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- PDB-7eda: Structure of monomeric photosystem II -

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Entry
Database: PDB / ID: 7eda
TitleStructure of monomeric photosystem II
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 17
  • Cytochrome c-550
KeywordsPHOTOSYNTHESIS / Photosystem / membrane protein
Function / homology
Function and homology information


photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II ...photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / extrinsic component of membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily ...Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / 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 CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / 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. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II 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. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / (3R)-beta,beta-caroten-3-ol / Chem-SQD / Unknown ligand / Photosystem II CP47 reaction center protein / Photosystem II extrinsic protein O / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II extrinsic protein V / Photosystem II reaction center protein Y / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein L / Photosystem II reaction center protein M / Photosystem II reaction center protein T / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II protein D1 / Photosystem II extrinsic protein U / Photosystem II reaction center protein J
Similarity search - Component
Biological speciesThermosynechococcus vulcanus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsYu, H. / Hamaguchi, T. / Nakajima, Y. / Kato, K. / kawakami, K. / Akita, F. / Yonekura, K. / Shen, J.R.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19K22396 Japan
Japan Society for the Promotion of Science (JSPS)JP20H03194 Japan
Japan Society for the Promotion of Science (JSPS)JP20H02914 Japan
Japan Society for the Promotion of Science (JSPS)JP17H06434 Japan
Japan Science and TechnologyJPMJPR16P1 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101072 Japan
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2021
Title: Cryo-EM structure of monomeric photosystem II at 2.78 Å resolution reveals factors important for the formation of dimer.
Authors: Huaxin Yu / Tasuku Hamaguchi / Yoshiki Nakajima / Koji Kato / Keisuke Kawakami / Fusamichi Akita / Koji Yonekura / Jian-Ren Shen /
Abstract: Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The ...Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The crystal structure of monomeric PSII has been solved at 3.6 Å resolution, but it is still not clear which factors contribute to the formation of the dimer. Here, we solved the structure of PSII monomer at a resolution of 2.78 Å using cryo-electron microscopy (cryo-EM). From our cryo-EM density map, we observed apparent differences in pigments and lipids in the monomer-monomer interface between the PSII monomer and dimer. One β-carotene and two sulfoquinovosyl diacylglycerol (SQDG) molecules are found in the monomer-monomer interface of the dimer structure but not in the present monomer structure, although some SQDG and other lipid molecules are found in the analogous region of the low-resolution crystal structure of the monomer, or cryo-EM structure of an apo-PSII monomer lacking the extrinsic proteins from Synechocystis sp. PCC 6803. In the current monomer structure, a large part of the PsbO subunit was also found to be disordered. These results indicate the importance of the β-carotene, SQDG and PsbO in formation of the PSII dimer.
History
DepositionMar 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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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
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
O: Photosystem II manganese-stabilizing polypeptide
T: Photosystem II reaction center protein T
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
Y: Photosystem II reaction center protein Ycf12
X: Photosystem II reaction center protein X
Z: Photosystem II reaction center protein Z
R: Photosystem II protein Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,02787
Polymers300,38520
Non-polymers52,64367
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area161460 Å2
ΔGint-1222 kcal/mol
Surface area67890 Å2

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Components

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Photosystem II ... , 17 types, 17 molecules ABCDHIJKLMOTUYXZR

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


Mass: 37029.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P51765, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / / PSII 47 kDa protein / Protein CP-47


Mass: 55939.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR1
#3: Protein Photosystem II CP43 reaction center protein / / PSII 43 kDa protein / Protein CP-43


Mass: 49207.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR7
#4: Protein Photosystem II D2 protein / / PSII D2 protein / Photosystem Q(A) protein


Mass: 38290.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR8, photosystem II
#7: Protein Photosystem II reaction center protein H / / PSII-H


Mass: 6986.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P19052
#8: Protein/peptide Photosystem II reaction center protein I / / PSII-I / PSII 4.4 kDa protein


Mass: 4438.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12240
#9: Protein/peptide Photosystem II reaction center protein J / / PSII-J


Mass: 4105.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: Q7DGD4
#10: Protein/peptide Photosystem II reaction center protein K / / PSII-K


Mass: 4101.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P19054
#11: Protein/peptide Photosystem II reaction center protein L / / PSII-L


Mass: 4299.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12241
#12: Protein/peptide Photosystem II reaction center protein M / / PSII-M


Mass: 3289.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12312
#13: Protein Photosystem II manganese-stabilizing polypeptide / / MSP / Extrinsic protein O of oxygen-evolving complex


Mass: 26651.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR2
#14: Protein/peptide Photosystem II reaction center protein T / / PSII-T / PSII-Tc


Mass: 3648.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12313
#15: Protein Photosystem II 12 kDa extrinsic protein / / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 11655.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P56152
#17: Protein/peptide Photosystem II reaction center protein Ycf12 /


Mass: 3228.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR3
#18: Protein/peptide Photosystem II reaction center protein X /


Mass: 4191.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR4
#19: Protein Photosystem II reaction center protein Z / / PSII-Z


Mass: 6766.187 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR5
#20: Protein/peptide Photosystem II protein Y /


Mass: 3859.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P0DM37

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

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


Mass: 9580.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12238
#6: Protein/peptide Cytochrome b559 subunit beta / / PSII reaction center subunit VI


Mass: 5067.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12239

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Protein / Sugars , 2 types, 5 molecules V

#16: Protein Cytochrome c-550 / Cytochrome c550 / Low-potential cytochrome c


Mass: 18046.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P0A387
#30: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 15 types, 79 molecules

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


Mass: 339.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CaMn4O5
#22: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#23: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#24: Chemical ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O5
#25: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#26: 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.: 2 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#28: 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 / Plastoquinone


Mass: 749.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H80O2
#29: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#32: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#33: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#34: Chemical ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin / Β-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H34FeN4O4
#36: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: Photosystem II / Type: COMPLEX / Entity ID: #1-#6, #8-#20 / Source: NATURAL
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173875 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0123735
ELECTRON MICROSCOPYf_angle_d1.49132786
ELECTRON MICROSCOPYf_dihedral_angle_d14.78814375
ELECTRON MICROSCOPYf_chiral_restr0.0623331
ELECTRON MICROSCOPYf_plane_restr0.0093924

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