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- PDB-9jzr: Structure of PSI-LHCI-LHCII supercomplex from Bryopsis corticulans -

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Basic information

Entry
Database: PDB / ID: 9jzr
TitleStructure of PSI-LHCI-LHCII supercomplex from Bryopsis corticulans
Components
  • (Chlorophyll a-b binding protein, ...) x 8
  • (Photosystem I ...) x 7
  • Lhcb-a
  • Lhcb-b
  • Lhcb-c
  • Lhcb-d
  • Lhcb-e
  • Lhcb-f
  • Lhcb-i
  • PSI subunit V
  • PsaE
  • PsaG
  • PsaH
  • PsaK
  • PsaO
  • photosystem I
KeywordsPHOTOSYNTHESIS / photosystem II
Function / homology
Function and homology information


plastid thylakoid membrane / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane ...plastid thylakoid membrane / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein domain specific binding / metal ion binding
Similarity search - Function
Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK ...Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I reaction centre subunit VIII superfamily / 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 PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / 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 / 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
Similarity search - Domain/homology
Siphonaxanthin / Siphonein / Chem-8CT / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-NEX ...Siphonaxanthin / Siphonein / Chem-8CT / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-NEX / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IX / PsaK / Photosystem I reaction center subunit XI, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / photosystem I / Chlorophyll a-b binding protein, chloroplastic / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II, chloroplastic / PsaE / Photosystem I reaction center subunit III / PsaH / Photosystem I reaction center subunit VIII
Similarity search - Component
Biological speciesBryopsis corticulans (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsLiu, X.Y. / Wang, W.D.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Structural insights into photosystem II supercomplex and PSI-LHCI-LHCII supercomplexes of a siphonous green algae Bryopsis corticulans
Authors: Liu, X.Y.
History
DepositionOct 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 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
0: Chlorophyll a-b binding protein, chloroplastic
1: Chlorophyll a-b binding protein, chloroplastic
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
5: Chlorophyll a-b binding protein, chloroplastic
6: Chlorophyll a-b binding protein, chloroplastic
7: Chlorophyll a-b binding protein, chloroplastic
8: Chlorophyll a-b binding protein, chloroplastic
9: Chlorophyll a-b binding protein, chloroplastic
A: Photosystem I P700 chlorophyll a apoprotein A1
B: photosystem I
D: Photosystem I reaction center subunit II, chloroplastic
E: PsaE
F: Photosystem I reaction center subunit III
G: PsaG
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: PSI subunit V
C: Photosystem I iron-sulfur center
K: PsaK
M: Photosystem I reaction center subunit XII
O: PsaO
a: Lhcb-a
c: Lhcb-c
b: Lhcb-b
d: Lhcb-d
f: Lhcb-f
g: Lhcb-d
h: Lhcb-a
H: PsaH
i: Lhcb-i
e: Lhcb-e
4: Chlorophyll a-b binding protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,282,500555
Polymers848,53833
Non-polymers433,963522
Water00
1


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

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Components

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Chlorophyll a-b binding protein, ... , 8 types, 10 molecules 0152367849

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


Mass: 26910.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H004
#2: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24458.012 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ6
#3: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 27808.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ7
#4: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 30409.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ8
#5: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 29300.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H000
#6: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 28621.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H001
#7: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 26575.912 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ9
#8: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24152.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H002

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Photosystem I ... , 7 types, 7 molecules ADFIJCM

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


Mass: 83412.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ2, photosystem I
#11: Protein Photosystem I reaction center subunit II, chloroplastic


Mass: 21733.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H006
#13: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 25129.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H008
#15: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 3859.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H010
#16: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4744.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ3
#18: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8880.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H005, photosystem I
#20: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3505.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence reference for source organism Bryopsis corticulans is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A1L2EDU0.
Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A1L2EDU0

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Protein , 14 types, 16 molecules BEGLKOahcbdgfHie

#10: Protein photosystem I


Mass: 82164.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H003, photosystem I
#12: Protein PsaE


Mass: 10096.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H007
#14: Protein PsaG


Mass: 18226.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#17: Protein PSI subunit V


Mass: 21338.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ5
#19: Protein PsaK


Mass: 12487.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ4
#21: Protein PsaO


Mass: 15052.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#22: Protein Lhcb-a


Mass: 27003.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#23: Protein Lhcb-c


Mass: 27448.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#24: Protein Lhcb-b


Mass: 27263.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#25: Protein Lhcb-d


Mass: 29898.654 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#26: Protein Lhcb-f


Mass: 27946.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#27: Protein PsaH


Mass: 14400.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H009
#28: Protein Lhcb-i


Mass: 30726.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#29: Protein Lhcb-e


Mass: 27045.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)

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Sugars , 1 types, 1 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 12 types, 521 molecules

#30: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 130 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 247 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical...
ChemComp-8CT / (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene


Mass: 536.873 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical...
ChemComp-0UR / Siphonein


Mass: 781.157 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C52H76O5 / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#35: 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
#36: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#37: Chemical
ChemComp-0IE / Siphonaxanthin


Mass: 600.870 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#38: 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
#39: 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
#40: 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
#42: 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 / Feature type: SUBJECT OF INVESTIGATION

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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: Bc-PSI-LHCI-LHCII / Type: COMPLEX / Entity ID: #1-#29 / Source: NATURAL
Source (natural)Organism: Bryopsis corticulans (plant)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI SPHERA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO2.25particle selection
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 213217 / Symmetry type: POINT
RefinementHighest resolution: 2.73 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00681763
ELECTRON MICROSCOPYf_angle_d1.887116835
ELECTRON MICROSCOPYf_dihedral_angle_d17.06827314
ELECTRON MICROSCOPYf_chiral_restr0.0499380
ELECTRON MICROSCOPYf_plane_restr0.00515024

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