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- EMDB-31373: Cryo-EM structure of cyanobacterial phycobilisome from Synechococ... -

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Basic information

Entry
Database: EMDB / ID: EMD-31373
TitleCryo-EM structure of cyanobacterial phycobilisome from Synechococcus sp. PCC 7002
Map data
Sample
  • Complex: Cryo-EM structure of cyanobacterial phycobilisome from Synechococcus sp. PCC 7002
    • Protein or peptide: x 10 types
  • Ligand: x 1 types
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
Allophycocyanin alpha subunit / Allophycocyanin subunit alpha-B / Allophycocyanin subunit beta-18 / Allophycocyanin beta subunit / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Phycobiliprotein ApcE / C-phycocyanin subunit alpha / C-phycocyanin subunit beta / Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod / Phycobilisome rod-core linker polypeptide CpcG
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7002 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZheng L / Zheng Z / Li X / Wang G / Zhang K / Wei P / Zhao J / Gao N
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 28, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateOct 6, 2021-
Current statusOct 6, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0167
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0167
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ext
  • Surface level: 0.0167
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31373.png

Downloads & links

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Map

FileDownload / File: emd_31373.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.055 Å
Density
Contour LevelBy AUTHOR: 0.0167 / Movie #1: 0.0167
Minimum - Maximum-0.028300187 - 0.082177125
Average (Standard dev.)-0.00019888715 (±0.0045821336)
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-0.0280.082-0.000

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of cyanobacterial phycobilisome from Synechococ...

EntireName: Cryo-EM structure of cyanobacterial phycobilisome from Synechococcus sp. PCC 7002
Components
  • Complex: Cryo-EM structure of cyanobacterial phycobilisome from Synechococcus sp. PCC 7002
    • Protein or peptide: Phycobilisome rod-core linker polypeptide CpcG
    • Protein or peptide: C-phycocyanin subunit alpha
    • Protein or peptide: C-phycocyanin subunit beta
    • Protein or peptide: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
    • Protein or peptide: Phycobiliprotein ApcE
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
    • Protein or peptide: Allophycocyanin alpha subunit
    • Protein or peptide: Allophycocyanin beta subunit
    • 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 Synechococ...

SupramoleculeName: Cryo-EM structure of cyanobacterial phycobilisome from Synechococcus sp. PCC 7002
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Synechococcus sp. PCC 7002 (bacteria)
Molecular weightTheoretical: 6 MDa

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Macromolecule #1: Phycobilisome rod-core linker polypeptide CpcG

MacromoleculeName: Phycobilisome rod-core linker polypeptide CpcG / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002
Molecular weightTheoretical: 28.540152 KDa
Recombinant expressionOrganism: Synechococcus sp. PCC 7002 (bacteria)
SequenceString: MTIPLLQYAP SSQNTRVAGY TVGGDEQPFV FTTDNVISDS DFDVLINAAY RQIFFHAFKC DRQQLLESQL RNGQITVRDF IRGLLLSET FIDSFYNKNS NYRFVEQCIQ RVLGRDPFSE QEKIAWSIVI CTKGLAAFVD QLLNTDEYME NFGYDTVPYQ R RRSLASRE ...String:
MTIPLLQYAP SSQNTRVAGY TVGGDEQPFV FTTDNVISDS DFDVLINAAY RQIFFHAFKC DRQQLLESQL RNGQITVRDF IRGLLLSET FIDSFYNKNS NYRFVEQCIQ RVLGRDPFSE QEKIAWSIVI CTKGLAAFVD QLLNTDEYME NFGYDTVPYQ R RRSLASRE QGEIPFNIKS PRYDAYYRSQ LGFPQVVWQN AVRRFRTPDR VPQAGDPALF LNMARSAQIP KVNVRVSAAD IS LAAVPYR N

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Macromolecule #2: C-phycocyanin subunit alpha

MacromoleculeName: C-phycocyanin subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 72 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002
Molecular weightTheoretical: 17.637695 KDa
Recombinant expressionOrganism: Synechococcus sp. PCC 7002 (bacteria)
SequenceString:
MKTPLTEAVA LADSQGRFLS NTELQYLYGR LRQGAFALEA AQTLTAKADT LVNGAAQAVY SKFPYTTSTP GNNFAADQRG KDKCARDIG YYLRMVTYCL VAGGTGPMDE YLIAGVDEIN RTFDLSPSWY VEALKHIKAN HGLTGDAATE TNNYIDYAIN A LS

