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- EMDB-9976: Structure of the phycobilisome from the red alga Porphyridium pur... -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-9976

Title

Structure of the phycobilisome from the red alga Porphyridium purpureum

Map data

Sample

Complex: Complex of phycobilisome from red alga P.purpureum.
- Protein or peptide: x 25 types
Ligand: x 3 types

Function / homology

Function and homology information

phycobilisome / chloroplast thylakoid membrane /

photosynthesis /

lyase activity
Similarity search - Function

Biological species

Porphyridium purpureum (eukaryote) /

Red alga (eukaryote)

Method

single particle reconstruction /

cryo EM / Resolution: 2.8 Å

Authors

Sui SF / Ma JF / You X / Sun S

Citation

Journal: Nature / Year: 2020
Title: Structural basis of energy transfer in Porphyridium purpureum phycobilisome.
Authors: Jianfei Ma / Xin You / Shan Sun / Xiaoxiao Wang / Song Qin / Sen-Fang Sui /

Abstract: Photosynthetic organisms have developed various light-harvesting systems to adapt to their environments. Phycobilisomes are large light-harvesting protein complexes found in cyanobacteria and red ...

History

Deposition	Jul 12, 2019	-
Header (metadata) release	Dec 11, 2019	-
Map release	Dec 11, 2019	-
Update	Mar 18, 2020	-
Current status	Mar 18, 2020	Processing site: PDBj / Status: Released

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Structure visualization

Movie	Surface view with section colored by density value Surface level: 0.02 Imaged by UCSF Chimera Download Surface view colored by cylindrical radius Surface level: 0.02 Imaged by UCSF Chimera Download Surface view with fitted model Atomic models: PDB-6kgx Surface level: 0.02 Imaged by UCSF Chimera Download Surface view with fitted model Atomic models: PDB-7lix Surface level: 0.015 Imaged by UCSF Chimera Download Surface view with fitted model Atomic models: PDB-7liy Surface level: 0.005 Imaged by UCSF Chimera Download Surface view with fitted model Atomic models: PDB-7liz Surface level: 0.015 Imaged by UCSF Chimera Download Surface view with fitted model Atomic models: PDB-7lj0 Surface level: 0.01 Imaged by UCSF Chimera Download Simplified surface model + fitted atomic model Atomic modelsPDB-6kgx Imaged by Jmol Download Simplified surface model + fitted atomic model Atomic modelsPDB-7lix Imaged by Jmol Download Simplified surface model + fitted atomic model Atomic modelsPDB-7liy Imaged by Jmol Download Simplified surface model + fitted atomic model Atomic modelsPDB-7liz Imaged by Jmol Download Simplified surface model + fitted atomic model Atomic modelsPDB-7lj0 Imaged by Jmol Download Movie viewer
Structure viewer	EM map: SurfViewMolmilJmol/JSmol
Supplemental images	emd_9976.png

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Downloads & links

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EMDB archive

Map data	emd_9976.map.gz	118.3 MB		EMDB map data format
Header (meta data)	emd-9976-v30.xml emd-9976.xml	37.5 KB 37.5 KB	Display Display	EMDB header
Images	emd_9976.png	113 KB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-9976 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9976	HTTPS FTP

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Related structure data

Related structure data	6kgxMC 7lixM 7liyM 7lizM 7lj0M 34529C 9977C 9978C 9979C 9980C 9981C 9982C 9983C 9984C 9985C 9986C 9987C 9988C M: atomic model generated by this map C: citing same article (ref.)
Similar structure data	4v5x-d 2482 2210 20504 11881 4308 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

EMDB pages	EMDB (EBI/PDBe) / EMDataResource

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Map

File

Download / File: emd_9976.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Voxel size

X=Y=Z: 1.091 Å

Density

Contour Level	By AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum	-0.08682697 - 0.14312163
Average (Standard dev.)	0.0006092488 (±0.004719709)

Symmetry

Space group: 1

Details

EMDB XML:

Map geometry

Axis order	X	Y	Z
Origin	0	0	0
Dimensions	560	560	560
Spacing	560	560	560

Cell

A=B=C: 610.95996 Å
α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.091	1.091	1.091
M x/y/z	560	560	560
origin x/y/z	0.000	0.000	0.000
length x/y/z	610.960	610.960	610.960
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	560	560	560
D min/max/mean	-0.087	0.143	0.001

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Supplemental data

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Sample components

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Entire : Complex of phycobilisome from red alga P.purpureum.

