[English] 日本語
Yorodumi
- EMDB-11081: RC-LH1(14)-W complex from Rhodopseudomonas palustris -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11081
TitleRC-LH1(14)-W complex from Rhodopseudomonas palustris
Map data
Sample
  • Complex: Reaction center-Light harvesting complex 1-Protein W
    • Protein or peptide: x 6 types
  • Ligand: x 11 types
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 transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane => GO:0016020 / membrane / metal ion binding / plasma membrane
Similarity search - Function
Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit ...Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit / 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 / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Reaction center protein M chain / H subunit of photosynthetic reaction center complex / Reaction center protein L chain / Uncharacterized protein / Light-harvesting complex 1 alpha chain / Light-harvesting complex 1 beta chain
Similarity search - Component
Biological speciesRhodopseudomonas palustris CGA009 (phototrophic) / Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsSwainsbury DJK / Qian P / Hitchcock A / Hunter CN
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M000265/1 United Kingdom
CitationJournal: Sci Adv / Year: 2021
Title: Structures of RC-LH1 complexes with open or closed quinone channels.
Authors: David J K Swainsbury / Pu Qian / Philip J Jackson / Kaitlyn M Faries / Dariusz M Niedzwiedzki / Elizabeth C Martin / David A Farmer / Lorna A Malone / Rebecca F Thompson / Neil A Ranson / ...Authors: David J K Swainsbury / Pu Qian / Philip J Jackson / Kaitlyn M Faries / Dariusz M Niedzwiedzki / Elizabeth C Martin / David A Farmer / Lorna A Malone / Rebecca F Thompson / Neil A Ranson / Daniel P Canniffe / Mark J Dickman / Dewey Holten / Christine Kirmaier / Andrew Hitchcock / C Neil Hunter /
Abstract: The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes ...The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes from A 2.65-Å resolution structure of the RC-LH1-W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16-subunit LH1 ring. Comparison of these structures provides insights into quinone dynamics within RC-LH1 complexes, including a previously unidentified conformational change upon quinone binding at the RC Q site, and the locations of accessory quinone binding sites that aid their delivery to the RC. The structurally unique protein-W prevents LH1 ring closure, creating a channel for accelerated quinone/quinol exchange.
History
DepositionMay 27, 2020-
Header (metadata) releaseJan 13, 2021-
Map releaseJan 13, 2021-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6z5s
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11081.png

Downloads & links

-
Map

FileDownload / File: emd_11081.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.048 Å
Density
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.20541248 - 0.8035115
Average (Standard dev.)0.0009778267 (±0.0148938885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z419.200419.200419.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2050.8040.001

-
Supplemental data

-
Sample components

+
Entire : Reaction center-Light harvesting complex 1-Protein W

EntireName: Reaction center-Light harvesting complex 1-Protein W
Components
  • Complex: Reaction center-Light harvesting complex 1-Protein W
    • Protein or peptide: Light harvesting complex 1 Protein WLight-harvesting complex
    • Protein or peptide: Reaction center protein M chainPhotosynthetic reaction centre
    • Protein or peptide: Reaction center protein L chainPhotosynthetic reaction centre
    • Protein or peptide: H subunit of photosynthetic reaction center complex
    • Protein or peptide: Light-harvesting complex 1 alpha chain
    • Protein or peptide: Light-harvesting complex 1 beta chain
  • Ligand: (6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S},28~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-24,28-dien-2-ol
  • Ligand: BACTERIOCHLOROPHYLL ABacteriochlorophyll
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: UBIQUINONE-10Coenzyme Q10
  • Ligand: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
  • Ligand: CARDIOLIPIN
  • Ligand: FE (III) ION
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: SPIRILLOXANTHIN
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: water

+
Supramolecule #1: Reaction center-Light harvesting complex 1-Protein W

SupramoleculeName: Reaction center-Light harvesting complex 1-Protein W / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: Reaction center-Light harvesting complex 1 containing protein W from Rhodopseudomonas palustris
Source (natural)Organism: Rhodopseudomonas palustris CGA009 (phototrophic) / Location in cell: Lamellar membranes
Molecular weightTheoretical: 3.20 MDa

+
Macromolecule #1: Light harvesting complex 1 Protein W

MacromoleculeName: Light harvesting complex 1 Protein W / type: protein_or_peptide / ID: 1 / Details: Light harvesting complex 1 Protein W / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009
Molecular weightTheoretical: 10.505632 KDa
SequenceString:
MMLLLVLTAI AFVATAVVAR VLAASAPEGK LYCQAAGAAS MVVGPFITLV AAFVLGKAGI GGEVLDATAM LRVAALPAFG TLFVGPVVF WFFRRQRRTV AAA

+
Macromolecule #2: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009
Molecular weightTheoretical: 34.453828 KDa
SequenceString: MAQYQNIFTQ VQVEGPAYAG VPLRPGSSPR ETQTTFNYWL GKIGDAQVGP VYLGFTGVCS LLCGFVAIEI IGLNMLASVD WSPIEFLRQ FCWLALEPPK PEYGLTIPPL KEGGWWLMAG FFLTVSIALW WVRTYRRSRA LGMGTHVSWA FASAILLYLA L GFIQPLLM ...String:
MAQYQNIFTQ VQVEGPAYAG VPLRPGSSPR ETQTTFNYWL GKIGDAQVGP VYLGFTGVCS LLCGFVAIEI IGLNMLASVD WSPIEFLRQ FCWLALEPPK PEYGLTIPPL KEGGWWLMAG FFLTVSIALW WVRTYRRSRA LGMGTHVSWA FASAILLYLA L GFIQPLLM GSWSEAPPFG VFPHLDWTNN FSIKYGNLYY NPFHCLSIAF LYGSALLFAM HGATILAVSR YGGEREIEQM LD RGTALER AALFWRWTMG FNATAESIHR WAWWFAVLCP LTGAIGIILT GPVVDNWFDW GVKHGLAPPR

