[English] 日本語
Yorodumi
- EMDB-39837: Photosynthetic LH1-RC complex from the purple bacterium Halorhodo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39837
TitlePhotosynthetic LH1-RC complex from the purple bacterium Halorhodospira halophila
Map datafull map
Sample
  • Complex: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Halorhodospira halophila
    • Complex: LH1-RC complex of Halorhodospira halophila
      • Protein or peptide: x 8 types
  • Ligand: x 14 types
KeywordsLH1-RC / PHOTOSYNTHESIS
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 / : / endomembrane system / metal ion binding / membrane / plasma membrane
Similarity search - Function
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 ...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 / : / 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 L chain / Reaction center protein M chain / Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsTani K / Kanno R / Nagashima KVP / Hiwatashi N / Kawakami M / Nakata K / Nagashima S / Inoue K / Takaichi S / Purba ER ...Tani K / Kanno R / Nagashima KVP / Hiwatashi N / Kawakami M / Nakata K / Nagashima S / Inoue K / Takaichi S / Purba ER / Hall M / Yu L-J / Madigan MT / Mizoguchi A / Humbel BM / Kimura Y / Wang-Otomo Z-Y
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101118 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101116 Japan
Japan Society for the Promotion of Science (JSPS)JP16H04174 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05153 Japan
Japan Society for the Promotion of Science (JSPS)20H05086 Japan
Japan Society for the Promotion of Science (JSPS)20H02856 Japan
CitationJournal: Commun Biol / Year: 2025
Title: A Native LH1-RC-HiPIP Supercomplex from an Extremophilic Phototroph.
Authors: Kazutoshi Tani / Ryo Kanno / Kenji V P Nagashima / Mai Kawakami / Naho Hiwatashi / Kazuna Nakata / Sakiko Nagashima / Kazuhito Inoue / Shinichi Takaichi / Endang R Purba / Malgorzata Hall / ...Authors: Kazutoshi Tani / Ryo Kanno / Kenji V P Nagashima / Mai Kawakami / Naho Hiwatashi / Kazuna Nakata / Sakiko Nagashima / Kazuhito Inoue / Shinichi Takaichi / Endang R Purba / Malgorzata Hall / Long-Jiang Yu / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Yukihiro Kimura / Zheng-Yu Wang-Otomo /
Abstract: Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic purple phototrophic bacterium and has been widely used as a model for exploring the osmoadaptive and ...Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic purple phototrophic bacterium and has been widely used as a model for exploring the osmoadaptive and photosynthetic strategies employed by phototrophic extreme halophiles that enable them to thrive in hypersaline environments. Here we present the cryo-EM structures of (1) a unique native Hlr. halophila triple-complex formed from light-harvesting (LH1), the reaction center (RC), and high-potential iron-sulfur protein (HiPIP) at 2.44 Å resolution, and (2) a HiPIP-free LH1-RC complex at 2.64 Å resolution. Differing from the LH1 in the Hlr. halophila LH1-LH2 co-complex where LH1 encircles LH2, the RC-associated LH1 complex consists of 16 (rather than 18) αβ-subunits circularly surrounding the RC. These distinct forms of LH1 indicate that the number of subunits in a Hlr. halophila LH1 complex is flexible and its size is a function of the photocomplex it encircles. Like LH1 in the LH1-LH2 co-complex, the RC-associated LH1 complex also contained two forms of αβ-polypeptides and both dimeric and monomeric molecules of bacteriochlorophyll a. The majority of the isolated Hlr. halophila LH1-RC complexes contained the electron donor HiPIP bound to the surface of the RC cytochrome subunit near the heme-1 group. The bound HiPIP consisted of an N-terminal functional domain and a long C-terminal extension firmly attached to the cytochrome subunit. Despite overall highly negative surface-charge distributions for both the cytochrome subunit and HiPIP, the interface between the two proteins was relatively uncharged and neutral, forming a pathway for electron tunneling. The structure of the Hlr. halophila LH1-RC-HiPIP complex provides insights into the mechanism of light energy acquisition coupled with a long-distance electron donating process toward the charge separation site in a multi-extremophilic phototroph.
History
DepositionApr 21, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_39837.png

Downloads & links

-
Map

FileDownload / File: emd_39837.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.09039431 - 0.22299995
Average (Standard dev.)0.000068375826 (±0.007822331)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: even-half map

Fileemd_39837_half_map_1.map
Annotationeven-half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: odd-half map

Fileemd_39837_half_map_2.map
Annotationodd-half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Photosynthetic LH1-RC complex from the purple phototrophic bacter...