Entire	Name: Complex of phycobilisome from red alga P.purpureum.
Components	Complex: Complex of phycobilisome from red alga P.purpureum. Protein or peptide: Phycoerythrin alpha subunit Protein or peptide: B-phycoerythrin beta chain Protein or peptide: LR7 Protein or peptide: LR2_Hb Protein or peptide: LR9 Protein or peptide: LR1 Protein or peptide: LR4 Protein or peptide: Phycobilisome rod-core linker polypeptide Protein or peptide: C-phycocyanin alpha subunit Protein or peptide: C-phycocyanin beta subunit Protein or peptide: LR2 Protein or peptide: LRC2 Protein or peptide: LR5 Protein or peptide: LR8 Protein or peptide: LR3 Protein or peptide: LRC3 Protein or peptide: Allophycocyanin alpha subunit Protein or peptide: Allophycocyanin beta subunit Protein or peptide: Allophycocyanin gamma subunit Protein or peptide: Allophycocyanin beta 18 subunit Protein or peptide: LC Protein or peptide: Phycobilisome linker polypeptide Protein or peptide: LRC4 Protein or peptide: LRC5 Protein or peptide: LRC6 Ligand: PHYCOERYTHROBILIN Ligand: PHYCOUROBILIN Ligand: PHYCOCYANOBILIN

Entire

Name: Complex of phycobilisome from red alga P.purpureum.

Components

Complex: Complex of phycobilisome from red alga P.purpureum.
- Protein or peptide: Phycoerythrin alpha subunit
- Protein or peptide: B-phycoerythrin beta chain
- Protein or peptide: LR7
- Protein or peptide: LR2_Hb
- Protein or peptide: LR9
- Protein or peptide: LR1
- Protein or peptide: LR4
- Protein or peptide: Phycobilisome rod-core linker polypeptide
- Protein or peptide: C-phycocyanin alpha subunit
- Protein or peptide: C-phycocyanin beta subunit
- Protein or peptide: LR2
- Protein or peptide: LRC2
- Protein or peptide: LR5
- Protein or peptide: LR8
- Protein or peptide: LR3
- Protein or peptide: LRC3
- Protein or peptide: Allophycocyanin alpha subunit
- Protein or peptide: Allophycocyanin beta subunit
- Protein or peptide: Allophycocyanin gamma subunit
- Protein or peptide: Allophycocyanin beta 18 subunit
- Protein or peptide: LC
- Protein or peptide: Phycobilisome linker polypeptide
- Protein or peptide: LRC4
- Protein or peptide: LRC5
- Protein or peptide: LRC6
Ligand: PHYCOERYTHROBILIN
Ligand: PHYCOUROBILIN
Ligand: PHYCOCYANOBILIN

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Supramolecule #1: Complex of phycobilisome from red alga P.purpureum.

Supramolecule	Name: Complex of phycobilisome from red alga P.purpureum. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#25
Source (natural)	Organism: Porphyridium purpureum (eukaryote)

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Macromolecule #1: Phycoerythrin alpha subunit

Macromolecule	Name: Phycoerythrin alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 254 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 17.824029 KDa
Sequence	String: MKSVITTVVS AADAAGRFPS NSDLESIQGN IQRSAARLEA AEKLAGNHEA VVKEAGDACF AKYAYLKNPG EAGENQEKIN KCYRDVDHY MRLVNYCLVV GGTGPLDEWG IAGAREVYRT LNLPTSAYVA SIAYTRDRLC VPRDMSAQAG VEFSAYLDYL I NALS

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Macromolecule #2: B-phycoerythrin beta chain

Macromolecule	Name: B-phycoerythrin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 274 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 18.584182 KDa
Sequence	String: MLDAFSRVVV NSDAKAAYVG GSDLQALKSF IADGNKRLDA VNSIVSNASC MVSDAVSGMI CENPGLISPG G(MEN)CYTN RRM AACLRDGEII LRYVSYALLA GDASVLEDRC LNGLKETYIA LGVPTNSSIR AVSIMKAQAV AFITNTATER KMSFAAG DC TSLASEVASY FDRVGAAIS

