[English] 日本語
Yorodumi
- EMDB-30823: Structure of GraFix PSI tetramer from Cyanophora paradoxa -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30823
TitleStructure of GraFix PSI tetramer from Cyanophora paradoxa
Map data
Sample
  • Complex: PSI tetramer
    • Protein or peptide: x 11 types
  • Ligand: x 7 types
Function / homology
Function and homology information


cyanelle thylakoid membrane / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding ...cyanelle thylakoid membrane / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / : / 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
Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit III / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit II, cyanelle
Similarity search - Component
Biological speciesCyanophora paradoxa (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsKato K / Nagao R / Akita F / Miyazaki N / Shen JR
CitationJournal: Biorxiv / Year: 2022
Title: Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes
Authors: Kato K / Nagao R / Ueno Y / Yokono M / Suzuki T / Jiang TY / Dohmae N / Akita F / Akimoto S / Miyazaki N / Shen JR
History
DepositionDec 25, 2020-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateFeb 16, 2022-
Current statusFeb 16, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7dr2
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30823.png

Downloads & links

-
Map

FileDownload / File: emd_30823.map.gz / Format: CCP4 / Size: 266.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 412 pix.
= 450.316 Å		1.09 Å/pix.
x 412 pix.
= 450.316 Å		1.09 Å/pix.
x 412 pix.
= 450.316 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.093 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.103816226 - 0.22017008
Average (Standard dev.)0.0006426144 (±0.005867366)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions412412412
Spacing412412412
CellA=B=C: 450.316 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0931.0931.093
M x/y/z412412412
origin x/y/z0.0000.0000.000
length x/y/z450.316450.316450.316
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS412412412
D min/max/mean-0.1040.2200.001

-
Supplemental data

-
Sample components

+
Entire : PSI tetramer

EntireName: PSI tetramer
Components
  • Complex: PSI tetramer
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I reaction center subunit II, cyanelle
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit PsaK 1
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

+
Supramolecule #1: PSI tetramer

SupramoleculeName: PSI tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 1.4 MDa

+
Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 83.397305 KDa
SequenceString: MRISPPEREA KKVKIVIDKD PVSTSFDKWA VPGHFSRTLA KGPKTTTWIW NLHADVHDFD SYTSDLEEVS RKIFSAHFGH LAVVFIWLS GAYFHGARFS NYEAWLSNPT TIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGLFQMWR ASGITTELQL Y VTAIGALV ...String:
MRISPPEREA KKVKIVIDKD PVSTSFDKWA VPGHFSRTLA KGPKTTTWIW NLHADVHDFD SYTSDLEEVS RKIFSAHFGH LAVVFIWLS GAYFHGARFS NYEAWLSNPT TIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGLFQMWR ASGITTELQL Y VTAIGALV MAALMLFAGW FHYHKAAPKL EWFQNAESMM NHHLGGLFGL GSLSWAGHQI HVSLPVNKLL DSGVSPQEIP LP HEFILNK DLIAQLYPSF GQGLTPFFTL NWNEYSDFLT FKGGLNPVTG GLWLSDSAHH HLAIAVLFIV AGHMYRTNWG IGH SMKEMY DSHKGPFTGE GHKGVYEIFT NSWHAQLSLN LALFGSLSII VAHHMYSMPP YPYLATDYAT SLCLFTHHVW IGGF LIVGA GAHAAIFMVR DYDPAQNYNN LVDRVLRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMRAL GRPQDMFSDA AIQLQ PVFA QWVQGVNSAA AGNTAPNALA NASYAFGGDI VSVGGKVAMM PISLGTADFL VHHIHAFTIH VTVLILLKGV LFARNS RLI PDKANLGFRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSL SVVLFHFSWK MQSDVWGNVT ADGAVSHITG NNFAQGA IT INGWLRDFLW AQASQVIQSY GSALSAYGLM FLGAHFIWAF SLMFLFSGRG YWQELIESIV WAHNKLKFAP SIQPRALS I TQGRAVGVAH YLLGGIATTW SFFHARIISV G

+
Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 82.316312 KDa
SequenceString: MGTKFPKASQ ALAQDPTTRR IWYGIATAND FETNDGITEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFEQWVKD PLNTRPIAH AISDPHFGQR AIEAFSQAGA SSPVNISYSG VYQWWYTQGM RTNEELYNGA IFLLILSALS LFAGWLHLQP K FRPNLSWF ...String:
MGTKFPKASQ ALAQDPTTRR IWYGIATAND FETNDGITEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFEQWVKD PLNTRPIAH AISDPHFGQR AIEAFSQAGA SSPVNISYSG VYQWWYTQGM RTNEELYNGA IFLLILSALS LFAGWLHLQP K FRPNLSWF KNAESRLNHH LGGLFGTSSL AWTGHIVHVA IPESRGQHVG WDNFLQVAPH PAGLQPFFTG NWGVYTENPD TA NHVFGSS DGAGTAILTF LGGFHPQTQS LWLTDIAHHH LAIAVLFIVA GHMYRTNFGI GHSIKEILNG HRPPGGRLGA GHV GLYDTV NNSLHFQLGL ALAALGVITS LVAQHMYSIP PYAYLARDFT TQAALYTHHQ YIAGFLMVGA FAHGAIFLVR DYDA EQNKN NVLARIIDHK EAIISHLSWV SLFLGFHTLG LYVHNDVVQA FGTPEKQILI EPVFAQWIQS VHGKSLYGFE VLLNN ADSI TRVAPGSAQP IWLPGWLDAI NSGNNSLFLT IGPGDFLVHH AIALGLHTTT LILVKGALDA RGSKLMPDKK DFGYSF PCD GPGRGGTCDI SAWDAFYLAV FWMLNTIGWT TFYWHWKHLG VWQGNVAQFN ESSTYLMGWF RDYLWLNSSQ LINGYNP FG MNNLSVWAWM FLFGHLIWAT GFMFLISWRG YWQELIETLV WAHERTPLAN LVRWKDKPVA LSIVQARLVG LAHFAVGY I VTYAAFLIAS TASKFG

