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- EMDB-31381: Cryo-EM structure of cyanobacterial phycobilisome from Anabaena s... -

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Basic information

Entry
Database: EMDB / ID: EMD-31381
TitleCryo-EM structure of cyanobacterial phycobilisome from Anabaena sp. PCC 7120
Map data
Sample
  • Complex: Cryo-EM structure of cyanobacterial phycobilisome from Anabaena sp. PCC 7120
    • Protein or peptide: x 12 types
  • Ligand: x 1 types
Keywordsphotosynthesis
Function / homology
Function and homology information


Lyases / 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. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit ...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. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit / 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
C-phycocyanin beta subunit / C-phycocyanin alpha subunit / Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod / Phycobilisome rod-core linker polypeptide CpcG1 / Phycobilisome rod-core linker polypeptide CpcG2 / Phycobilisome rod-core linker polypeptide CpcG4 / Allophycocyanin subunit alpha 1 / Allophycocyanin subunit alpha-B / Allophycocyanin subunit beta / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core ...C-phycocyanin beta subunit / C-phycocyanin alpha subunit / Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod / Phycobilisome rod-core linker polypeptide CpcG1 / Phycobilisome rod-core linker polypeptide CpcG2 / Phycobilisome rod-core linker polypeptide CpcG4 / Allophycocyanin subunit alpha 1 / Allophycocyanin subunit alpha-B / Allophycocyanin subunit beta / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Phycobiliprotein ApcE / Allophycocyanin subunit beta-18
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZheng L / Zheng Z
Funding support1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)
CitationJournal: Nat Commun / Year: 2021
Title: Structural insight into the mechanism of energy transfer in cyanobacterial phycobilisomes.
Authors: Lvqin Zheng / Zhenggao Zheng / Xiying Li / Guopeng Wang / Kun Zhang / Peijun Wei / Jindong Zhao / Ning Gao /
Abstract: Phycobilisomes (PBS) are the major light-harvesting machineries for photosynthesis in cyanobacteria and red algae and they have a hierarchical structure of a core and peripheral rods, with both ...Phycobilisomes (PBS) are the major light-harvesting machineries for photosynthesis in cyanobacteria and red algae and they have a hierarchical structure of a core and peripheral rods, with both consisting of phycobiliproteins and linker proteins. Here we report the cryo-EM structures of PBS from two cyanobacterial species, Anabaena 7120 and Synechococcus 7002. Both PBS are hemidiscoidal in shape and share a common triangular core structure. While the Anabaena PBS has two additional hexamers in the core linked by the 4th linker domain of ApcE (L). The PBS structures predict that, compared with the PBS from red algae, the cyanobacterial PBS could have more direct routes for energy transfer to ApcD. Structure-based systematic mutagenesis analysis of the chromophore environment of ApcD and ApcF subunits reveals that aromatic residues are critical to excitation energy transfer (EET). The structures also suggest that the linker protein could actively participate in the process of EET in both rods and the cores. These results provide insights into the organization of chromophores and the mechanisms of EET within cyanobacterial PBS.
History
DepositionMay 30, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0195
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0195
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7eyd
  • Surface level: 0.0195
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31381.png

Downloads & links

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Map

FileDownload / File: emd_31381.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 500 pix.
= 527.5 Å		1.06 Å/pix.
x 500 pix.
= 527.5 Å		1.06 Å/pix.
x 500 pix.
= 527.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0195 / Movie #1: 0.0195
Minimum - Maximum-0.034992184 - 0.08293841
Average (Standard dev.)0.00041137394 (±0.005623475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 527.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0551.0551.055
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z527.500527.500527.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0350.0830.000

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of cyanobacterial phycobilisome from Anabaena s...

EntireName: Cryo-EM structure of cyanobacterial phycobilisome from Anabaena sp. PCC 7120
Components
  • Complex: Cryo-EM structure of cyanobacterial phycobilisome from Anabaena sp. PCC 7120
    • Protein or peptide: Phycobilisome rod-core linker polypeptide CpcG2
    • Protein or peptide: C-phycocyanin alpha subunit
    • Protein or peptide: C-phycocyanin beta subunit
    • Protein or peptide: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
    • Protein or peptide: Phycobilisome rod-core linker polypeptide CpcG4
    • Protein or peptide: Phycobilisome rod-core linker polypeptide CpcG1
    • Protein or peptide: Allophycocyanin subunit alpha 1
    • Protein or peptide: Allophycocyanin subunit beta
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
    • Protein or peptide: Phycobiliprotein ApcE
    • Protein or peptide: Allophycocyanin subunit beta-18
    • Protein or peptide: Allophycocyanin subunit alpha-B
  • Ligand: PHYCOCYANOBILIN

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Supramolecule #1: Cryo-EM structure of cyanobacterial phycobilisome from Anabaena s...

