[English] 日本語
Yorodumi
- EMDB-63604: structure of bundle-shaped PBS with both long rod and (ApcA2B3Apc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63604
Titlestructure of bundle-shaped PBS with both long rod and (ApcA2B3ApcD) trimer
Map datastructure of bundle-shaped PBS with long rod
Sample
  • Complex: phycobilisome
    • Protein or peptide: Allophycocyanin alpha subunit
    • Protein or peptide: Allophycocyanin beta subunit
    • Protein or peptide: Allophycocyanin-B
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
    • Protein or peptide: Phycobiliprotein ApcE
  • Ligand: PHYCOCYANOBILIN
Keywordsphycobilisome / light-harvesting complex / photosynthesis
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity
Similarity search - Function
Allophycocyanin linker protein / Allophycocyanin linker chain / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. ...Allophycocyanin linker protein / Allophycocyanin linker chain / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Allophycocyanin beta subunit / Phycobiliprotein ApcE
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsMa J / Sui S-F
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670745 China
National Natural Science Foundation of China (NSFC)31861143048 China
CitationJournal: Nat Commun / Year: 2025
Title: Light-induced structural adaptation of the bundle-shaped phycobilisome from thylakoid-lacking cyanobacterium Gloeobacter violaceus.
Authors: Jianfei Ma / Xin You / Shan Sun / Sen-Fang Sui /
Abstract: Gloeobacter diverged from other lineages early in cyanobacterial evolution, preferentially growing under low light intensity conditions. Among cyanobacteria, G. violaceus exhibits unique features, ...Gloeobacter diverged from other lineages early in cyanobacterial evolution, preferentially growing under low light intensity conditions. Among cyanobacteria, G. violaceus exhibits unique features, including lack of a thylakoid membrane and bundle-shaped antenna phycobilisomes (PBSs), densely packed and well-organized on the plasma membrane. However, without high-resolution structures, it has remained unclear how G. violaceus PBSs assemble into a bundle-shaped configuration. Here we solve the cryo-EM structures of PBSs from G. violaceus cells cultured under low (Sr-PBS) or moderate (Lr-PBS) light intensity. These structures reveal two unique linker proteins, L and L, that play a key role in the PBS architecture. Analysis of the bilin arrangement indicates that the bundle-shaped structure allows efficient energy transfer among rods. Moreover, comparison between Lr-PBS and Sr-PBS uncovers a distinct mode of adaption to increased light intensity wherein the ApcA-ApcB-ApcD layer can be blocked from binding to the core by altering structural elements exclusively found in the G. violaceus L. This study illustrates previously unrecognized mechanisms of assembly and adaptation to varying light intensity in the bundle-shaped PBS of G. violaceus.
History
DepositionMar 2, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_63604.png

Downloads & links

-
Map

FileDownload / File: emd_63604.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of bundle-shaped PBS with long rod
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 580 pix.
= 636.782 Å		1.1 Å/pix.
x 580 pix.
= 636.782 Å		1.1 Å/pix.
x 580 pix.
= 636.782 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.51835763 - 1.669809
Average (Standard dev.)0.0070418175 (±0.06594328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions580580580
Spacing580580580
CellA=B=C: 636.78204 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: structure of bundle-shaped PBS with long rod half map 2

Fileemd_63604_half_map_1.map
Annotationstructure of bundle-shaped PBS with long rod half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: structure of bundle-shaped PBS with long rod half map 1

Fileemd_63604_half_map_2.map
Annotationstructure of bundle-shaped PBS with long rod half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : phycobilisome

EntireName: phycobilisome
Components
  • Complex: phycobilisome
    • Protein or peptide: Allophycocyanin alpha subunit
    • Protein or peptide: Allophycocyanin beta subunit
    • Protein or peptide: Allophycocyanin-B
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
    • Protein or peptide: Phycobiliprotein ApcE
  • Ligand: PHYCOCYANOBILIN

-
Supramolecule #1: phycobilisome

SupramoleculeName: phycobilisome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria) / Strain: PCC 7421
Molecular weightTheoretical: 7 MDa

-
Macromolecule #1: Allophycocyanin alpha subunit

MacromoleculeName: Allophycocyanin alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 44 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 17.539039 KDa
SequenceString:
MSVLTKAIVN ADAEARYLSP GELDRIKSFV ASGERRLRIA QTLTEARERI VKQAGDQLFQ IRPDVVSPGG NAYGEKMTAL CLRDLDYYL RLVTYGIVAG DVTPIEEIGI IGVKEMYNSL QTPIPAVAEG VRAMKNVATS LLSGDDAAEA GFYFDYLVGA M Q

-
Macromolecule #2: Allophycocyanin beta subunit

MacromoleculeName: Allophycocyanin beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 48 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 17.241664 KDa
SequenceString:
MQDAITAVIN NYDVQGKYLD GAALDKLKAY FTTGAVRVRA AAVISSNATT IIKEAAAKAL IYSDLTRPGG (MEN)MYTTR RYA ACIRDMDYFL RYATYAMLAG DPSILDERVL NGLKETYNSL GVPIAATVGG IQAMKEVVGG LVGPDAAKEA SIYFDYL SS GLS

UniProtKB: Allophycocyanin beta subunit

-
Macromolecule #3: Allophycocyanin-B

MacromoleculeName: Allophycocyanin-B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 18.050812 KDa
SequenceString:
MSVVLTTIMN ADQQLRYPSV GELEQIKNFM EDSALRLKVA KTLSDANDRV VKQASAGLFQ RRPDLNNPGG NAYGEKRLGS CIRDLGWYY RLITYSIVAG NNEPVERIGL TGIFEMYRVL EVPIPAMIES MRLLKKEALE LLSPAEAEIA APYFDYVIGA M Q

-
Macromolecule #4: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associa...