+
Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 8.850221 KDa
SequenceString:
MAHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCRANQIA SAPRTEDCVG CKRCESACPT DFLSIRVYLG AETTRSMGLG Y

+
Macromolecule #4: Photosystem I reaction center subunit II, cyanelle

MacromoleculeName: Photosystem I reaction center subunit II, cyanelle / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 23.693258 KDa
SequenceString: MNAFVASVAP IAVAGSATLS SAVCAQKKAF FGAQVAAKKT TFEAAPARFI VRAEEEEAAP AEKVEKKAAA PKPFSVPTLN LNAPTPIFG GSTGGLLRKA EVEEFYSITW TGKSETVFEL PTGGAAIMRA GENLLRLARK EQCIALGAQL KDKFKITDYK I YRVYPSGE ...String:
MNAFVASVAP IAVAGSATLS SAVCAQKKAF FGAQVAAKKT TFEAAPARFI VRAEEEEAAP AEKVEKKAAA PKPFSVPTLN LNAPTPIFG GSTGGLLRKA EVEEFYSITW TGKSETVFEL PTGGAAIMRA GENLLRLARK EQCIALGAQL KDKFKITDYK I YRVYPSGE VQFLHPKDGV FPEKVNPGRV AVGSNKRRIG QNPDPAKLKF KGQETFDSDL KL

+
Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 8.058164 KDa
SequenceString:
MVQRGSKVRI LRKESYWYQE IGTVASIDQS GIKYPVIVRF EKVNYSNVNS NNFSLDEVVE VEPPPSKKKA

+
Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 20.697777 KDa
SequenceString:
MRKLFLLMFC LSGLILTTDI RPVRADVAGL IPCSQSDAFE RRLKNTTQRL ENRLKKYEPG SAPAEALQKQ IDKTQQRFDK YRNSGLLCG ADGLPHLITD GRWSHAGEFT IPGLLFLYIA GFIGWSGRSY LQAVAASDNS TEKEIIIDIP VALQSVSKGF V WPLAALQE FSSGKLTARD EEITISPR

+
Macromolecule #7: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 3.77262 KDa
SequenceString:
MVSNLPSILV PMVGIVLPAI VMALLFVYIE TDEIA

+
Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 4.483274 KDa
SequenceString:
MSFSKYLSTA PVIGTLTAFF LAGLLIEINR FNPDLLVYPF

+
Macromolecule #9: Photosystem I reaction center subunit PsaK 1

MacromoleculeName: Photosystem I reaction center subunit PsaK 1 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 15.704348 KDa
SequenceString:
MAFVAPAPLA PARKFDAAQA RNVCIRGAAV RPAAKPAAQP AVSFEVEAAD KKAKFVAAAS VASAIFLAHT GAAHAAEMVP VIAGAMTQS VGEAAEKSFV MLASVLFAGA VGGPGIKMKG QGPAWPFNAQ IPFTPSEFLA VTALGHIIGT GVILGIGL

+
Macromolecule #10: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 10 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 15.376591 KDa
SequenceString:
MAKDAVKPFY DDAFIGHLST PISNSSAVNG LLANLPAYRK GLTPRLRGLE IGMAHGYFLT GPFVELGPLR NTDGGILYGS LSAVGLVVI LTACLALYGK ANFSGSSKSK DATLWESGEG WSDFVSGWLI GGAGSVGFAY LLLQYIL

+
Macromolecule #11: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 11 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Molecular weightTheoretical: 3.334065 KDa
SequenceString:
MLADGQIFTA LAVALVPGIL ALRLALELYK F

+
Macromolecule #12: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 12 / Number of copies: 4 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

+
Macromolecule #13: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 13 / Number of copies: 326 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #14: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 14 / Number of copies: 8 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

+
Macromolecule #15: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 15 / Number of copies: 76 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #16: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 16 / Number of copies: 8 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

+
Macromolecule #17: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 17 / Number of copies: 12 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

+
Macromolecule #18: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 18 / Number of copies: 4 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.048 mg/mL
BufferpH: 6.5 / Component:
ConcentrationFormula
50.0 mMMES-NaOH
0.03 %DDM
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 723316
CTF correctionSoftware - Name: Gctf (ver. 1.18)
Startup modelType of model: OTHER / Details: De novo generation
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 40679
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationSoftware - Name: RELION (ver. 3)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-7dr2:
Structure of GraFix PSI tetramer from Cyanophora paradoxa

+
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