[English] 日本語
Yorodumi
- EMDB-51760: Cryo-EM structure of RC-dLH complex model I from Gem. groenlandic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51760
TitleCryo-EM structure of RC-dLH complex model I from Gem. groenlandica strain TET16
Map data
Sample
  • Complex: RC-dLH complex model I from Gemmatimonas groenlandica
    • Protein or peptide: x 9 types
  • Ligand: x 11 types
Keywordsreaction centre light harvesting complex / RC-dLH / photosynthetic bacteria / gemmatimonas groenlandica / PHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / endomembrane system / electron transfer activity / iron ion binding / heme binding / metal ion binding ...organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / endomembrane system / 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, M subunit / Photosynthetic reaction centre, L subunit / Multiheme cytochrome superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Reaction center protein M chain / Light-harvesting protein / Reaction center protein L chain / Uncharacterized protein / Light-harvesting protein / Light-harvesting protein / Photosynthetic reaction center cytochrome c subunit
Similarity search - Component
Biological speciesGemmatimonas groenlandica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsGardiner A / Qian P / Koblizek M / Jing Y / Joosten M / Jakobi A / Bina D / Mujakic I / Gardian Z / Kaftan D / Castro-Hartmann P
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Czech Science Foundation19-28778X Czech Republic
CitationJournal: To Be Published
Title: Cryo-EM structure of RC-dLH complex model I from Gem. groenlandica strain TET16
Authors: Gardiner A / Qian P / Koblizek M / Jing Y / Joosten M / Jakobi A / Bina D / Mujakic I / Gardian Z / Kaftan D / Castro-Hartmann P
History
DepositionOct 9, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_51760.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 600 pix.
= 439.2 Å
0.73 Å/pix.
x 600 pix.
= 439.2 Å
0.73 Å/pix.
x 600 pix.
= 439.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density
Contour LevelBy AUTHOR: 0.0687
Minimum - Maximum-0.22585393 - 0.5475419
Average (Standard dev.)0.00059466774 (±0.012089587)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 439.19998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: z-flip

Fileemd_51760_half_map_1.map
Annotationz-flip
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: z-flip

Fileemd_51760_half_map_2.map
Annotationz-flip
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire : RC-dLH complex model I from Gemmatimonas groenlandica

EntireName: RC-dLH complex model I from Gemmatimonas groenlandica
Components
  • Complex: RC-dLH complex model I from Gemmatimonas groenlandica
    • Protein or peptide: Light-harvesting protein
    • Protein or peptide: Light-harvesting protein
    • Protein or peptide: Light-harvesting protein
    • Protein or peptide: Photosynthetic reaction center cytochrome c subunit
    • Protein or peptide: reaction centre Ht sub unit
    • Protein or peptide: reaction centre Hc sub unit
    • Protein or peptide: Reaction center protein L chain
    • Protein or peptide: Reaction center protein M chain
    • Protein or peptide: reaction centre S sub unit
  • Ligand: (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{Z},24~{E},26~{E},28~{E})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
  • Ligand: MENAQUINONE 8
  • Ligand: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: FE (III) ION
  • Ligand: SPIRILLOXANTHIN
  • Ligand: HEME C
  • Ligand: water

+
Supramolecule #1: RC-dLH complex model I from Gemmatimonas groenlandica

SupramoleculeName: RC-dLH complex model I from Gemmatimonas groenlandica / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #9, #1-#2, #8, #6-#7, #4-#5, #3 / Details: a single monomer complex
Source (natural)Organism: Gemmatimonas groenlandica (bacteria)
Molecular weightTheoretical: 650 KDa

+
Macromolecule #1: Light-harvesting protein

MacromoleculeName: Light-harvesting protein / type: protein_or_peptide / ID: 1 / Details: helix / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas groenlandica (bacteria)
Molecular weightTheoretical: 7.697123 KDa
SequenceString:
MHRIWLMFDP RRVMVAMVGF LAVLALVIHF ILLSSQRYSW IENGTLSAAQ APVGASAPAA AAEMSPLPPG R

UniProtKB: Light-harvesting protein

+
Macromolecule #2: Light-harvesting protein

MacromoleculeName: Light-harvesting protein / type: protein_or_peptide / ID: 2 / Details: helix / Number of copies: 40 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas groenlandica (bacteria)
Molecular weightTheoretical: 5.183985 KDa
SequenceString:
MMEKGGMTED EARRFHGYFV TGTLGYIIVA AVAHFLAWQW RPWF