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Macromolecule #3: LR7

Macromolecule	Name: LR7 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 36.924992 KDa
Sequence	String: MAAFVVGAQV SSGFMGCAAP RKEQTRVGGA AKAAVSMRII IQDKNSYRKY QTNTSTSKWD KLLNTKPMKR QVQPNPPTNE TRALNLGNT FRSPAFKFLG TLKRSKDPSG LRLGFYGRKA DDFMARSIAM QAKASAAGSG VYTTQCSEGA SKGMAENART A SLAKQFRQ ...String: MAAFVVGAQV SSGFMGCAAP RKEQTRVGGA AKAAVSMRII IQDKNSYRKY QTNTSTSKWD KLLNTKPMKR QVQPNPPTNE TRALNLGNT FRSPAFKFLG TLKRSKDPSG LRLGFYGRKA DDFMARSIAM QAKASAAGSG VYTTQCSEGA SKGMAENART A SLAKQFRQ AQRSAREMSF DYYEGRKYAM KAVGHICNYE EKIFQQYNKT AAAYVMGKQE TLLSCDRYAQ PANKAEEYIQ KS VQMQMKK RSIPYGVYTT SCADGTVKGM AENARVAKES ANFRARQMSA GAKAAARFNA RRVANDWHNN GCNYEEKLTS RFP AAASSV RPTTNRY

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Macromolecule #4: LR2_Hb

Macromolecule	Name: LR2_Hb / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 43.968605 KDa
Sequence	String: MAAFISSFAG AQLAHARPSK QTALRAALTL PGTAETNLAV PSNAVRKVQP YPIAKPPSYS SVDSLRPARV SRMDADWATI YEQVRRQVM GNAYVMEGEA PDIDVAFSQL KGGNLTVREF VRAVGKSASY RTRFMEAKSS YNFVLLNFKH FLGRAPTQEE V STHIQILA ...String: MAAFISSFAG AQLAHARPSK QTALRAALTL PGTAETNLAV PSNAVRKVQP YPIAKPPSYS SVDSLRPARV SRMDADWATI YEQVRRQVM GNAYVMEGEA PDIDVAFSQL KGGNLTVREF VRAVGKSASY RTRFMEAKSS YNFVLLNFKH FLGRAPTQEE V STHIQILA TSGLEAEIDS YIDSDEYKAL FGDHVVPYVV YRGTYLSSER FNRMVKANPG GATSDKAKSN LNMIATVAAD LP TDAIDVM RGLPSPITSE TLAFGTAYYW AKVEKEASEG RSASPIGEKI GKFDHAPIST YTSLCSYDKV NKAPQISVTN VGS DEHSYV SVTSKYIAPD MAAAAQMLAD CQKYKAGGNA PTGKWMKYYP GTTVNMAPYI SLNDTGSDSS RTVSVTLDKV KISP NKIGK

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Macromolecule #5: LR9

Macromolecule	Name: LR9 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 31.332955 KDa
Sequence	String: MAAKPYESGY IAEDDFWRGR GIAAWVYATG ANKVIAQIVK DFNLTDKKFM VFIPNDGAFA RLSPQLRKAM MEDSRLVYDM LAGHIFTSK GSAMLKDLQG AGYLQPAYGE AIGYVGTGRV IKIGNAQVIP ESSDILRKNL GFSAHTLDTF IVPKALTKKV S IEAGFSPV ...String: MAAKPYESGY IAEDDFWRGR GIAAWVYATG ANKVIAQIVK DFNLTDKKFM VFIPNDGAFA RLSPQLRKAM MEDSRLVYDM LAGHIFTSK GSAMLKDLQG AGYLQPAYGE AIGYVGTGRV IKIGNAQVIP ESSDILRKNL GFSAHTLDTF IVPKALTKKV S IEAGFSPV TPAKYVSTTK ADLRYVGATK PAAVGGRRAM NLMKQQPFWM YGPPYNAVTQ DEYEPISAAA PKAFVDYQIF AP GTVKVSP DSVNANELNP VSGMSKYIGK TQKLVGDQGI SDRSDKLPMG Q