EntireName: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Halorhodospira halophila
Components
  • Complex: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Halorhodospira halophila
    • Complex: LH1-RC complex of Halorhodospira halophila
      • Protein or peptide: Photosynthetic reaction center cytochrome c subunit
      • Protein or peptide: Reaction center protein L chain
      • Protein or peptide: Reaction center protein M chain
      • Protein or peptide: Photosynthetic reaction center H subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
  • Ligand: HEME C
  • Ligand: MAGNESIUM ION
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
  • Ligand: PALMITIC ACID
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: Ubiquinone-8
  • Ligand: CARDIOLIPIN
  • Ligand: FE (III) ION
  • Ligand: MENAQUINONE 8
  • Ligand: SPIRILLOXANTHIN
  • Ligand: water

+
Supramolecule #1: Photosynthetic LH1-RC complex from the purple phototrophic bacter...

SupramoleculeName: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Halorhodospira halophila
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5, #7-#8, #6
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622

+
Supramolecule #2: LH1-RC complex of Halorhodospira halophila

SupramoleculeName: LH1-RC complex of Halorhodospira halophila / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5, #7-#8, #6
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622

+
Macromolecule #1: Photosynthetic reaction center cytochrome c subunit

MacromoleculeName: Photosynthetic reaction center cytochrome c subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 40.439383 KDa
SequenceString: MSSKMYLNRS LAVGALSAGL AVVVGCERPP VDTEQKGYRG TGMEEVNNPR LRDDDLHLAP EAADPVSAEG PRAGEIYQNV EVLDDLSVA EFTRLMQSMT DWVSPDEGCT YCHDGNDFAS EELYTYQVSR QMIEMNRYVN ANWDSHMDDT GVTCYTCHRG E NLPEESWF ...String:
MSSKMYLNRS LAVGALSAGL AVVVGCERPP VDTEQKGYRG TGMEEVNNPR LRDDDLHLAP EAADPVSAEG PRAGEIYQNV EVLDDLSVA EFTRLMQSMT DWVSPDEGCT YCHDGNDFAS EELYTYQVSR QMIEMNRYVN ANWDSHMDDT GVTCYTCHRG E NLPEESWF AEPTPDVNMA GLGNTMMQNL ASEKTEYTSL PRNAFERYLL GHDDLRVEGD TILPHLDEWD VSLQDTEASY SL MMHMSAA TGSNCTTCHN TGRLGQWDES PEEREISWHG IRMTRDINAN WIEPLEAGQP EVRLGPTGDI AKVQCATCHY GEQ LPLDGA KMVDDYPGLM GEEDADFDFL QFGDLGTDGL RDRNAE

+
Macromolecule #2: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 30.718809 KDa
SequenceString: MAMLDFEKKY RVRGGTLLGG DLFDFWIGPF YVGIFGVLTA IFAVLGTVLI IYGASQDTFN LWQISIAPPD LSYGLALAPM MEGGLWQII TVCALGAFIT WALRQAEISK KLGMGYHVPV AFAVAILAYA TLVVFRPLLM GAWGHGFPYG ILSHLDWVSN V GYQYLHFH ...String:
MAMLDFEKKY RVRGGTLLGG DLFDFWIGPF YVGIFGVLTA IFAVLGTVLI IYGASQDTFN LWQISIAPPD LSYGLALAPM MEGGLWQII TVCALGAFIT WALRQAEISK KLGMGYHVPV AFAVAILAYA TLVVFRPLLM GAWGHGFPYG ILSHLDWVSN V GYQYLHFH YNPAHMLAVT FFFTTTLALA LHGGLILSVT NPKKGEPVKT AEHENTFFRD VIGYSIGSLG IHRLGLFLAL NA GFWSAVC IIISGPFWTR GWPEWWNWWL NVPIWSWGG

UniProtKB: Reaction center protein L chain

+
Macromolecule #3: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 35.925391 KDa
SequenceString: MAEYQNIFTR VQVRGPTDPG VELPAADWPR TKGATHSWLL GKIGDAQVGP IYLGTTGVMS ILFGIVSIVI IGMNMLASVD WSPLEFIRQ FFWVALEPPP PEYGLSLPPL NDGGWWLIAG FTLTLSVLLW FARTYNRARA LGLGTHVAWA FAAAIFLFLA I GFIWPVLM ...String:
MAEYQNIFTR VQVRGPTDPG VELPAADWPR TKGATHSWLL GKIGDAQVGP IYLGTTGVMS ILFGIVSIVI IGMNMLASVD WSPLEFIRQ FFWVALEPPP PEYGLSLPPL NDGGWWLIAG FTLTLSVLLW FARTYNRARA LGLGTHVAWA FAAAIFLFLA I GFIWPVLM GSWAKSVPFG IFPHLDWTTA FSLRYGNLYY NPFHMLSIVF LFGSALLFAM HGATILAAGR YNAEREIEQI TD RGTAAER SALFWRWTMG FNATMESIHR WGYWFAILCV ITGGIGILLT GTVVENWYLW GVHHGIAPEY PEFFTPAVDP AAG GTE

