[English] 日本語
Yorodumi
- PDB-7ymm: PSII-Pcb Tetramer of Acaryochloris Marina -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ymm
TitlePSII-Pcb Tetramer of Acaryochloris Marina
Components
  • (High light inducible ...) x 4
  • (Photosystem II ...) x 14
  • Cytochrome b559 subunit alpha
  • Unknown protein
KeywordsPHOTOSYNTHESIS / Photosystem II / Pcb
Function / homology
Function and homology information


photosystem / 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 II / response to herbicide / chlorophyll binding ...photosystem / 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 II / response to herbicide / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / : / phosphate ion binding / photosynthesis, light reaction / photosynthesis / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbY / Photosystem II PsbX, type 1 subfamily / 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 PsbY / Photosystem II PsbX, type 1 subfamily / 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 reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / 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 cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Chem-8CT / BICARBONATE ION / CHLOROPHYLL D / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / Chem-PL9 ...Chem-8CT / BICARBONATE ION / CHLOROPHYLL D / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Chem-ZEX / Photosystem II protein D1 2 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II D2 protein 1 / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein Y / High light inducible protein / High light inducible protein / High light inducible protein / Photosystem II protein PsbI / Photosystem II protein PsbT / High light inducible protein / Photosystem II reaction center protein L / Cytochrome b559 subunit alpha / Photosystem II reaction center protein K / Photosystem II 10 kDa phosphoprotein PsbH / Photosystem II reaction center protein M / Photosystem II CP47 reaction center protein
Similarity search - Component
Biological speciesAcaryochloris marina MBIC11017 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsShen, L.L. / Gao, Y.Z. / Wang, W.D. / Zhang, X. / Shen, J.R. / Wang, P.Y. / Han, G.Y.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDY-SSW-SMC003 China
Chinese Academy of SciencesXDB17000000 China
National Basic Research Program of China (973 Program)2015CB150100 China
CitationJournal: Sci Adv / Year: 2024
Title: Structure of a unique PSII-Pcb tetrameric megacomplex in a chlorophyll -containing cyanobacterium.
Authors: Liangliang Shen / Yuanzhu Gao / Kailu Tang / Ruxi Qi / Lutang Fu / Jing-Hua Chen / Wenda Wang / Xiaomin Ma / Peiyao Li / Min Chen / Tingyun Kuang / Xing Zhang / Jian-Ren Shen / Peiyi Wang / Guangye Han /
Abstract: is a unique cyanobacterium using chlorophyll (Chl ) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of associates with a number of prochlorophyte Chl- ... is a unique cyanobacterium using chlorophyll (Chl ) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of associates with a number of prochlorophyte Chl-binding (Pcb) proteins to act as the light-harvesting system. We report here the cryo-electron microscopic structure of a PSII-Pcb megacomplex from at a 3.6-angstrom overall resolution and a 3.3-angstrom local resolution. The megacomplex is organized as a tetramer consisting of two PSII core dimers flanked by sixteen symmetrically related Pcb proteins, with a total molecular weight of 1.9 megadaltons. The structure reveals the detailed organization of PSII core consisting of 15 known protein subunits and an unknown subunit, the assembly of 4 Pcb antennas within each PSII monomer, and possible pathways of energy transfer within the megacomplex, providing deep insights into energy transfer and dissipation mechanisms within the PSII-Pcb megacomplex involved in far-red light utilization.
History
DepositionJul 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
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 / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1A: Photosystem II protein D1 2
1B: Photosystem II CP47 reaction center protein
1C: Photosystem II CP43 reaction center protein
1D: Photosystem II D2 protein 1
1E: Cytochrome b559 subunit alpha
1F: Photosystem II protein Y
1H: Photosystem II 10 kDa phosphoprotein PsbH
1I: Photosystem II protein PsbI
1K: Photosystem II reaction center protein K
1L: Photosystem II reaction center protein L
1M: Photosystem II reaction center protein M
1T: Photosystem II reaction center protein T
1X: Photosystem II reaction center X protein
1Y: Photosystem II reaction center protein Ycf12
1Z: Photosystem II reaction center protein Z
12: High light inducible protein
1G: Unknown protein
11: High light inducible protein
13: High light inducible protein
14: High light inducible protein
2A: Photosystem II protein D1 2
2B: Photosystem II CP47 reaction center protein
2C: Photosystem II CP43 reaction center protein
2D: Photosystem II D2 protein 1
2E: Cytochrome b559 subunit alpha
2F: Photosystem II protein Y
2H: Photosystem II 10 kDa phosphoprotein PsbH
2I: Photosystem II protein PsbI
2K: Photosystem II reaction center protein K
2L: Photosystem II reaction center protein L
2M: Photosystem II reaction center protein M
2T: Photosystem II reaction center protein T
2X: Photosystem II reaction center X protein
2Y: Photosystem II reaction center protein Ycf12
2Z: Photosystem II reaction center protein Z
22: High light inducible protein
2G: Unknown protein
21: High light inducible protein
23: High light inducible protein
24: High light inducible protein
3A: Photosystem II protein D1 2
3B: Photosystem II CP47 reaction center protein
3C: Photosystem II CP43 reaction center protein
3D: Photosystem II D2 protein 1
3E: Cytochrome b559 subunit alpha
3F: Photosystem II protein Y
3H: Photosystem II 10 kDa phosphoprotein PsbH
3I: Photosystem II protein PsbI
3K: Photosystem II reaction center protein K
3L: Photosystem II reaction center protein L
3M: Photosystem II reaction center protein M
3T: Photosystem II reaction center protein T
3X: Photosystem II reaction center X protein
3Y: Photosystem II reaction center protein Ycf12
3Z: Photosystem II reaction center protein Z
32: High light inducible protein
3G: Unknown protein
31: High light inducible protein
33: High light inducible protein
34: High light inducible protein
4A: Photosystem II protein D1 2
4B: Photosystem II CP47 reaction center protein
4C: Photosystem II CP43 reaction center protein
4D: Photosystem II D2 protein 1
4E: Cytochrome b559 subunit alpha
4F: Photosystem II protein Y
4H: Photosystem II 10 kDa phosphoprotein PsbH
4I: Photosystem II protein PsbI
4K: Photosystem II reaction center protein K
4L: Photosystem II reaction center protein L
4M: Photosystem II reaction center protein M
4T: Photosystem II reaction center protein T
4X: Photosystem II reaction center X protein
4Y: Photosystem II reaction center protein Ycf12
4Z: Photosystem II reaction center protein Z
42: High light inducible protein
4G: Unknown protein
41: High light inducible protein
43: High light inducible protein
44: High light inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,158,031704
Polymers1,650,17280
Non-polymers507,858624
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Photosystem II ... , 14 types, 56 molecules 1A2A3A4A1B2B3B4B1C2C3C4C1D2D3D4D1F2F3F4F1H2H3H4H1I2I3I4I1K2K...

