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- EMDB-62201: structure of bundle-shaped PBS with short rod -

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Basic information

Entry
Database: EMDB / ID: EMD-62201
Titlestructure of bundle-shaped PBS with short rod
Map datastructure of bundle-shaped PBS with short rod at 2.80A
Sample
  • Complex: phycobilisome
    • Protein or peptide: x 2 types
  • Protein or peptide: x 9 types
  • Ligand: x 1 types
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 / Phycobilisome linker protein / 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 ...Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / 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
Phycocyanin beta chain / Phycocyanin alpha chain / Phycocyanin-associated rod linker protein / Glr2806 protein / CpcD protein / Glr1262 protein / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Allophycocyanin beta subunit / Allophycocyanin alpha subunit / Phycobiliprotein ApcE / Phycocyanin-associated rod linker protein
Similarity search - Component
Biological speciesPorphyridium purpureum (eukaryote) / Gloeobacter violaceus PCC 7421 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSui S-F / Ma J / You X / Sun S
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
DepositionOct 28, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62201.png

Downloads & links

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Map

FileDownload / File: emd_62201.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of bundle-shaped PBS with short rod at 2.80A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 560 pix.
= 614.824 Å		1.1 Å/pix.
x 560 pix.
= 614.824 Å		1.1 Å/pix.
x 560 pix.
= 614.824 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-1.4110602 - 2.8998883
Average (Standard dev.)0.006232031 (±0.06676307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 614.82404 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: structure of bundle-shaped PBS with short rod at 2.80A halfB

Fileemd_62201_half_map_1.map
Annotationstructure of bundle-shaped PBS with short rod at 2.80A halfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: structure of bundle-shaped PBS with short rod at 2.80A halfA

Fileemd_62201_half_map_2.map
Annotationstructure of bundle-shaped PBS with short rod at 2.80A halfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : phycobilisome

EntireName: phycobilisome
Components
  • Complex: phycobilisome
    • Protein or peptide: Glr2806 protein
    • Protein or peptide: Phycocyanin-associated rod linker protein
  • Protein or peptide: Allophycocyanin beta subunit
  • Protein or peptide: Phycocyanin alpha chain
  • Protein or peptide: Phycocyanin beta chain
  • Protein or peptide: Phycocyanin-associated rod linker protein
  • Protein or peptide: CpcD protein
  • Protein or peptide: Allophycocyanin alpha subunit
  • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
  • Protein or peptide: Phycobiliprotein ApcE
  • Protein or peptide: Glr1262 protein
  • Ligand: PHYCOCYANOBILIN

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Supramolecule #1: phycobilisome

SupramoleculeName: phycobilisome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #6, #5
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 14700 kDa/nm

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Macromolecule #1: Allophycocyanin beta subunit

MacromoleculeName: Allophycocyanin beta subunit / type: protein_or_peptide / ID: 1 / Number of copies: 42 / 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

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Macromolecule #2: Phycocyanin alpha chain

MacromoleculeName: Phycocyanin alpha chain / type: protein_or_peptide / ID: 2 / Number of copies: 84 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 17.679852 KDa
SequenceString:
MKTVITEVIA SADSQGRFLN NTELQAANGR FQRATASMEA ARALTSNADS LVKGAVQEVY NKFPYLTQPG QMGYGDTNQA KCARDISHY LRFITYSLVA GGTGPLDDYI VAGLREVNRT FNLSPSWYIE ALKHIKGKVG SQLSGQPLTE ANAYIDYCIN A LS

UniProtKB: Phycocyanin alpha chain

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Macromolecule #3: Phycocyanin beta chain

MacromoleculeName: Phycocyanin beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 84 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 18.478953 KDa
SequenceString:
MQDAFTKAIV AADLRGSFLS EQELNQLTNL VKESNKRLDA VNAITGNAAE IISDAAHKLF AEQTDLIRPG GNAYPNRRMA ACLRDMEII LRYVSYALLA GDASVLEDRC LNGLKETYVA LGTPTRSVAR AVQLMKETAI GYVNSPSGVT RGDCSALVNE A ATYFDKAA ASIA

UniProtKB: Phycocyanin beta chain

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Macromolecule #4: Phycocyanin-associated rod linker protein

