[English] 日本語
Yorodumi
- PDB-6sl5: Dunaliella Photosystem I Supercomplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sl5
TitleDunaliella Photosystem I Supercomplex
Components
  • (Chlorophyll a-b binding protein, ...) x 2
  • (Photosystem I ...) x 4
  • Lhca2
  • Lhca4
  • Lhca5
  • Lhca6
  • PsaD
  • PsaE
  • PsaF
  • PsaG
  • PsaH
  • PsaI
  • PsaK
  • PsaL
  • PsaO
KeywordsPHOTOSYNTHESIS / membrane complex / photosystem I / dunaliella / light harvesting / excitation transfer
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Single helix bin / SH3 type barrels. - #50 / Alpha-Beta Plaits - #20 / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaJ, reaction centre subunit IX ...Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Single helix bin / SH3 type barrels. - #50 / Alpha-Beta Plaits - #20 / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / : / 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 / 4Fe-4S dicluster domain / Helicase, Ruva Protein; domain 3 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Tripalmitoylglycerol / BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LMK ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Tripalmitoylglycerol / BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LMK / Chem-LUT / octadecanal / Chem-P3H / PHYLLOQUINONE / PHOSPHATIDYLETHANOLAMINE / IRON/SULFUR CLUSTER / Chem-SQD / Chem-XAT / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2
Similarity search - Component
Biological speciesDunaliella salina (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsNelson, N. / Caspy, I. / Malavath, T. / Klaiman, D. / Shkolinsky, Y.
Funding support Israel, Belgium, 2items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
European Research Council (ERC)723991 Belgium
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2020
Title: Structure and energy transfer pathways of the Dunaliella Salina photosystem I supercomplex.
Authors: Ido Caspy / Tirupathi Malavath / Daniel Klaiman / Maria Fadeeva / Yoel Shkolnisky / Nathan Nelson /
Abstract: Oxygenic photosynthesis evolved more than 3 billion years ago in cyanobacteria. The increased complexity of photosystem I (PSI) became apparent from the high-resolution structures that were obtained ...Oxygenic photosynthesis evolved more than 3 billion years ago in cyanobacteria. The increased complexity of photosystem I (PSI) became apparent from the high-resolution structures that were obtained for the complexes that were isolated from various organisms, ranging from cyanobacteria to plants. These complexes are all evolutionarily linked. In this paper, the researchers have uncovered the increased complexity of PSI in a single organism demonstrated by the coexistance of two distinct PSI compositions. The Large Dunaliella PSI contains eight additional subunits, six in PSI core and two light harvesting complexes. Two additional chlorophyll a molecules pertinent for efficient excitation energy transfer in state II transition were identified in PsaL and PsaO. Short distances between these newly identified chlorophylls correspond with fast excitation transfer rates previously reported during state II transition. The apparent PSI conformations could be a coping mechanism for the high salinity.
History
DepositionAug 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 15, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0May 22, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10236
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: PsaD
E: PsaE
F: PsaF
J: Photosystem I reaction center subunit IX
G: PsaG
H: PsaH
I: PsaI
K: PsaK
L: PsaL
O: PsaO
1: Chlorophyll a-b binding protein, chloroplastic
2: Lhca2
3: Chlorophyll a-b binding protein, chloroplastic
4: Lhca4
5: Lhca5
6: Lhca6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)644,178311
Polymers410,77419
Non-polymers233,404292
Water00
1


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

-
Components

-
Photosystem I ... , 4 types, 4 molecules ABCJ

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


Mass: 81877.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXV2, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 81671.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXZ0, photosystem I
#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8717.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXW7, photosystem I
#7: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4614.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXW0

-
Protein , 12 types, 12 molecules DEFGHKLO2456

#4: Protein PsaD


Mass: 16214.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#5: Protein PsaE


Mass: 7297.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#6: Protein PsaF


Mass: 18115.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#8: Protein PsaG


Mass: 10928.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#9: Protein PsaH


Mass: 10012.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#11: Protein PsaK


Mass: 8191.218 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#12: Protein PsaL


Mass: 16189.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#13: Protein PsaO


Mass: 9635.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#15: Protein Lhca2


Mass: 22813.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#17: Protein Lhca4


Mass: 23131.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#18: Protein Lhca5


Mass: 21676.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#19: Protein Lhca6


Mass: 19559.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)

-
Protein/peptide , 1 types, 1 molecules I

#10: Protein/peptide PsaI


Mass: 4236.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)

-
Chlorophyll a-b binding protein, ... , 2 types, 2 molecules 13

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


Mass: 21305.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: C1K003
#16: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24585.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: C1K004*PLUS

-
Sugars , 2 types, 8 molecules

#27: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#28: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15

-
Non-polymers , 18 types, 284 molecules

#20: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#21: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 172 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#22: 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
#23: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#24: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C40H56
#25: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#26: Chemical ChemComp-OCD / octadecanal


Mass: 268.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O
#29: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H77O8P
#30: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#31: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C45H86O10
#32: Chemical ChemComp-4RF / Tripalmitoylglycerol / propane-1,2,3-triyl trihexadecanoate


Mass: 807.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H98O6
#33: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#34: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN


Mass: 568.871 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C40H56O2
#35: 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.: 6 / Source method: obtained synthetically / Formula: C40H56O4
#36: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#37: 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.: 3 / Source method: obtained synthetically / Formula: C41H78O12S
#38: Chemical ChemComp-LMK / trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium


Mass: 773.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H94NO7
#39: Chemical ChemComp-P3H / [(2~{R})-1-nonanoyloxy-3-[oxidanyl-[(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z})-heptadeca-5,8-dienoate


Mass: 722.841 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H63O13P

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Large dunaliella salina photosystem I-LHC supercomplex
Type: COMPLEX / Entity ID: #1-#19 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Dunaliella salina (plant)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 2.5 sec blotting before plunging

-
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 42.68 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4306

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.18rc4_3812refinement
PHENIX1.18rc4_3812refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7PHENIX1.18model fitting
9PHENIX1.18model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 720711
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189006 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 83 / Protocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 1.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011546189
ELECTRON MICROSCOPYf_angle_d2.261865216
ELECTRON MICROSCOPYf_chiral_restr0.16815653
ELECTRON MICROSCOPYf_plane_restr0.010511924
ELECTRON MICROSCOPYf_dihedral_angle_d26.487819083

+
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