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Macromolecule #6: LR1

Macromolecule	Name: LR1 / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 39.727625 KDa
Sequence	String: MAAFVTGMGA APRSQMRSVS GSAVCVRSDS VRAPGALTMR LGTVSGNSSL DKLGLDKFLS ESNRAYTPRA QPGFSSEYEQ IISATYKQL FGNAYIMDSE RAEMAKQESM FRDGQLTLKD FCRALAKTEQ YKKRFFDSRP LYGAIELNFK NILGRTPDGL E HYRAKSAV ...String: MAAFVTGMGA APRSQMRSVS GSAVCVRSDS VRAPGALTMR LGTVSGNSSL DKLGLDKFLS ESNRAYTPRA QPGFSSEYEQ IISATYKQL FGNAYIMDSE RAEMAKQESM FRDGQLTLKD FCRALAKTEQ YKKRFFDSRP LYGAIELNFK NILGRTPDGL E HYRAKSAV YDTKGYEAFV DAFFDDGEYD EVYDDYTVPF YRGYKTEANL SMAAFTHFFR MVRGSSTSDK ANPNSMQKDI PL NYYGITK TPLAVIAPGA AGTAYTESFA GTGSWQSGRA GLNAARVALG VPATANGKSF RVEVTGYTQP GFGITAGTAV GKL YKANKL SRYPRSNKSY VVGFDELTPL YQRITKNGGT IASITPL

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Macromolecule #7: LR4

Macromolecule	Name: LR4 / type: protein_or_peptide / ID: 7 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 31.792982 KDa
Sequence	String: MAAFVSGFHG VQVGAPAENK LVCRAAKPAQ LTMLTGYDSK SSPNFPNRAA TRERRTVSFN ARVARNKSQA KKILEKADEF FARSVTMQY KAFACPNGVY DIQCTEGTVK GAAYEKRAMA VSAAFRAKQA SPAAKARALF ENRRHAIIAS HECQHEEDLF V RFPKLSAA ...String: MAAFVSGFHG VQVGAPAENK LVCRAAKPAQ LTMLTGYDSK SSPNFPNRAA TRERRTVSFN ARVARNKSQA KKILEKADEF FARSVTMQY KAFACPNGVY DIQCTEGTVK GAAYEKRAMA VSAAFRAKQA SPAAKARALF ENRRHAIIAS HECQHEEDLF V RFPKLSAA YMMGKTEAMR TCSRYVVPDS LEEEYMAASV DRQMKERACP GGVYASSCVE GNAKGQAEQA RVAALATAFR SA QKSASKT TAERYSSAAY GRDHFAHGCS YEESVFNTYP ATAAAMRSKS YNY

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Macromolecule #8: Phycobilisome rod-core linker polypeptide

Macromolecule	Name: Phycobilisome rod-core linker polypeptide / type: protein_or_peptide / ID: 8 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 26.996689 KDa
Sequence	String: MSIPILKYSL STQNQRVESF EVNPGDEQYR IYSTDSLPSS SEVDQIIWAA YRQIFSEHQI LKSTKQPFLE SQLRFNQISI KDFIKGLVL SAPFRDLNYN VNNNYRFVEI CVQRVLGRDI YNEREKIAWS IIIATQGLEG FIDTLLNTQE YLSNFGDSIV P FQRRRIIP ...String: MSIPILKYSL STQNQRVESF EVNPGDEQYR IYSTDSLPSS SEVDQIIWAA YRQIFSEHQI LKSTKQPFLE SQLRFNQISI KDFIKGLVL SAPFRDLNYN VNNNYRFVEI CVQRVLGRDI YNEREKIAWS IIIATQGLEG FIDTLLNTQE YLSNFGDSIV P FQRRRIIP QRSKGEMPFN LKTPRYGIEF RSKLAATQFS WASPIRRFRP QEQQPKAGDP ALFLNMVQEM GPGL

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Macromolecule #9: C-phycocyanin alpha subunit