+
Macromolecule #3: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009
Molecular weightTheoretical: 30.857777 KDa
SequenceString: MAMLSFEKKY RVRGGTLIGG DLFDFWVGPF YVGIFGVMTV FFALIGIALI AWNTALGPTW NLWQISVNPP DAKYGLGFAP LAEGGIWQW VSICATGAFV TWALREVEIC RKLGIGFHVP FAFSFAIFAY VTLVVIRPVL MGSWSYGFPY GIFTHLDWVS N TGYSYGQF ...String:
MAMLSFEKKY RVRGGTLIGG DLFDFWVGPF YVGIFGVMTV FFALIGIALI AWNTALGPTW NLWQISVNPP DAKYGLGFAP LAEGGIWQW VSICATGAFV TWALREVEIC RKLGIGFHVP FAFSFAIFAY VTLVVIRPVL MGSWSYGFPY GIFTHLDWVS N TGYSYGQF HYNPAHMIAI TFFFTTCLAL ALHGGLVLSA LNPDRGEPVK SPEHENTVFR DLVGYSIGTI GIHRLGLFLA LS AVFFSAV CMIISGPVLA EGGSWPDWWN WWRNLPIWNP

+
Macromolecule #4: H subunit of photosynthetic reaction center complex

MacromoleculeName: H subunit of photosynthetic reaction center complex / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009
Molecular weightTheoretical: 27.268223 KDa
SequenceString: MQPGAYLDLA QVTLYVFWIF FAGLLFYLRR EDKREGYPLV ADAGSGTRLA KIGVPAPPDP KTYLLRGGAT KTVPSTSNDR PNVALTPAA PWPGAPFVPT GNPFADGVGP GSYAQRADVP ELGLDNLPII VPLRAAKGMF LDPRDPNPVG MPVVGCDGVV G GTVTEVWV ...String:
MQPGAYLDLA QVTLYVFWIF FAGLLFYLRR EDKREGYPLV ADAGSGTRLA KIGVPAPPDP KTYLLRGGAT KTVPSTSNDR PNVALTPAA PWPGAPFVPT GNPFADGVGP GSYAQRADVP ELGLDNLPII VPLRAAKGMF LDPRDPNPVG MPVVGCDGVV G GTVTEVWV DRAEVLARYL EVEVAKSRKR VLLPVPFALI NDPFGKVSVD AIRGDQFAGV PTTSKGDQVS KLEEDKICAY YG AGTLYAT PLRSESLV

+
Macromolecule #5: Light-harvesting complex 1 alpha chain

MacromoleculeName: Light-harvesting complex 1 alpha chain / type: protein_or_peptide / ID: 5 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009
Molecular weightTheoretical: 7.276766 KDa
SequenceString:
(FME)WRIWLLFDP RRALVLLFVF LFGLAIIIHF ILLSTSRFNW LDGPRAAKAA SISLPFTPPS MPV

+
Macromolecule #6: Light-harvesting complex 1 beta chain

MacromoleculeName: Light-harvesting complex 1 beta chain / type: protein_or_peptide / ID: 6 / Details: Light-harvesting LH1 beta subunit / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009
Molecular weightTheoretical: 7.284456 KDa
SequenceString:
MSDGSISGLS EAEAKEFHSI FVTSFFLFIV VAVVAHILAW MWRPWLPKAT GYAMDSVHQL TSFLC

+
Macromolecule #7: (6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S},28~{E})-2,6,10,1...

MacromoleculeName: (6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S},28~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-24,28-dien-2-ol
type: ligand / ID: 7 / Number of copies: 1 / Formula: QAK
Molecular weightTheoretical: 575.047 Da
Chemical component information

ChemComp-QAK:
(6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S},28~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-24,28-dien-2-ol

+
Macromolecule #8: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 8 / Number of copies: 32 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll

+
Macromolecule #9: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 9 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A / Pheophytin

+
Macromolecule #10: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 10 / Number of copies: 3 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10 / Coenzyme Q10

+
Macromolecule #11: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-...

MacromoleculeName: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
type: ligand / ID: 11 / Number of copies: 3 / Formula: 6PL
Molecular weightTheoretical: 763.1 Da
Chemical component information

ChemComp-6PL:
(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / phospholipid*YM

+
Macromolecule #12: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 12 / Number of copies: 6 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

+
Macromolecule #13: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 13 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #14: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 14 / Number of copies: 29 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #15: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 15 / Number of copies: 13 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

+
Macromolecule #16: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 16 / Number of copies: 1 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM / Phosphatidylglycerol

+
Macromolecule #17: water

MacromoleculeName: water / type: ligand / ID: 17 / Number of copies: 10 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
200.0 mMNaClSodium chlorideNaClSodium chloride
0.03 % w/vC24H46O11n-Dodecyl-beta-D-Maltopyranoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 298 K / Instrument: LEICA EM GP
DetailsThis sample was monodisperse

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 46.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 849359 / Details: Autopicked in RELION
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Software - details: Executed within RELION3.0
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 377703
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-6z5s:
RC-LH1(14)-W complex from Rhodopseudomonas palustris

+
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