#1: Protein
Photosystem II protein D1 2 / PSII D1 protein 2 / Photosystem II Q(B) protein 2


Mass: 39695.211 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: A5A8K9, photosystem II
#2: Protein
Photosystem II CP47 reaction center protein


Mass: 56518.746 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0CFM2
#3: Protein
Photosystem II CP43 reaction center protein


Mass: 53978.320 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C1V7
#4: Protein
Photosystem II D2 protein 1 / PSII D2 protein 1 / Photosystem Q(A) protein 1


Mass: 39291.852 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C1V6, photosystem II
#6: Protein
Photosystem II protein Y


Mass: 11277.320 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C2V2
#7: Protein
Photosystem II 10 kDa phosphoprotein PsbH


Mass: 7683.901 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0CDZ2
#8: Protein/peptide
Photosystem II protein PsbI


Mass: 3948.692 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C5R5
#9: Protein/peptide
Photosystem II reaction center protein K / PSII-K


Mass: 4939.008 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6Z7
#10: Protein/peptide
Photosystem II reaction center protein L / PSII-L


Mass: 4254.045 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6T1
#11: Protein/peptide
Photosystem II reaction center protein M / PSII-M


Mass: 3614.302 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0CFM0
#12: Protein/peptide
Photosystem II reaction center protein T


Mass: 5442.383 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C605
#13: Protein/peptide
Photosystem II reaction center X protein


Mass: 4443.303 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0BYW9
#14: Protein/peptide
Photosystem II reaction center protein Ycf12


Mass: 4015.932 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria)
#15: Protein
Photosystem II reaction center protein Z / PSII-Z


Mass: 6395.632 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C0S7

-
High light inducible ... , 4 types, 16 molecules 12223242112131411323334314243444

#16: Protein
High light inducible protein / Light harvesting chlorophyll d-binding protein 2 (PcbA)


Mass: 38753.934 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C3E5
#18: Protein
High light inducible protein / Light harvesting chlorophyll d-binding protein 1 (PcbA)


Mass: 38612.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C576
#19: Protein
High light inducible protein / Light harvesting chlorophyll d-binding protein 3 (PcbA)


Mass: 38707.781 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6I0
#20: Protein
High light inducible protein / Light harvesting chlorophyll d-binding protein 4 (PcbC)


Mass: 37967.473 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C3E6

-
Protein / Protein/peptide / Sugars , 3 types, 16 molecules 1E2E3E4E1G2G3G4G

#17: Protein/peptide
Unknown protein


Mass: 3507.314 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria)
#27: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION
#5: Protein
Cytochrome b559 subunit alpha / PSII reaction center subunit V / PsbE


Mass: 9495.788 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6T2

-
Non-polymers , 11 types, 616 molecules

#21: Chemical...
ChemComp-CL7 / CHLOROPHYLL D


Mass: 895.462 Da / Num. of mol.: 424 / Source method: obtained synthetically / Formula: C54H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C55H74N4O5 / Feature type: SUBJECT OF INVESTIGATION
#23: 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.: 44 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#25: 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.: 28 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#28: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#30: 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 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical...
ChemComp-ZEX / (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: PSII-Pcb Tetramer of Acaryochloris Marina / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132346 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00871866
ELECTRON MICROSCOPYf_angle_d1.055100892
ELECTRON MICROSCOPYf_dihedral_angle_d20.0823108
ELECTRON MICROSCOPYf_chiral_restr0.0919290
ELECTRON MICROSCOPYf_plane_restr0.00512792

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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

Read more