MacromoleculeName: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
type: protein_or_peptide / ID: 4 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 7.765004 KDa
SequenceString:
MSRYFKVTAC IPSLKRVRTG RELQNTFFTK LVPYENWFTE QQRIQKAGGK VLSVKLFTGV QGANTGVGA

UniProtKB: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

-
Macromolecule #5: Phycobiliprotein ApcE

MacromoleculeName: Phycobiliprotein ApcE / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 130.002258 KDa
SequenceString: MSIRGTSGST VARPRLFRTV MTETINGINA EDRYPNSGEV SQLDQFFGDG QRRIAIVAKL TENAEMIVSR AANRIFVGGS PMAYSERQK AKAKSPLAND EFGNEPIVED RGGFLESLKS IFSTRGGGGR ASADFAVPPD FEPINIARYG PERMQKSIRD L DWFLRYTT ...String:
MSIRGTSGST VARPRLFRTV MTETINGINA EDRYPNSGEV SQLDQFFGDG QRRIAIVAKL TENAEMIVSR AANRIFVGGS PMAYSERQK AKAKSPLAND EFGNEPIVED RGGFLESLKS IFSTRGGGGR ASADFAVPPD FEPINIARYG PERMQKSIRD L DWFLRYTT YAILAGDPSI LEANCLGLRE ILEKSCSISA TIVALLEMRK NAARLFKDEA DSKLVSSYIS VVIRALDADR SD APADIVR PSSEDRPGLT LPYIYKLSAD SLTTFKMTAI YGADGRPKVN LSSDEKERVV RAAYRQVFER DLKAYGQSVS EAE SKVKNG EISVREFVRR LGKSELYRRE FYQPFINSRV LELAFKHFLG RAPESRAEVQ KYFSIISSPI VRGQSSMPSG GLYA LIDAL IDSEEYTSIF GEDTVPYLRN LGVEAQPSWN WGAAYDLYNY AAPRRKVPQF ITLFADYTQP LPNQHPYGAG NDPLE IQFG AIFKNSTINP AERAAPIGKD VKRILIRNGS PTSNERGNPT GMSEGATTLG PKIFKLTQNV GFRSKGMVQN AGVVTV EGS VQALITAAYQ QIFGRQLYQG QRLKVAEIKL ENGETTVKEF VRALGRSEIF RKLYWEPFYV CKAIEYIHRR LLGRPTY DR VENNRYFDIA SKKGFYGVVD AMLNSNEYQE VFGEDVLPYE RYLTPAGLSL RKGRFGSSDV LTTPGGITPR GDAARMMD K IQELGTPINE RSIPEMYVNQ GVPALKRQRK VFKQSQATDR ESFDALVTAA YVQVFDKDIA SYIRSEFSAL ESRLRNRET SVKEFVRLLG FSALYRKQFH DRYPNTKVVE FAFKHFLGRA VKNQAELIKY HGLLGRKGIK ALIGALVDGE EYGRLYGEDT VPSWQFPTL PAANYPNSVE LYNRFTRQDD SLVVPSFKPI RSKMDIASMP LVQAALKEQQ ATKTALDMSR PMFLELGRSF K GADGQSVE VGVGTLRRQL EHIYRIAPDA TRSEKDVAIN AIYRQVLDVF AGIPPSYLRL SEAESKLKNN EISVREFVRR LG RSENYRK RFFEPYSSPK VVELLTKHFL GRAPISQQEI STYVQILGTK GLAAAVDAIV ESPEYLTIFN EDIVPYRRYP TLP AGNYRA SVRVNDEELI SQSWSSLSPT YTGYQYVTR

UniProtKB: Phycobiliprotein ApcE

-
Macromolecule #6: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 6 / Number of copies: 96 / Formula: CYC
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-CYC:
PHYCOCYANOBILIN

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
Component:
ConcentrationFormulaName
0.75 mol/LNa2HPO4disodium hydrogen phosphate
0.75 mol/LKH2PO4Monobasic Potassium Phosphate
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 18 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMin: 77.0 K / Max: 77.0 K
Specialist opticsSpherical aberration corrector: Spherical aberration (Cs) corrector
Energy filter - Name: GIF Quantum ER / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 2 / Number real images: 10942 / Average exposure time: 8.2 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.3000000000000003 µm / Calibrated defocus min: 1.3 µm / Calibrated magnification: 64000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 605750
CTF correctionSoftware - Name: CTFFIND (ver. 4.15) / Type: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.2) / Number images used: 192814
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.2)
Final 3D classificationNumber classes: 2 / Avg.num./class: 192814 / Software - Name: cryoSPARC (ver. 4.0.2)

-
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: 62.05 / Target criteria: 0,99
Output model

PDB-9m3j:
structure of bundle-shaped PBS with both long rod and (ApcA2B3ApcD) trimer

+
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