[English] 日本語
Yorodumi
- EMDB-39683: Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39683
TitleCryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with magnesium solutions
Map dataCryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with magnesium-containing solutions
Sample
  • Complex: tri-heme cytochrome-associated RC-LH1 complex
    • Protein or peptide: x 7 types
  • Ligand: x 9 types
KeywordsPhotosynthesis / Reaction center / Energy transfer / Photosynthetic bacteria
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / electron transfer activity / iron ion binding / heme binding ...organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Uncharacterized protein / Antenna pigment protein beta chain / Antenna pigment protein alpha chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit / Reaction center protein H chain
Similarity search - Component
Biological speciesDinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsChen JH / Zheng Q / Zhang X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100202 China
CitationJournal: Adv Sci (Weinh) / Year: 2025
Title: Cryo-EM Analysis of a Tri-Heme Cytochrome-Associated RC-LH1 Complex from the Marine Photoheterotrophic Bacterium Dinoroseobacter Shibae.
Authors: Weiwei Wang / Yanting Liu / Jiayi Gu / Shaoya An / Cheng Ma / Haichun Gao / Nianzhi Jiao / Jian-Ren Shen / John Thomas Beatty / Michal Koblížek / Xing Zhang / Qiang Zheng / Jing-Hua Chen /
Abstract: The reaction center-light harvesting 1 (RC-LH1) complex converts solar energy into electrical energy, driving the initiation of photosynthesis. The authors present a cryo-electron microscopy ...The reaction center-light harvesting 1 (RC-LH1) complex converts solar energy into electrical energy, driving the initiation of photosynthesis. The authors present a cryo-electron microscopy structure of the RC-LH1 isolated from a marine photoheterotrophic bacterium Dinoroseobacter shibae. The RC comprises four subunits, including a three-heme cytochrome (Cyt) c protein, and is surrounded by a closed LH ring composed of 17 pairs of antenna subunits. Notably, a novel subunit with an N-terminal "helix-turn-helix" motif embedded in the gap between the RC and the LH ring is identified. The purified RC-LH1 complex exhibits high stability in solutions containing Mg or Ca. The periplasmic Cyt c is predicted to bind at the junction between the Cyt subunit and the membrane plane, enabling electron transfer from Cyt c to the proximal heme of the tri-heme Cyt, and subsequently to the special pair of bacteriochlorophylls. These findings provide structural insights into the efficient energy and electron transfer processes within a distinct type of RC-LH1, and shed light on evolutionary adaptations of photosynthesis.
History
DepositionApr 5, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_39683.png

Downloads & links

-
Map

FileDownload / File: emd_39683.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with magnesium-containing solutions
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.46003747 - 0.6976571
Average (Standard dev.)0.0015505309 (±0.031468928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex...

Fileemd_39683_half_map_1.map
AnnotationCryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with magnesium-containing solutions-half-map-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex...

Fileemd_39683_half_map_2.map
AnnotationCryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with magnesium-containing solutions-half-map-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : tri-heme cytochrome-associated RC-LH1 complex

EntireName: tri-heme cytochrome-associated RC-LH1 complex
Components
  • Complex: tri-heme cytochrome-associated RC-LH1 complex
    • Protein or peptide: Reaction center protein O chain
    • Protein or peptide: Antenna pigment protein beta chain
    • Protein or peptide: Antenna pigment protein alpha chain
    • Protein or peptide: Reaction center protein M chain
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein H chain
    • Protein or peptide: Photosynthetic reaction center cytochrome c subunit
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: (4~{E},16~{E},26~{E})-2-methoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-3-one
  • Ligand: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate
  • Ligand: FE (III) ION
  • Ligand: UBIQUINONE-10
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: CARDIOLIPIN
  • Ligand: HEME C

+
Supramolecule #1: tri-heme cytochrome-associated RC-LH1 complex

SupramoleculeName: tri-heme cytochrome-associated RC-LH1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1, #4-#7
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)

+
Macromolecule #1: Antenna pigment protein alpha chain

MacromoleculeName: Antenna pigment protein alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 6.195409 KDa
SequenceString:
MSKFYKIWLI FDPRRVFVAQ GVFLFLLAAM IHLVLLSTEH FNWFELAAAN AAM

