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- PDB-9kc5: PSI-LHCI of the red alga Galdieria sulphuraria NIES-3638 -

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Basic information

Entry
Database: PDB / ID: 9kc5
TitlePSI-LHCI of the red alga Galdieria sulphuraria NIES-3638
Components
  • (Light-harvesting complex ...) x 6
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 6
  • (Photosystem I subunit ...) x 2
  • PSI-K
  • Photosystem I iron-sulfur center
  • Psa28
  • RedCAP
KeywordsPHOTOSYNTHESIS / Photosystem I / ELECTRON TRANSPORT
Function / homology
Function and homology information


plastid thylakoid membrane / thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid / chlorophyll binding ...plastid thylakoid membrane / thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I PsaO / PsaO transmembrane domain / 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 PsaO / PsaO transmembrane domain / 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 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 / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / 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
: / : / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / (3R)-beta,beta-caroten-3-ol / IRON/SULFUR CLUSTER / Unknown ligand ...: / : / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / (3R)-beta,beta-caroten-3-ol / IRON/SULFUR CLUSTER / Unknown ligand / Photosystem I subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit III / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / PSI-K / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit XII / Light-harvesting complex protein / Light-harvesting complex protein / Light-harvesting complex protein / Light-harvesting complex protein / Light-harvesting complex protein / Uncharacterized protein / Photosystem I subunit O / Uncharacterized protein / Light-harvesting complex protein
Similarity search - Component
Biological speciesGaldieria sulphuraria (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsKato, K. / Nakajima, Y. / Shen, J.R. / Nagao, R.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23K14211 Japan
Japan Society for the Promotion of Science (JSPS)JP22H04916 Japan
Japan Society for the Promotion of Science (JSPS)JP23H02423 Japan
CitationJournal: Sci Adv / Year: 2025
Title: Structure of a photosystem I supercomplex from close to an ancestral red alga.
Authors: Koji Kato / Minoru Kumazawa / Yoshiki Nakajima / Takehiro Suzuki / Naoshi Dohmae / Jian-Ren Shen / Kentaro Ifuku / Ryo Nagao /
Abstract: Red algae exhibit unique photosynthetic adaptations, characterized by photosystem I (PSI) supercomplexes containing light-harvesting complexes (LHCs), forming PSI-LHCI supercomplexes. In this study, ...Red algae exhibit unique photosynthetic adaptations, characterized by photosystem I (PSI) supercomplexes containing light-harvesting complexes (LHCs), forming PSI-LHCI supercomplexes. In this study, we solved the PSI-LHCI structure of NIES-3638 at 2.19-angstrom resolution using cryo-electron microscopy, revealing a PSI monomer core associated with seven LHCI subunits. Structural analysis uncovered the absence of phylloquinones, the common secondary electron acceptor in PSI of photosynthetic organisms, suggesting adaptation to a benzoquinone-like molecule. Phylogenetic analysis suggests that retains traits characteristic of an ancestral red alga, including distinctive LHCI binding and interaction patterns. Variations in LHCI composition and interactions across red algae, particularly in red-lineage chlorophyll /-binding-like protein and red algal LHCs, highlight evolutionary divergence and specialization. These findings not only deepen our understanding of red algal PSI-LHCI diversification but also enable us to predict features of an ancestral red algal PSI-LHCI supercomplex, providing a framework to explore evolutionary adaptations from an ancestral red alga.
History
DepositionNov 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: 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 subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: PSI-K
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
O: Photosystem I subunit O
Z: Psa28
1: RedCAP
2: Light-harvesting complex protein
3: Light-harvesting complex protein
4: Light-harvesting complex protein
5: Light-harvesting complex protein
6: Light-harvesting complex protein
7: Light-harvesting complex protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)643,559318
Polymers399,74120
Non-polymers243,818298
Water10,953608
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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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

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


Mass: 82528.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: E3UIU0, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 82418.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: E3UIU1, photosystem I

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Protein , 4 types, 4 molecules CKZ1

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


Mass: 8719.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: E3UIU2, photosystem I
#9: Protein PSI-K / Photosystem I subunit X


Mass: 6874.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: E3UIU8
#13: Protein Psa28