Macromolecule	Name: C-phycocyanin alpha subunit / type: protein_or_peptide / ID: 9 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 17.478664 KDa
Sequence	String: MKTPITEAIA TADNQGRFLS NTELQAVNGR YQRATASLTA AKALTGSAQR LITGAAQAVY NKFPYTTQMP GPAYASSAIG KAKCARDIG YYLRMVTYCL VVGGTGPMDE YLVAGLEEIN RSFDLSPSWY IEALQYIKNS HGLSGQVANE ANAYIDYAIN T LS

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Macromolecule #10: C-phycocyanin beta subunit

Macromolecule	Name: C-phycocyanin beta subunit / type: protein_or_peptide / ID: 10 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 18.242705 KDa
Sequence	String: MLDAFAKVVA QADARGEFLS NTQIDALSKM VKEGNQRLDI VNKVTSNASA IVTNSARALF AEQPQLIQPG G(MEN)AYTS RRM AACLRDMEIV LRYVSYAMIA GDSSVLDDRC LNGLRETYQA LGTPGSSVAV AIQKMKDASV ALANDTTGTP IGDCSSL VA ELAGYFDRAA VSVV

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Macromolecule #11: LR2

Macromolecule	Name: LR2 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 32.886242 KDa
Sequence	String: MEAVGFVHVG AWRVGSSSAA AAAAGVAGKR CGALPVSFGA HAPRRAASAS QVKMMAFSSI QNVLTDAPLG TPSAMGFLDE RTEKPLMGP SEMDELVYAV YKQVFGNAHI MESERAELRD AESLFRYLRD VREFVRALAK SNAYTSRFLQ GNQQYRFFEL N FKHLLGRG ...String: MEAVGFVHVG AWRVGSSSAA AAAAGVAGKR CGALPVSFGA HAPRRAASAS QVKMMAFSSI QNVLTDAPLG TPSAMGFLDE RTEKPLMGP SEMDELVYAV YKQVFGNAHI MESERAELRD AESLFRYLRD VREFVRALAK SNAYTSRFLQ GNQQYRFFEL N FKHLLGRG PRSLEEMASH SALYAEGGFE AVIDAILDSD EYAQEFGSTV VPYCRFKGEY PTNEEFNRML VLKGANSTSD KA GKGRSKL CYSIAAGCSQ NWLSMSKALP FGTEKGTGFN LISSSRNPAA RPRIGTKIPG GVVFSS

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Macromolecule #12: LRC2

Macromolecule	Name: LRC2 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 53.601336 KDa
Sequence	String: MAFVNGFSGG AAAVPRRGVA RVCAQRVVMK VVDRLDSQPS AAFEQTKQVY TFSRYILGPH RAVVAPVAMD PSEKEVVLRA VYRQVFGNA YIMEEERAEL RVMESQFLLG ELSVKELVRA LAKSSTYKVR FFEGAVQYRF IELCFKHLLG RAPDNHEEIA V HMRKYQQE ...String: MAFVNGFSGG AAAVPRRGVA RVCAQRVVMK VVDRLDSQPS AAFEQTKQVY TFSRYILGPH RAVVAPVAMD PSEKEVVLRA VYRQVFGNA YIMEEERAEL RVMESQFLLG ELSVKELVRA LAKSSTYKVR FFEGAVQYRF IELCFKHLLG RAPDNHEEIA V HMRKYQQE GYDAEIDSYL DAGEYDNVFG DDTVPFLRFR GVYTPCDSFN RQCALQGGWA NSDKAMGGAA LSGYNGSDGR QM STMIGNY ISGKPIPYEK VAADTPLKST APNWYARPNP ALAPQPAYVS AKEIAELRSR VSKLEAAWSV AVKQSAAAKD TVE TWRAAA KEMAAMRGIS PMGEAYFGGI AQKVDNGALA QLGNKASSYK KYLYAIETDE VSRLEVDLEE AKGQLRVLEA AMAK STPMT RTAEFKTLTK NVAAVTAAEK ADPLSKRPRI SASRPKPTPA AAKMAAAEKK KGPFGLSVPS LPNLPNLPKL PSLSL PKVS LPFGKK