MacromoleculeName: Phycocyanin-associated rod linker protein / type: protein_or_peptide / ID: 4
Details: There is no expression tag in the Phycocyanin-associated rod linker proteins (MA, M3, M4, M8, M9 and M1) or the Phycocyanin-associated rod linker proteins (NA, N3, Z4, N9, Z8 and N1). We ...Details: There is no expression tag in the Phycocyanin-associated rod linker proteins (MA, M3, M4, M8, M9 and M1) or the Phycocyanin-associated rod linker proteins (NA, N3, Z4, N9, Z8 and N1). We align all amino acids by their electron density map.
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 30.913822 KDa
SequenceString: MNVLTTSSQR GGKLFKVTMT LSPALSHHPW PSLDTYEPSQ NSYSVVVPLD RLLAEMTYIK NKGGRVLDIS PADLEALGPP DISSVAIPL KVELWAKADV SDVQAAIVAA YKQIFGNTYV LESERLTSAE SLLRNGSISV REFVRLLAKS ELYKERFFFC T SNNRFTEL ...String:
MNVLTTSSQR GGKLFKVTMT LSPALSHHPW PSLDTYEPSQ NSYSVVVPLD RLLAEMTYIK NKGGRVLDIS PADLEALGPP DISSVAIPL KVELWAKADV SDVQAAIVAA YKQIFGNTYV LESERLTSAE SLLRNGSISV REFVRLLAKS ELYKERFFFC T SNNRFTEL NFKHFLGRAP YNQSEIAAHL DRYQTFGYDA EIDSYIDSDE YIQAFGENVV PYYRGFKSQS GQTVESFNRM FK LYRGDAG SDTNLNLQGQ KRRVDPKNLL RSGRGIV

UniProtKB: Phycocyanin-associated rod linker protein

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Macromolecule #5: Phycocyanin-associated rod linker protein

MacromoleculeName: Phycocyanin-associated rod linker protein / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 31.085066 KDa
SequenceString: MSVLTGDNQQ RGSKLFKITI ALSPTLAHHP WPGLDTHEPS QSSYSTIVSL ERLLPEMTRI KRNGGRILEI TEGEASESRA NFPAVMEPP VVELYPRAGE AEVQAVIAVA YKQVFGNIHV MESERIVSAE SLLRNRSISV REFVRLLAKS DLYKESFFHC T SNNRFIEL ...String:
MSVLTGDNQQ RGSKLFKITI ALSPTLAHHP WPGLDTHEPS QSSYSTIVSL ERLLPEMTRI KRNGGRILEI TEGEASESRA NFPAVMEPP VVELYPRAGE AEVQAVIAVA YKQVFGNIHV MESERIVSAE SLLRNRSISV REFVRLLAKS DLYKESFFHC T SNNRFIEL NFKHLLGRAP YNHSEIIEHL DRYQSQGYDA EIDSYIDSDE YVKTFGENVV PYHRGFKSQV GQQSVAAFER MI RLFGGDA SSDTSLNRTG QKRLVDPKQL LRSGRGIV

UniProtKB: Phycocyanin-associated rod linker protein

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Macromolecule #6: Glr2806 protein

MacromoleculeName: Glr2806 protein / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 81.544312 KDa
SequenceString: MSATTYDWRK VIDSIKIEDP VKPGDFANFL DMARGIESRT GVWSISYESL RTLGPPEGGM LRPAVGGTAE AAAQKQLGIT AVAPASVVE LRPNASEEDL QGVLRAVYRQ VLGNTYVMES ERPTQAESLL RNGSISVREF VRRIAKSDLY KERFFNKASN N RFIELNFK ...String:
MSATTYDWRK VIDSIKIEDP VKPGDFANFL DMARGIESRT GVWSISYESL RTLGPPEGGM LRPAVGGTAE AAAQKQLGIT AVAPASVVE LRPNASEEDL QGVLRAVYRQ VLGNTYVMES ERPTQAESLL RNGSISVREF VRRIAKSDLY KERFFNKASN N RFIELNFK HLLGRAPYNH GEIQEHFGLY HKAGYDVEID SYIDSDEYIE TFGENIVPYF RGFKYQTNQS AGGFPRMVKL WG GDAGSDT DRGKNGQRTL VTTKDLIGPT KIFVPFVAPG RDADMVSGDY TRLAFGLSGE AAAQRQLGIA SVAPAPICQL RPN ASEEDL QGVLRAVYRQ VLGNTYVMES ERPTQAESLL RNGSISVREF VRRIAKSDLY KERFFNKASN NRFIELNFKH LLGR APYNH GEIQEHFGLY HKAGYDVEID SYIDSDEYIE TFGENIVPYF RGFKYQTNQS AGGFPRMVKL WGGDAGSDTD RATGG QRTL VTTRELVKTL PLLTEIPAVP ATRGFEQVLN QLKRPAPGGT GEAQGQKQLG ITAVAPAPIC QLRPNASEED LQGVLR AVY RQVLGNTYVM ESERPTQAES LLRNGSISVR EFVRRIAKSD LYKERFFNKA SNNRFIELNF KHLLGRAPYN HGEIQEH FG LYHKAGYDAE IDSYIDSDEY LLTFGEDVVP YFRGFKYQTN QSAGGFPRFT KLYGGDAGSD TDRGKNGQRT LVTTKDLV V SGQFSKPV