Mass: 9030.552 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: M2Y646
#14: Protein RedCAP


Mass: 19435.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: M2XW22

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Photosystem I reaction center subunit ... , 6 types, 6 molecules DFIJLM

#4: Protein Photosystem I reaction center subunit II


Mass: 15669.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: E3UIU3
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 18254.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: E3UIU5
#7: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 3879.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: E3UIU6
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4754.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: E3UIU7
#10: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 15206.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: E3UIU9
#11: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3067.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: E3UIV0

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Photosystem I subunit ... , 2 types, 2 molecules EO

#5: Protein Photosystem I subunit IV


Mass: 7330.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: A0A075W2R1
#12: Protein Photosystem I subunit O


Mass: 10522.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: M2XWX3

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Light-harvesting complex ... , 6 types, 6 molecules 234567

#15: Protein Light-harvesting complex protein


Mass: 18228.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: M2X4C9
#16: Protein Light-harvesting complex protein


Mass: 14670.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: M2XR49
#17: Protein Light-harvesting complex protein


Mass: 19949.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: M2X090
#18: Protein Light-harvesting complex protein


Mass: 19901.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: M2VTV2
#19: Protein Light-harvesting complex protein


Mass: 20512.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: M2VZV1
#20: Protein Light-harvesting complex protein


Mass: 18787.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: M2Y652

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Sugars , 2 types, 5 molecules

#28: 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
#30: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 10 types, 901 molecules

#21: 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
#22: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 167 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical ChemComp-A1L64 / Coenzyme Q4 / Ubiquinone-4 / 2,3-dimethoxy-5-methyl-6-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]cyclohexa-2,5-diene-1,4-dione


Mass: 454.641 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H42O4 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#25: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#26: 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
#27: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 949.299 Da / Num. of mol.: 52 / Source method: obtained synthetically
#29: Chemical...
ChemComp-5X6 / Zeaxanthin / (1R)-4-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4R)-4-hydroxy-2,6,6-trimethylcyclohexen-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenyl]-3,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical
ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56O / Feature type: SUBJECT OF INVESTIGATION
#32: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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-LHCI / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL
Molecular weightValue: 0.68 MDa / Experimental value: NO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMMESMES-NaOH1
20.03 %DDMDDM1
SpecimenConc.: 2.5 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 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

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
4CTFFIND4.1CTF correction
7UCSF Chimera1.16model fitting
9RELION4initial Euler assignment
10RELION4final Euler assignment
11RELION4classification
12RELION43D reconstruction
13Servalcat0.4.32model refinement
14REFMAC5.8.0419model refinement
15PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2583694
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110313 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Atomic model buildingDetails: Phyre2 server / Source name: Other / Type: in silico model
RefinementResolution: 2.19→204.54 Å / Cor.coef. Fo:Fc: 0.862 / SU B: 3.851 / SU ML: 0.088 / ESU R: 0.13
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.24629 --
obs0.24629 878705 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 70.414 Å2
Refinement stepCycle: 1 / Total: 41435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01442991
ELECTRON MICROSCOPYr_bond_other_d00.01740255
ELECTRON MICROSCOPYr_angle_refined_deg1.8082.18560729
ELECTRON MICROSCOPYr_angle_other_deg0.7962.07791717
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.58353504
ELECTRON MICROSCOPYr_dihedral_angle_2_deg13.3775750
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.837104634
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0730.25081
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0246662
ELECTRON MICROSCOPYr_gen_planes_other0.0080.029568
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it3.1156.32614085
ELECTRON MICROSCOPYr_mcbond_other3.1156.32614085
ELECTRON MICROSCOPYr_mcangle_it5.09711.3817566
ELECTRON MICROSCOPYr_mcangle_other5.09711.38117567
ELECTRON MICROSCOPYr_scbond_it3.897.25428906
ELECTRON MICROSCOPYr_scbond_other3.897.25428907
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other6.52213.23743128
ELECTRON MICROSCOPYr_long_range_B_refined9.31267.9951386
ELECTRON MICROSCOPYr_long_range_B_other9.31267.9951387
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.597 65228 -
obs--100 %

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