD1


Mass: 41899.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4HJZ8, superoxide dismutase
#2: Protein Superoxide dismutase [Fe] / SOD2


Mass: 29931.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4FB02, superoxide dismutase

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Protein , 2 types, 2 molecules Af

#3: Protein photosystem I


Mass: 44801.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: D9IXI2, photosystem I
#16: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 31759.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4I0G6

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Photosystem I ... , 11 types, 11 molecules CDEFILMRuaB

#4: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8961.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: D9IXG0, photosystem I
#5: Protein Photosystem I reaction center subunit II


Mass: 30636.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4H942
#6: Protein Photosystem I reaction center subunit IV


Mass: 14430.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4H6U3
#7: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 35865.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4GX86
#8: Protein Photosystem I protein (PsaI)


Mass: 22553.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4HFQ7
#9: Protein Photosystem I reaction center subunit V / PSI subunit V / PsaL / Photosystem I reaction center subunit V


Mass: 29700.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4GX71
#10: Protein Photosystem I protein (PsaM)


Mass: 22135.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12
#11: Protein Photosystem I protein (PsaR) / PsaR


Mass: 22594.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4FDJ8
#17: Protein Photosystem I protein (PsaV) / PsaV


Mass: 45973.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4HRT4
#18: Protein Photosystem I P700 chlorophyll a apoprotein A1


Mass: 29865.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12
#19: Protein Photosystem I protein (PsaB) / PsaB


Mass: 128908.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: D9IXI4, photosystem I

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Plastid light harvesting ... , 4 types, 4 molecules bcde

#12: Protein Plastid light harvesting protein / PFCb


Mass: 32446.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4ID45
#13: Protein Plastid light harvesting protein / FCPc


Mass: 26235.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4FL36
#14: Protein Plastid light harvesting protein


Mass: 24313.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4HNB1
#15: Protein Plastid light harvesting protein / FCPe


Mass: 24079.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chromera velia (eukaryote) / Strain: RM12 / References: UniProt: A0A0G4HMN0

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Sugars , 4 types, 79 molecules

#20: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#21: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#29: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION
#30: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 71 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 13 types, 1727 molecules

#22: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 114 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#27: 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.: 22 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical ChemComp-AV0 / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside / 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 1005.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H88O22
#33: Chemical
ChemComp-A1L6D / [(1~{R},5~{S})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{Z})-3,7,12,16-tetramethyl-17-oxidanyl-19-oxidanylidene-19-[(1~{R},4~{S})-1,2,2-trimethyl-4-oxidanyl-cyclopentyl]nonadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate


Mass: 658.906 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H58O6 / Feature type: SUBJECT OF INVESTIGATION
#34: 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.: 1 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical ChemComp-A1I05 / [(2~{R})-3-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate


Mass: 1025.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C61H116O11 / Feature type: SUBJECT OF INVESTIGATION
#36: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1558 / Source method: isolated from a natural source / Formula: H2O

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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: PSI super complex from Chrome velia / Type: COMPLEX
Details: A complex containing PSI as a core with other components for example PsaA-, PsaB, Psa
Entity ID: #1-#2, #8, #3-#7, #9-#13, #15-#19 / Source: NATURAL
Molecular weightValue: 0.6544 MDa / Experimental value: NO
Source (natural)Organism: Chromera velia (eukaryote) / Strain: RM12
Buffer solutionpH: 6.5
Details: 20 mM MES pH 6.5, 0.15M NaCl and 0.01% Lauryl maltose neopentyl glycol
Buffer componentConc.: 20 mM / Name: MES / Formula: C6H13NO4S
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Protein sample in buffer solution of 20 mM MES pH 6.5, 0.15M NaCl and 0.01% Lauryl maltose neopentyl glycol
Specimen supportDetails: GloQube Plus instrument (Quorum Technologies, UK) was used for glow discharge with the currency of 35 mA For the sample from Gel, glow discharge time is 30, waiting time is 5 sec and blowing time is 3 seconds
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blotting time 2.5 sec.

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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: 165000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 800 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 / Temperature (max): 81 K / Temperature (min): 79 K
Image recordingAverage exposure time: 3.16 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 32897
Details: Two dataset were collected and merged together during data processing.
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13RELION3D reconstruction
Image processingDetails: Motion correction and CTF estimation were performed on the raw data in cryoSPARC's Live session
CTF correctionDetails: CTF estimation were performed on the raw data in cryoSPARC's Live session
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5807142 / Details: Blob picking was selected initially.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 1.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 532822 / Algorithm: BACK PROJECTION
Details: The particles from both datasets were converted into star files using csparc2star from the PyEM suite for further processing in RELION v5.0.0b.
Symmetry type: POINT
Atomic model buildingB value: 21.6 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: CCC in ChimeraX
Atomic model buildingSource name: SwissModel / Type: in silico model
RefinementHighest resolution: 1.84 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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