UniProtKB: Antenna pigment protein alpha chain

+
Macromolecule #2: Reaction center protein O chain

MacromoleculeName: Reaction center protein O chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 25.206586 KDa
SequenceString: MATQRKDMTC TITCWGIGVL LGIMTTVGLM VVGWSFLQGA FMGVLAWLIV GGVLAVAVCG ETGRPKDNAE QIRAEMAAAR ERVRGATPG ITPKPAPSVP ADVRSKVQPS AALAGEAELA GRKGSWSYDS GAGHASGAGH DAGTDAAKPA TLTAARDGKA D DLKKIKGV ...String:
MATQRKDMTC TITCWGIGVL LGIMTTVGLM VVGWSFLQGA FMGVLAWLIV GGVLAVAVCG ETGRPKDNAE QIRAEMAAAR ERVRGATPG ITPKPAPSVP ADVRSKVQPS AALAGEAELA GRKGSWSYDS GAGHASGAGH DAGTDAAKPA TLTAARDGKA D DLKKIKGV GPKLEEMLHS MGFYHFDQVA SWSEQELAWV DENLEGFKGR ASRDEWVAQA KLLAQGGETE FSKRVDGGDV Y

UniProtKB: Uncharacterized protein

+
Macromolecule #3: Antenna pigment protein beta chain

MacromoleculeName: Antenna pigment protein beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 5.578334 KDa
SequenceString:
MADKSDLSFT GLTDEQAQEL HSVYMSGLWL FSAVAVVAHL ATFIWRPWF

UniProtKB: Antenna pigment protein beta chain

+
Macromolecule #4: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 37.583723 KDa
SequenceString: MPEYQNIFTQ VQVQGPAELG VDNENNLTEE RTTGTGFSQL IGWIGNAQLG PIYLGWFGII SLVTGTLWFN IVGFNMLSQV GYSIPEFIR QLFWLALEPP SPEYGLRMPP LDDGGWFIIA SFFLLVSVIS WWLRSYQLAE MHKMGKHVAW AFAAAIWLFL V LGLFRPIL ...String:
MPEYQNIFTQ VQVQGPAELG VDNENNLTEE RTTGTGFSQL IGWIGNAQLG PIYLGWFGII SLVTGTLWFN IVGFNMLSQV GYSIPEFIR QLFWLALEPP SPEYGLRMPP LDDGGWFIIA SFFLLVSVIS WWLRSYQLAE MHKMGKHVAW AFAAAIWLFL V LGLFRPIL MGSWSEAVPY GIFPHLDWTT AFSIRYGNLY YNPFHALSIV FLYGSVLLFA MHGATILAVT RFGGDRELEQ IY DRGTASE RAGLFWRWTM GFNATMEGIH RWAWWFAVLT PITGGIGILL TGTVVDNWFL WAVEHNFAPD YTQDYGYEAY TTY DGFLGR EEGN

UniProtKB: Reaction center protein M chain

+
Macromolecule #5: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 31.197178 KDa
SequenceString: MALLSFERKY RVRGGTLIGG DLFDFWVGPF YVGFFGVTTA FFALLGTILI FWGASQQGTF NPWLINIAPP DLSYGLGMAP LMEGGLWQI ITICAIGAFV SWALREVEIC RKLGMGYHVP FAFSVAIFAY VTLVVFRPLL MGAWGHGFPY GIWSHLDWVS N TGYAYLHF ...String:
MALLSFERKY RVRGGTLIGG DLFDFWVGPF YVGFFGVTTA FFALLGTILI FWGASQQGTF NPWLINIAPP DLSYGLGMAP LMEGGLWQI ITICAIGAFV SWALREVEIC RKLGMGYHVP FAFSVAIFAY VTLVVFRPLL MGAWGHGFPY GIWSHLDWVS N TGYAYLHF HYNPAHMIAV TFFFTTTLAL ALHGALVLSA ANPPKGEEVK GPDNEDTFFR DFIGYSIGTL GIHRVGLLLA LN AGFWSAV CIIISGPVWT KGWPEWWNWW LEMPIWPSQV DC