UniProtKB: Reaction center protein M chain

+
Macromolecule #4: Photosynthetic reaction center H subunit

MacromoleculeName: Photosynthetic reaction center H subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 30.904004 KDa
SequenceString: MEGTGALTDY MNVAQMTLYA FWLFLAGLIV YLRMEDKREG YPLQAEANEN CNRTPEKKLG FPAPPSPKVF KLADGRSIQV PRAEKTDYE LNTQLRAEPT APWDGAPLEP TGNPMVDGLG PAAWAKREDE PEVTHGGKQK ICPLRVATEF EVGMSRDVAR F WPEIDPDP ...String:
MEGTGALTDY MNVAQMTLYA FWLFLAGLIV YLRMEDKREG YPLQAEANEN CNRTPEKKLG FPAPPSPKVF KLADGRSIQV PRAEKTDYE LNTQLRAEPT APWDGAPLEP TGNPMVDGLG PAAWAKREDE PEVTHGGKQK ICPLRVATEF EVGMSRDVAR F WPEIDPDP RGYQVLGCDG KVAGKIVDIW VDRGELRPMY LEMDLSGVGS SGDRVLLPIN FARVGYDSKV RVNAITGQQF TD VPRLREA DRISPQEEDF ITGYFGGGVL YAVPGRTEPF L

+
Macromolecule #5: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 5 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 7.2755 KDa
SequenceString:
MWRLWKLYDP RRVLIGIFSW LAVLALVIHF ILLSTDRFNW VGGAAVSSVS ESAEEVSALP PRQV

UniProtKB: Antenna complex, alpha/beta subunit

+
Macromolecule #6: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 6 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 8.068154 KDa
SequenceString:
MADNMSLTGL SDEEAKEFHS IFMQSFLIFT AVAVVAHFLA WAWRPWIPGA EGYGSVIEGV HNVTAAVSQI APLAG

UniProtKB: Antenna complex, alpha/beta subunit

+
Macromolecule #7: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 7 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 7.664882 KDa
SequenceString:
MWRMWKILDY RRTVVLAHVG MAVLALLIHF ILLSTENFNW LQGNPYGDAE SAAEVADAAV MPQQREV

UniProtKB: Antenna complex, alpha/beta subunit

+
Macromolecule #8: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 8 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 7.893913 KDa
SequenceString:
MADEMRNVSD EEAKEFHAMF SQAFTVYIGV AVVAHILAWA WRPWIPGDEG FGAALIEGAN AVTAAVQSIA PIAA

UniProtKB: Antenna complex, alpha/beta subunit

+
Macromolecule #9: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 9 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

+
Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #11: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

MacromoleculeName: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / type: ligand / ID: 11 / Number of copies: 1 / Formula: Z41
Molecular weightTheoretical: 568.911 Da
Chemical component information

ChemComp-Z41:
(2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

+
Macromolecule #12: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 12 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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

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

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

+
Macromolecule #14: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 14 / Number of copies: 42 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM

+
Macromolecule #15: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 15 / Number of copies: 45 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

+
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: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 17 / Number of copies: 3 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

+
Macromolecule #18: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 18 / Number of copies: 9 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

+
Macromolecule #19: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #20: MENAQUINONE 8

MacromoleculeName: MENAQUINONE 8 / type: ligand / ID: 20 / Number of copies: 1 / Formula: MQ8
Molecular weightTheoretical: 717.116 Da
Chemical component information

ChemComp-MQ8:
MENAQUINONE 8

+
Macromolecule #21: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 21 / Number of copies: 9 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

+
Macromolecule #22: water

MacromoleculeName: water / type: ligand / ID: 22 / Number of copies: 5 / 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

Concentration6.0 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
DetailsThis sample was monodisperse.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 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: 2.7 µm / Nominal defocus min: 1.1 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 331335
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 44938
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5y5s


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 20 / Target criteria: Correlation coefficient
Output model

PDB-8z83:
Photosynthetic LH1-RC complex from the purple bacterium Halorhodospira halophila

+
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