SupramoleculeName: Cryo-EM structure of cyanobacterial phycobilisome from Anabaena sp. PCC 7120
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 7 MDa

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Macromolecule #1: Phycobilisome rod-core linker polypeptide CpcG2

MacromoleculeName: Phycobilisome rod-core linker polypeptide CpcG2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Strain: PCC 7120
Molecular weightTheoretical: 28.688434 KDa
Recombinant expressionOrganism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
SequenceString: MSIPLLEYKP SSQNQRVPGY EVPNEDTPRI YRIEDAAYDS ELKELIWATY RQVFSEHVIL KFFRQGNLES QLKNRAISVR DFVRGLAKS EAFKTLVIKS NSNYRLVELA LKRLLGRAPY NKDEEIAWSI KIATNGWDGF VDALLDSEEY QSNFGENIVP Y QRRRYKDR ...String:
MSIPLLEYKP SSQNQRVPGY EVPNEDTPRI YRIEDAAYDS ELKELIWATY RQVFSEHVIL KFFRQGNLES QLKNRAISVR DFVRGLAKS EAFKTLVIKS NSNYRLVELA LKRLLGRAPY NKDEEIAWSI KIATNGWDGF VDALLDSEEY QSNFGENIVP Y QRRRYKDR PFNLVTPRYG NYWRDKLESE RYIEGDIKNF LELAKSIEIK TVTFTPVSTA NIKIPDTTRN TTPTGIPISV NP SANFPVR

UniProtKB: Phycobilisome rod-core linker polypeptide CpcG2

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Macromolecule #2: C-phycocyanin alpha subunit

MacromoleculeName: C-phycocyanin alpha subunit / type: protein_or_peptide / ID: 2 / Number of copies: 84 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Strain: PCC 7120
Molecular weightTheoretical: 17.475451 KDa
Recombinant expressionOrganism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
SequenceString:
MVKTPITEAI AAADTQGRFL GNTELQSARG RYERAAASLE AARGLTSNAQ RLIDGATQAV YQKFPYTTQT PGPQFAADSR GKSKCARDV GHYLRIITYS LVAGGTGPLD EYLIAGLAEI NSTFDLSPSW YVEALKHIKA NHGLSGQAAN EANTYIDYAI N ALS

UniProtKB: C-phycocyanin alpha subunit

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Macromolecule #3: C-phycocyanin beta subunit

MacromoleculeName: C-phycocyanin beta subunit / type: protein_or_peptide / ID: 3 / Number of copies: 84 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Strain: PCC 7120
Molecular weightTheoretical: 18.403758 KDa
Recombinant expressionOrganism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
SequenceString:
MTLDVFTKVV SQADSRGEFL SNEQLDALAN VVKEGNKRLD VVNRITSNAS AIVTNAARAL FEEQPQLIAP GGNAYTNRRM AACLRDMEI ILRYVTYAIL AGDASVLDDR CLNGLRETYQ ALGTPGSSVA VGVQKMKDAA VGIANDPNGI TKGDCSQLIS E VASYFDRA AAAVG

UniProtKB: C-phycocyanin beta subunit

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Macromolecule #4: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod

MacromoleculeName: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
type: protein_or_peptide / ID: 4 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Strain: PCC 7120
Molecular weightTheoretical: 32.254086 KDa
Recombinant expressionOrganism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
SequenceString: MAITTAASRL GTEPFSDAPK VELRPKASRE EVESVIRAVY RHVLGNDYIL ASERLVSAES LLRDGNLTVR EFVRSVAKSE LYKKKFFYN SFQTRLIELN YKHLLGRAPY DESEVVYHLD LYQNKGYDAE IDSYIDSWEY QSNFGDNVVP YYRGFETQVG Q KTAGFNRI ...String:
MAITTAASRL GTEPFSDAPK VELRPKASRE EVESVIRAVY RHVLGNDYIL ASERLVSAES LLRDGNLTVR EFVRSVAKSE LYKKKFFYN SFQTRLIELN YKHLLGRAPY DESEVVYHLD LYQNKGYDAE IDSYIDSWEY QSNFGDNVVP YYRGFETQVG Q KTAGFNRI FRLYRGYANS DRAQVEGTKS RLARELASNK ASTIVGPSGT NDSWGFRASA DVAPKKNLGN AVGEGDRVYR LE VTGIRSP GYPSVRRSST VFIVPYERLS DKIQQVHKQG GKIVSVTSA

UniProtKB: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod

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Macromolecule #5: Phycobilisome rod-core linker polypeptide CpcG4