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Macromolecule #3: C-phycocyanin subunit beta

MacromoleculeName: C-phycocyanin subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 72 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002
Molecular weightTheoretical: 18.353852 KDa
Recombinant expressionOrganism: Synechococcus sp. PCC 7002 (bacteria)
SequenceString:
MFDIFTRVVS QADARGEFIS SDKLEALKKV VAEGTKRSDA VSRMTNNASS IVTNAARQLF ADQPQLIAPG GNAYTNRRMA ACLRDMEII LRYVTYATFT GDASVLNDRC LNGLRETYVA LGVPGASVAA GVRAMGKAAV AIVMDPAGVT SGDCSSLQQE I ELYFETAA KAVE

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Macromolecule #4: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod

MacromoleculeName: Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod
type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002
Molecular weightTheoretical: 32.308896 KDa
Recombinant expressionOrganism: Synechococcus sp. PCC 7002 (bacteria)
SequenceString: MPVTVAASRL GTAAFDQSPV ELRANYSRDD AQTVIRAVYR QVLGNDYVMS SERLTAAESL FTNGFISVRD FVRAVAQSEL YKEKFLYNN FQTRVIELNF KHLLGRAPYD EAEVIEHLDR YQNEGFEADI NSYIDSAEYT ENFGDNIVPY IRSYVVQTGH R TVGFTRMF ...String:
MPVTVAASRL GTAAFDQSPV ELRANYSRDD AQTVIRAVYR QVLGNDYVMS SERLTAAESL FTNGFISVRD FVRAVAQSEL YKEKFLYNN FQTRVIELNF KHLLGRAPYD EAEVIEHLDR YQNEGFEADI NSYIDSAEYT ENFGDNIVPY IRSYVVQTGH R TVGFTRMF SLQRGYANSD RAQIAGNASR LAQELARNTT SAVVGPSGVN EGWAFRSAAD DYHPGQSLGG STGLSADDQV VR VEVAALS TPRYPRIRRS SRVFFVPVSR LSQKLQEIQR MGGRVASISP AGQ

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Macromolecule #5: Phycobiliprotein ApcE

MacromoleculeName: Phycobiliprotein ApcE / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: Lyases
Source (natural)Organism: Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002
Molecular weightTheoretical: 99.391656 KDa
Recombinant expressionOrganism: Synechococcus sp. PCC 7002 (bacteria)
SequenceString: MTIKASGGSS LARPQLYQTV PLSNISQAEQ QDRYLESGEL TALKTFYDSG LKRLAIAQAI KLSSQLIVSR AANRIFAGGS PLAYLDQPE TDTDDSDLGV SMAVGDASGA TGIFGGVKNL FLGSGGGKIP AGFRPISVSR YGPRNMTKSL RDMAWFLRYT T YAIVAGDP ...String:
MTIKASGGSS LARPQLYQTV PLSNISQAEQ QDRYLESGEL TALKTFYDSG LKRLAIAQAI KLSSQLIVSR AANRIFAGGS PLAYLDQPE TDTDDSDLGV SMAVGDASGA TGIFGGVKNL FLGSGGGKIP AGFRPISVSR YGPRNMTKSL RDMAWFLRYT T YAIVAGDP SILVVNTRGL KEVIENACSI PATIVAIQEM KAASLDLFRG DREAQETVVQ YFDVLITEMQ TQVPNDKLRQ RP SIDAQGL QLPQSYFNAA EKRQKFVMKP GLSALEKNSV VKAAYRQIFE RDITRAYSQS ISYLESQVKS GDISMKEFVR RLA KSPLYR KQFFEPFINS RALELAFRHI LGRGPSSREE VQEYFAIVSS GGLAALVDAL VDSQEYADYF GEETVPYLRG LGQE AQECR NWGMQQDLFK YSAPFRKVPQ FITTFASYNQ PLPDQHVYGS GNDALEIQFG AIFPKATRSP SASPAPFNKD TRRIL IHRG PGINNQLGNP RARATQPGSL GAKVFRLNNE LPSGKTTNVS FSESATQKVI EAAYRQVFGR MVYAGQRQKV AEIKLE NGE ITLREFIRAL AKSDVFRNTY WSSLYVTKAV EYIHRRLLGR PTYGRQEINS YFDTCAKKGF YALVDAIIDS KEYEEAF GE DTVPYERYLT PGGYSLRQTR PGALREDVGV KVKVEKTARF IELGTSSTKN LPVTDVDARL KQGVNIQRQQ TKAFKLTD T FNKVELKTAI AAAYRQIFER DIEPYIVDAQ FTALESKLGN REINMKEFIE GLGCSELYQK EFYTPYPNTK VIEMGTKHF LGRAPLDQQE IRKYNQILAS QGLKAFIGAM VNSMEYLDNF GEDTVPFRRF PTLPAANFPN TERLYNQLTK QNRDLVVPSF EPAVKR