UniProtKB: Reaction center protein L chain

+
Macromolecule #6: Reaction center protein H chain

MacromoleculeName: Reaction center protein H chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 28.739449 KDa
SequenceString: MEETFFGNFD LASLSLWLFY GFFALLIYYL QTENMREGYP LEDDDGNTAA NQGPFPLPKE KTFKLQHGRG ELTLPGEDVQ RRDNLALRK TAHGNGFPME PTGDPMLDGV GPASWSKRRD VPELDAHGHP KIVPMSAAEG FGVSAGTDPR GLPVMAGDGE I VGLVSDMW ...String:
MEETFFGNFD LASLSLWLFY GFFALLIYYL QTENMREGYP LEDDDGNTAA NQGPFPLPKE KTFKLQHGRG ELTLPGEDVQ RRDNLALRK TAHGNGFPME PTGDPMLDGV GPASWSKRRD VPELDAHGHP KIVPMSAAEG FGVSAGTDPR GLPVMAGDGE I VGLVSDMW IDEAEQLVRY LEIELDPEWG DGKRLVQREM VRIKSDRVKV RSIYGKHFKN VPKTKSPNQV TLLEEDKIMA YY AGGTLYA DESRLEPQL

UniProtKB: Reaction center protein H chain

+
Macromolecule #7: Photosynthetic reaction center cytochrome c subunit

MacromoleculeName: Photosynthetic reaction center cytochrome c subunit / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Molecular weightTheoretical: 39.977367 KDa
SequenceString: MLPKWFDEWN SKNPTDIYKP AIVVGVAGGA VFAAALLVSW GQPLATDSMQ TGPRGTGMSV PEFVSDLDTP DPTIEVFLAS TSDPVIPEE GAQTAGEAYE NVDPVLADLT VENYDRLLAA MRSWTGIPDL LEDPDHYQSK VAINMIQMNQ TINEEWAGHV Y ANAEVGVT ...String:
MLPKWFDEWN SKNPTDIYKP AIVVGVAGGA VFAAALLVSW GQPLATDSMQ TGPRGTGMSV PEFVSDLDTP DPTIEVFLAS TSDPVIPEE GAQTAGEAYE NVDPVLADLT VENYDRLLAA MRSWTGIPDL LEDPDHYQSK VAINMIQMNQ TINEEWAGHV Y ANAEVGVT CFTCHRGQAV PSEVWYRIDP VTENTSGWAS VQNRATSLSQ FTSLPSDALY QYLLNYEQIA VHDLESRVET LP GDPTWQN TERTYSLMNY FSNSLGRNCV FCHNSRAFYD PAQHTPQWAT AMLGISMVQE LNNEWIVPIG EAHLPPERLG PVY NDVPKL ACKTCHKGYQ QPLQGLNVVA DWPELATTEG PFYD

UniProtKB: Photosynthetic reaction center cytochrome c subunit

+
Macromolecule #8: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 8 / Number of copies: 38 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

+
Macromolecule #9: (4~{E},16~{E},26~{E})-2-methoxy-2,6,10,14,19,23,27,31-octamethyl-...

MacromoleculeName: (4~{E},16~{E},26~{E})-2-methoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-3-one
type: ligand / ID: 9 / Number of copies: 35 / Formula: A1EFU
Molecular weightTheoretical: 582.898 Da

+
Macromolecule #10: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24l...

MacromoleculeName: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate
type: ligand / ID: 10 / Number of copies: 12 / Formula: MW9
Molecular weightTheoretical: 777.06 Da
Chemical component information

ChemComp-MW9:
(21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate

+
Macromolecule #11: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #12: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 12 / Number of copies: 2 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

+
Macromolecule #13: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 13 / Number of copies: 5 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

+
Macromolecule #14: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 14 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

+
Macromolecule #15: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 15 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

+
Macromolecule #16: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 16 / Number of copies: 3 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 194156
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationNumber classes: 10 / Software - Name: cryoSPARC (ver. 4.2.1)

+
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