MacromoleculeName: Phycobilisome rod-core linker polypeptide CpcG4 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Strain: PCC 7120
Molecular weightTheoretical: 29.362826 KDa
Recombinant expressionOrganism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
SequenceString: MALPLLQYKP SSQNHRVTSF GAADQNEDTP YIYRIEDVSS YTDIQNIIWA SYRQVFSEHE ILKFNRQKTL ESQVKNGSIS VRDFIRGLA KSEAFYRLVV SVNNNYRLVD ITLKRLLGRS SYNKDEQIAW SIVIGTKGFS GFVDALIDSE EYTKNFGENI V PYQRKRME ...String:
MALPLLQYKP SSQNHRVTSF GAADQNEDTP YIYRIEDVSS YTDIQNIIWA SYRQVFSEHE ILKFNRQKTL ESQVKNGSIS VRDFIRGLA KSEAFYRLVV SVNNNYRLVD ITLKRLLGRS SYNKDEQIAW SIVIGTKGFS GFVDALIDSE EYTKNFGENI V PYQRKRME GRPHNLVTPR YGEDFQEKAG TVQTDWRFTL DKFYSRKSQE KQLREGDPRK FADLAASVGN QGNYAQRISA FD IDYLNAV PNRSRR

UniProtKB: Phycobilisome rod-core linker polypeptide CpcG4

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Macromolecule #6: Phycobilisome rod-core linker polypeptide CpcG1

MacromoleculeName: Phycobilisome rod-core linker polypeptide CpcG1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Strain: PCC 7120
Molecular weightTheoretical: 31.973932 KDa
Recombinant expressionOrganism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
SequenceString: MSIPLLEYAP SSQNQRVEGY EVPNEDTPTI YRLAAAIDDA DVDAIIWAGY RQIFSEHLII KSNRQSFLES QLRNRAINVR DFIRGLGKS EVYRTQVADL NSNYRLVDIT LKRFLGRAAY NQDEEIAWSI VIGSQGLHGF IDALLDSDEY RENFGDDIVP Y QRRRYKDR ...String:
MSIPLLEYAP SSQNQRVEGY EVPNEDTPTI YRLAAAIDDA DVDAIIWAGY RQIFSEHLII KSNRQSFLES QLRNRAINVR DFIRGLGKS EVYRTQVADL NSNYRLVDIT LKRFLGRAAY NQDEEIAWSI VIGSQGLHGF IDALLDSDEY RENFGDDIVP Y QRRRYKDR PFNLVNPRYN AYWRDRQTLN ALGGRSFYSA RTSGTLTKDD IRRAIPANFM ALAGKILTPE RNYQRTIASV TS QIKDIKI PDTSREVTTP EVTVKPVAVA LPYRYIPGNK TT

UniProtKB: Phycobilisome rod-core linker polypeptide CpcG1

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Macromolecule #7: Allophycocyanin subunit alpha 1

MacromoleculeName: Allophycocyanin subunit alpha 1 / type: protein_or_peptide / ID: 7 / Number of copies: 44 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Strain: PCC 7120
Molecular weightTheoretical: 17.362617 KDa
Recombinant expressionOrganism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
SequenceString:
MSIVTKSIVN ADAEARYLSP GELDRIKSFV AGGQQRLRIA QALTDNRERL VKQAGDQLFQ KRPDVVSPGG NAYGQEMTAT CLRDLDYYL RLVTYGIVAG DVTPIEEIGV IGVREMYKSL GTPIEAVGEG VRALKNAAST LLSAEDAAEA GSYFDYVVGA L Q

UniProtKB: Allophycocyanin subunit alpha 1

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Macromolecule #8: Allophycocyanin subunit beta

MacromoleculeName: Allophycocyanin subunit beta / type: protein_or_peptide / ID: 8 / Number of copies: 46 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Strain: PCC 7120
Molecular weightTheoretical: 17.320695 KDa
Recombinant expressionOrganism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
SequenceString:
MAQDAITAVI NSADVQGKYL DTAALEKLKA YFSTGELRVR AATTISANAA AIVKEAVAKS LLYSDITRPG GNMYTTRRYA ACIRDLDYY LRYATYAMLA GDPSILDERV LNGLKETYNS LGVPVGATVQ AIQAIKEVTA SLVGADAGKE MGIYLDYISS G LS

UniProtKB: Allophycocyanin subunit beta

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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: 8 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Strain: PCC 7120
Molecular weightTheoretical: 7.852082 KDa
Recombinant expressionOrganism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
SequenceString:
MSRLFKITAL VPSLSRTRTQ RELQNTYFTK LVPYENWFRE QQRIQKAGGK IIKVELATGK QGTNAGLQ