UniProtKB: Light-harvesting protein

+
Macromolecule #3: reaction centre S sub unit

MacromoleculeName: reaction centre S sub unit / type: protein_or_peptide / ID: 3 / Details: native protein / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas groenlandica (bacteria)
Molecular weightTheoretical: 21.641564 KDa
SequenceString: MMLRQDRPRV LSRVSTVVGI GALVAVAMAA RSQGGQQATP PSAPQPPVAA PSAAPAATDS TMQDSTQRAD TTAKADSMLA MPDSMMMQH TAAAPAPQAS AMWPVDPVTG QTIINGEPVV GRVFIMQKTD GTVKLGKWQA QYDGEPTAPE AANVGSSYTV P APEHTRRM ...String:
MMLRQDRPRV LSRVSTVVGI GALVAVAMAA RSQGGQQATP PSAPQPPVAA PSAAPAATDS TMQDSTQRAD TTAKADSMLA MPDSMMMQH TAAAPAPQAS AMWPVDPVTG QTIINGEPVV GRVFIMQKTD GTVKLGKWQA QYDGEPTAPE AANVGSSYTV P APEHTRRM RGIMIQSTLW SIDGKRSARE RRHYRPQTTG AALGQQ

UniProtKB: Uncharacterized protein

+
Macromolecule #4: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 4 / Details: native protein / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas groenlandica (bacteria)
Molecular weightTheoretical: 30.54274 KDa
SequenceString: MAMLSFEKKY RVRGGTLIGG DLFDFWFGPF YVGFFGVTTI FFVTLGTLLC VWGAAMGPTW NLWQISIAPP DLKYGLGLAP LREGGLWQI ITLCALGAFG SWALRQAEIS RKLGMGMHIP WAYGGAVLAY ATLVVIRPML LGAWGHGFPY GIFSHLDWVS N VGYQYLHF ...String:
MAMLSFEKKY RVRGGTLIGG DLFDFWFGPF YVGFFGVTTI FFVTLGTLLC VWGAAMGPTW NLWQISIAPP DLKYGLGLAP LREGGLWQI ITLCALGAFG SWALRQAEIS RKLGMGMHIP WAYGGAVLAY ATLVVIRPML LGAWGHGFPY GIFSHLDWVS N VGYQYLHF HYNPAHMIAV TFFFTNCLAL AMHGSLILSV TNPKKGTPVG TSETENVFFR DLLGYSIGAI GIHRLGLFLA VG AAVWSAI CIVISGPFWT KGWPEWWNWW LNLPIWR

UniProtKB: Reaction center protein L chain

+
Macromolecule #5: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 5 / Details: native proteins / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas groenlandica (bacteria)
Molecular weightTheoretical: 43.396742 KDa
SequenceString: MLEYQNLFTR VQVRTVPEAG IEIDESTGTR YGTGTFSYLA GKFGDAQIGP IYLGWAGVLS LIFGFMAFEI IGLNMWASVG WDPVEFIRQ LPWLALEPPP PQYGLRVPPL AQGGWYLMAG FFLTISILLW WVRVYRRARA LNMGTHLPWA FASAIFLYST F FFQPLLVG ...String:
MLEYQNLFTR VQVRTVPEAG IEIDESTGTR YGTGTFSYLA GKFGDAQIGP IYLGWAGVLS LIFGFMAFEI IGLNMWASVG WDPVEFIRQ LPWLALEPPP PQYGLRVPPL AQGGWYLMAG FFLTISILLW WVRVYRRARA LNMGTHLPWA FASAIFLYST F FFQPLLVG SWSEMVPFGI FPHLDWTSAF SIRYGNLYYN PFHALSIAFL YGSAVLFAMH GATILAVARL GGEREIEQIT DR GTAAERS MLFWRWTMGF NATMESIHRW SWWFAVLTTF SGGIGILLTG TVVDNWYLWG VKHGLVAPYP AQNTLTEEQQ QLL RGRYQG TAPDSFPSYV APQPAMMLDS TAMMAPADSM KADSTKVDSA AAPSAPAAAA PPPAKPPAPS VGGKTP

UniProtKB: Reaction center protein M chain

+
Macromolecule #6: reaction centre Ht sub unit

MacromoleculeName: reaction centre Ht sub unit / type: protein_or_peptide / ID: 6 / Details: helix / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas groenlandica (bacteria)
Molecular weightTheoretical: 7.202296 KDa
SequenceString:
MQYIDGAQIA LYAFWLFFFG LIIYIRREDK REGYPLESPQ GPREGWPAMP EKKTYIHRPT

+
Macromolecule #7: reaction centre Hc sub unit

MacromoleculeName: reaction centre Hc sub unit / type: protein_or_peptide / ID: 7 / Details: native proteins / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas groenlandica (bacteria)
Molecular weightTheoretical: 19.538121 KDa
SequenceString:
SDIKAVPADS YNGSALIPTG DPMIDGVGPS SWANRSDTPD MTFHNTAKIV PMRLDPTYSI AKGDPDPRGL PVVAADKQVA GTVIELWVN RAEPQVTYYE VQLTGSERRV MLPAGFVQWP NFGLWGNDKL LVKAITAAQF ANVPALKRDD QITLLEEDMV C AYYAGGHL YAMAERSEPI I