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Macromolecule #6: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associa...

MacromoleculeName: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002
Molecular weightTheoretical: 7.806188 KDa
Recombinant expressionOrganism: Synechococcus sp. PCC 7002 (bacteria)
SequenceString:
MRMFKITACV PSQSRIRTQR ELQNTYFTKL VPYDNWFREQ QRIMKMGGKI VKVQLATGKP GTNTGLT

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Macromolecule #7: Allophycocyanin alpha subunit

MacromoleculeName: Allophycocyanin alpha subunit / type: protein_or_peptide / ID: 7 / Number of copies: 32 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002
Molecular weightTheoretical: 17.30266 KDa
Recombinant expressionOrganism: Synechococcus sp. PCC 7002 (bacteria)
SequenceString:
MSIVTKSIVN ADAEARYLSP GELDRIKAFV TSGESRLRIA ETLTGSRERI IKSAGDALFQ KRPDVVSPGG NAYGEEMTAT CLRDMDYYL RLITYGVVAG DVTPIEEIGL VGVREMYKSL GTPVDAVAQA VREMKAVATG MMSGDDAAEA GAYFDYVIGA M E

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Macromolecule #8: Allophycocyanin beta subunit

MacromoleculeName: Allophycocyanin beta subunit / type: protein_or_peptide / ID: 8 / Number of copies: 34 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002
Molecular weightTheoretical: 17.23759 KDa
Recombinant expressionOrganism: Synechococcus sp. PCC 7002 (bacteria)
SequenceString:
MQDAITSVIN SADVQGKYLD GSAMDKLKAY FTTGALRVRA ASTISANAAA IVKEAVAKSL LYSDVTRPGG NMYTTRRYAA CIRDLDYYL RYATYAMLAG DPSILDERVL NGLKETYNSL GVPVGSTVQA IQAMKEVTAG LVGADAGREM GVYFDYICSG L S

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Macromolecule #9: Allophycocyanin subunit beta-18

MacromoleculeName: Allophycocyanin subunit beta-18 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002
Molecular weightTheoretical: 18.742137 KDa
Recombinant expressionOrganism: Synechococcus sp. PCC 7002 (bacteria)
SequenceString:
MRDAVTSLIR NYDTTGRYFD RDAIESLKDY FASGNDRITV AAMINSQSAE IVKAAANSLF EAVPELLLAG GNAYTTRRFS ACLRDMDYY LRYGTYALIA GDMDVLNERV LQGLRETYNS LGVPIAPTVR GIQFLKDAIK EMAAAAGIAN TAFIDEPFDH M TRELSEVD L

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Macromolecule #10: Allophycocyanin subunit alpha-B

MacromoleculeName: Allophycocyanin subunit alpha-B / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002
Molecular weightTheoretical: 17.72127 KDa
Recombinant expressionOrganism: Synechococcus sp. PCC 7002 (bacteria)
SequenceString:
MSVVSQVILR ADDELRYPSS GELSGIKNFL ATGAVRIRIA EALADNEKKI VDQAQKQLFS IHPEYRTSGG NAATTKQYNQ CLRDYGWYL RLVTYGILAG DKDPIERIGL IGVKEMYNAL GVPVPGMVDA IRCLKDAALG VLDSEEARIA APYFDFITQA M S

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Macromolecule #11: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 11 / Number of copies: 288 / 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64268
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING

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