UniProtKB: Glr2806 protein

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Macromolecule #7: CpcD protein

MacromoleculeName: CpcD protein / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 7.776872 KDa
SequenceString:
MYNNVTANTE WGRKVFKITV AQFPDADGLD TDNLSQSNYF VTVPLARLLP EMQLIKNKGG KVLSVEPVVS

UniProtKB: CpcD protein

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Macromolecule #8: Allophycocyanin alpha subunit

MacromoleculeName: Allophycocyanin alpha subunit / type: protein_or_peptide / ID: 8 / Number of copies: 40 / 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

UniProtKB: Allophycocyanin alpha subunit

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Macromolecule #9: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associa...

MacromoleculeName: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
type: protein_or_peptide / ID: 9 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 7.633809 KDa
SequenceString:
SRYFKVTACI PSLKRVRTGR ELQNTFFTKL VPYENWFTEQ QRIQKAGGKV LSVKLFTGVQ GANTGVGA

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

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Macromolecule #10: Phycobiliprotein ApcE

MacromoleculeName: Phycobiliprotein ApcE / type: protein_or_peptide / ID: 10 / 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

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Macromolecule #11: Glr1262 protein

MacromoleculeName: Glr1262 protein / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 92.127602 KDa
SequenceString: MSTVLDDQSK AYAPGSANGP TAGLEPFVRM SRMIRSGVPE DREEPDELWL SMVRDIFGRG YMDRLSQTRA IDYSAFVRPA DQATADGAA QTKLGITAIA PDQGVELRPN FTEADVITVI RAAYKQLFGN TYILESERVI QAESLLRNGS ISVREFIRIL A KSDLYKER ...String:
MSTVLDDQSK AYAPGSANGP TAGLEPFVRM SRMIRSGVPE DREEPDELWL SMVRDIFGRG YMDRLSQTRA IDYSAFVRPA DQATADGAA QTKLGITAIA PDQGVELRPN FTEADVITVI RAAYKQLFGN TYILESERVI QAESLLRNGS ISVREFIRIL A KSDLYKER FFRCTSNNRF IELNLKHLLG RAPYNQGEIA EHLDRYCQSG YDAEIDSYID SDEYRRVFGE NTVPYFRGFK YQ VGQSAAA FERMRALYSG DAGSDTDRNQ NGQRTELTSG LADPAQPVRA RTDYALTRVD IPGGNGAAGR LAALDESLGS WLD AARDLI SQNDYSQKAI EVEPKRVAPY AQYLTPAVEA TPDAAAQTKL GITAVAPDQA VELRPNFGEA EVQAVIRAAY KQIF GNTYI LEADRVVIAE SLLRNGSISV REFVRLLAKS DLYRDRFFRT ASNNRFIELN FKHFLGRAPY SQAEIGEHFN RYHKS GYDA EIDSYIDSDE YRRVFGENTV PYFRGFKYQV GQAARGFDQM QQLFAGDAGS DTDRGIGAQP AAKLTFPLSR PLGVTS AYF PSSQGGAATS DGLEMFTRMA RELTVTPVSA RRTTSPTAPT APAMPLAGYY SRPAPRATAD GDAQTKLGIT AVAPAQA VE LRPNFGETEL QAVIRATYKQ LFGNTYILEA DRVVQAESLL RNGSINVREF VRLLAKSELY KERFFHCTSN NRFIELTF K HLLGRAPYNQ SEFVEHLDRY QKSGYDAEID SYIDSDEYRR VFGENTVPYF RGFKYQTGQA AGVFERTLKL YGGDADSDT NRNRQGQLRQ VDPQELLRSG RGIV

UniProtKB: Glr1262 protein

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Macromolecule #12: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 12 / Number of copies: 336 / Formula: CYC
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-CYC:
PHYCOCYANOBILIN

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
Component:
ConcentrationFormulaName
0.75 mol/LNa2HPO4disodium hydrogen phosphate
0.75 mol/LKH2PO4Monobasic Potassium Phosphate
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / 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

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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 K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 2 / Number real images: 6438 / 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

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Image processing

Particle selectionNumber selected: 1042622
CTF correctionSoftware - Name: CTFFIND (ver. 4.15) / Type: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1beta) / Number images used: 389430
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1beta)
Final 3D classificationNumber classes: 6 / Avg.num./class: 389430 / Software - Name: RELION (ver. 3.1beta)

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Atomic model buiding 1

Initial modelPDB ID:

6kgx


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 62.05 / Target criteria: 0,99
Output model

PDB-9k9w:
structure of bundle-shaped PBS with short rod

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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

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