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 / EC number: Lyases
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Strain: PCC 7120
Molecular weightTheoretical: 127.045812 KDa
Recombinant expressionOrganism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
SequenceString: MSVKASGGSS VARPQLYQTL AVATITQAEQ QDRFLGRGEL DELASYFASG AKRLEIAQLL TENSEIIVSR AANRIFVGGS PMAFLEKPR EPELAMAAVG GGGDVRESMK LGTVTYVETR GGFLENLRSI FNTSPSGPTP PGFRPINIAR YGPSNMAKSL R DLSWFLRY ...String:
MSVKASGGSS VARPQLYQTL AVATITQAEQ QDRFLGRGEL DELASYFASG AKRLEIAQLL TENSEIIVSR AANRIFVGGS PMAFLEKPR EPELAMAAVG GGGDVRESMK LGTVTYVETR GGFLENLRSI FNTSPSGPTP PGFRPINIAR YGPSNMAKSL R DLSWFLRY ATYAIVAGDP NIIVVNTRGL REIIENACSG EATIVALQEI KAASLSYFRK DPEAAEIVSQ YMDVLITEFK AP TPSNKLR QRPSGDQQGL QLPQIYFSAA ERRPKFVMKT GLSATEKNEV IKAAYRQIFE RDITRAYSLS ISDLESKVKN GDI SMKEFV RRLAKSPLYQ KQFYQPFINS RVIELAFRHI LGRGPSSREE VQKYFSIISN GGLPALVDAL VDSAEYSDYF GEET VPYLR GLGQEAQECR NWGPQQDLFN YSAPFRKVPQ FITTFAAYDR PLPDQHPYGS GNDPLEIQFG AIFPKETRNP STSPA PFGK DTRRILIHQG PGINNQVSNP SARGLAPGSL GPKVFKLDQL PGTIGKKAAK GASVKFSESS TQAVIKATYL QVFGRD VYE GQRLKVQEIK LENGEISVRD FVRALAKSDL FRKLYWTPFY VCKAIEYIHR RLLGRPTYGR QENNKYFDIA SKKGLYA VV DAILDSLEYT ETFGEDTVPY ERYLTPAGVA LRQLRVGTIR EDVANVEKQE TPRFVELGTV KENRTQPDID FRINQGVT K QREQTKVFKR VAGIKDKAAI KTLISAAYRQ IFERDIAPYI AQNEFSGWES KLGNGEITVK EFIEGLGYSN LYLKEFYTP YPNTKVIELG TKHFLGRAPI DQAEIRKYNQ ILATQGIRAF INALVNSQEY NEVFGEDTVP YRRFPTLPAA NFPNTQKLYN QLTKQNNDV VIPSFKPVQA RIQSDKTPIL AKAIADLAAQ AKQMDKSKPL FIELGRSYND GRGQSVEVGV GTTRRKPARI Y RLTNGIGQ AEKQLVINAI YRQVLDVFSG QVPDYYRRTE LDSKLRNGEI SVREFVREIA SSEIYRKRFY TPYPNTKVIE FL FRHLLGR APATQGEIRQ YNKLLADNGL RAAVEAIVDS PEYSRYFGED VVPYPRFPSL PAGNYLGSVQ AAADLVKQSW SSL SPSTLT GRPGDR

UniProtKB: Phycobiliprotein ApcE

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Macromolecule #11: Allophycocyanin subunit beta-18

MacromoleculeName: Allophycocyanin subunit beta-18 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Strain: PCC 7120
Molecular weightTheoretical: 18.657016 KDa
Recombinant expressionOrganism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
SequenceString:
MRDAVTSLIK NYDVAGRYFD RNAIDTLKDY FDSGTARVQA AAAINSNAAA LVKQAGSKLF EELPELIRPG GNAYTTRRLA ACLRDMDYY LRYATYALVA GNTNVLDERV LQGLRETYNS LGVPIGPTVR GVQILKDLVK EQVAGAGIAN TTFVEEPFDH I TRELSERD V

UniProtKB: Allophycocyanin subunit beta-18

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Macromolecule #12: Allophycocyanin subunit alpha-B

MacromoleculeName: Allophycocyanin subunit alpha-B / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) / Strain: PCC 7120
Molecular weightTheoretical: 17.828438 KDa
Recombinant expressionOrganism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
SequenceString:
MTVISQVILQ ADDELRYPSS GELKSISDFL QTGVQRTRIV ATLAENEKKI VQEATKQLWQ KRPDFIAPGG NAYGERQRAL CIRDFGWYL RLITYGVLAG DIEPIEKIGI IGVREMYNSL GVPVPGMVEA INSLKKASLD LLSSEDAAAA APYFDYIIQA M S

UniProtKB: Allophycocyanin subunit alpha-B

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Macromolecule #13: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 13 / Number of copies: 348 / 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62439
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING

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  • 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

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