+
Macromolecule #8: Photosynthetic reaction center cytochrome c subunit

MacromoleculeName: Photosynthetic reaction center cytochrome c subunit / type: protein_or_peptide / ID: 8 / Details: native protein / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas groenlandica (bacteria)
Molecular weightTheoretical: 40.302758 KDa
SequenceString: MSILRRSIGL VAPLALLSLG ACGDTATDSV QVGYRGTGME QNYDHGDLKK QFAQVKIPTP LPPAGESPPG PLPWQNVQVL NDISVGEFN RTMVAMSTWV AGTGNCAYCH NIANLAADTL PNGKPLYTKL VARRMLQMTR QINGQYSQHV KNTGVTCYTC H MGKPLPNG ...String:
MSILRRSIGL VAPLALLSLG ACGDTATDSV QVGYRGTGME QNYDHGDLKK QFAQVKIPTP LPPAGESPPG PLPWQNVQVL NDISVGEFN RTMVAMSTWV AGTGNCAYCH NIANLAADTL PNGKPLYTKL VARRMLQMTR QINGQYSQHV KNTGVTCYTC H MGKPLPNG LWFYSSQTDY LRHYLDRDGA RVVTRDVAPS NANRSSVKQT EWTYALMISQ SRSLGVNCTY CHNTRQFASW KE APPARVT AYHGILMLRD VNQNYLSPLQ PVYPSVRLGT QGDAPKAQCV TCHNGNYKPL YGAQMVKDYP ALWGRADWNG VPF QGLSPK ADTTSAGAAP AAPAAAAPVP AVKRSSARTV PAPTVIGGAV GSPNTPK

UniProtKB: Photosynthetic reaction center cytochrome c subunit

+
Macromolecule #9: Light-harvesting protein

MacromoleculeName: Light-harvesting protein / type: protein_or_peptide / ID: 9 / Details: helix / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Gemmatimonas groenlandica (bacteria)
Molecular weightTheoretical: 6.413583 KDa
SequenceString:
MHRIWQGMDP QIIMSGLGFF LAGLALIIHM WAYSITGWPK YKKAQYNAQT PPTAVR

UniProtKB: Light-harvesting protein

+
Macromolecule #10: (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{...

MacromoleculeName: (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{Z},24~{E},26~{E},28~{E})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid
type: ligand / ID: 10 / Number of copies: 40 / Formula: V7N
Molecular weightTheoretical: 610.865 Da
Chemical component information

ChemComp-V7N:
(2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{Z},24~{E},26~{E},28~{E})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid

+
Macromolecule #11: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 11 / Number of copies: 84 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

+
Macromolecule #12: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 12 / Number of copies: 48 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #13: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

MacromoleculeName: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / type: ligand / ID: 13 / Number of copies: 17 / Formula: PEX
Molecular weightTheoretical: 522.632 Da
Chemical component information

ChemComp-PEX:
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

+
Macromolecule #14: MENAQUINONE 8

MacromoleculeName: MENAQUINONE 8 / type: ligand / ID: 14 / Number of copies: 3 / Formula: MQ8
Molecular weightTheoretical: 717.116 Da
Chemical component information

ChemComp-MQ8:
MENAQUINONE 8

+
Macromolecule #15: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(te...

MacromoleculeName: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate
type: ligand / ID: 15 / Number of copies: 2 / Formula: CD4
Molecular weightTheoretical: 1.241633 KDa
Chemical component information

ChemComp-CD4:
(2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate

+
Macromolecule #16: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 16 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

+
Macromolecule #17: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #18: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 18 / Number of copies: 1 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

+
Macromolecule #19: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 19 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

+
Macromolecule #20: water

MacromoleculeName: water / type: ligand / ID: 20 / Number of copies: 38 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4.0 mg/mL
BufferpH: 8 / Component - Concentration: 20.0 mM / Component - Name: Tris-HCL / Details: 20 mM Tris-HCL, 50 mM NaCl, pH 8.0, 0.02% beta-DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 3 seconds, blot force, 3.
DetailsProtein in buffer solution with detergent of beta-DDM

-
Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 88.0 K / Max: 92.0 K
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Details: Thermofisher Titan Krios G3 with energy filter selectrisX
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 23012 / Average exposure time: 5.13 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsTiff format was used for image recording.
Particle selectionNumber selected: 935540
Details: Initially, particles were selected by the use of cryosparc blob model automatically. Model reference then was used later for final 3D reconstruction.
CTF correctionSoftware - Name: CTFFIND (ver. 4.0) / Details: CTF was performed within cryosparc / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: a subset data was used for ab-initial model establishment
Details: within cryosparc package
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 129052
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4.2.1)
Details: This complex has two confirmations. The final dataset was used for 3D classification within 2 classes
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 60 / Target criteria: model to map
Output model

PDB-9h19:
Cryo-EM structure of RC-dLH complex model I from Gem. groenlandica strain TET16

+
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