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Macromolecule #13: LR5

Macromolecule	Name: LR5 / type: protein_or_peptide / ID: 13 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 29.453639 KDa
Sequence	String: MAAFVGSAAS AFTGASAVKA NEKRSVCSLQ MVAMPQTGLV NSKFSARMAK KTAKQTKNKV DEYMARSVQR QYKQAAVATG VYGTQCTEG TVKGAAEASR SAALSRQFRI KQRSAFSKAH DLFEFRKHAI IAAAGCSYEE KMVTRFPKLA AAMVLGQTEM M RTCSRYVV ...String: MAAFVGSAAS AFTGASAVKA NEKRSVCSLQ MVAMPQTGLV NSKFSARMAK KTAKQTKNKV DEYMARSVQR QYKQAAVATG VYGTQCTEG TVKGAAEASR SAALSRQFRI KQRSAFSKAH DLFEFRKHAI IAAAGCSYEE KMVTRFPKLA AAMVLGQTEM M RTCSRYVV PESVEEEYMA ASVDKQMKRR GAPGGVYSLS CAEGVAKGQA EIARVSALGA AYRAASKSAS AVTAERYNSM AY GRVHFAH GCSYEEQQFN KYPAAAAAMR SDSYGY

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Macromolecule #14: LR8

Macromolecule	Name: LR8 / type: protein_or_peptide / ID: 14 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 31.358787 KDa
Sequence	String: METAFVSGFM GKAAVAKFGA TAVCDKTARR SSSSNSQVHM VTGAVSSVNM RRFQRVPKVS GFSAKVTKKN VNKALDKADM FFAKSVTME GKAAAIPYGV YGIQCMEGSA KGMAHEKRAM ALSAAFRMNQ RSAAEKTGAM YENRRLALIL AQNDHQEKQY I KYPKLAAA ...String: METAFVSGFM GKAAVAKFGA TAVCDKTARR SSSSNSQVHM VTGAVSSVNM RRFQRVPKVS GFSAKVTKKN VNKALDKADM FFAKSVTME GKAAAIPYGV YGIQCMEGSA KGMAHEKRAM ALSAAFRMNQ RSAAEKTGAM YENRRLALIL AQNDHQEKQY I KYPKLAAA ALMASTEVTR ACQRYAVPES IEEEFLAASV DKVNKMRGTT ASGVYKSSCV EGNAKGQAEQ ARVAALAVAF RS AQKSASQ FAAERYAQSK YGRDLFSSTH FEEGYANTYP AMAAAKRASS YGY

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Macromolecule #15: LR3

Macromolecule	Name: LR3 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 37.175957 KDa
Sequence	String: MAFVTGGVGA VVRPGTAVSR GVVCARQQAR PRAAALQMGV SDVSITLSGV AASQPVSAPA KMSLEDRQLL VLQAIKQVFG NAYVMEEER ASFAKQESMF LSGELSVREF VRELALSDTY RRRFFEPCGP YRFVELNMKH LLGRGPISQA EVSQHVQCYV N NGYEAEIS ...String: MAFVTGGVGA VVRPGTAVSR GVVCARQQAR PRAAALQMGV SDVSITLSGV AASQPVSAPA KMSLEDRQLL VLQAIKQVFG NAYVMEEER ASFAKQESMF LSGELSVREF VRELALSDTY RRRFFEPCGP YRFVELNMKH LLGRGPISQA EVSQHVQCYV N NGYEAEIS SYVDSDEYYE RFGEDTVPYE QFRGTYMTAE DFNRMVSMYG APGQSDKSLT SRARSTGVAN SNKVLSLEGA GR SSKTVGR VATNTASSLT SVKSGIPPRP DIDQPRGQSS KRLVGRRLEI VPGSYMYLSP AEAAEYRAQQ AAVSQVSAAF SAD VQSKMA QVSKLKRELA ALGLSV

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Macromolecule #16: LRC3

Macromolecule	Name: LRC3 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 55.146727 KDa
Sequence	String: MAFVGAMPGG GGEPRAVRMM MQTDARSLSS GSSAAVPFST AVRFESPSGG LDRYSRVDPA APGPNVITRF LFKDRPVRRS DPSLSEVDR EATMRTVYRN VMGNAYVMEE ERAELATLES QFLVGAISTR DFVRGVAKSA TYKKRFFESV SQFRFIELNF K HFMGRAPL ...String: MAFVGAMPGG GGEPRAVRMM MQTDARSLSS GSSAAVPFST AVRFESPSGG LDRYSRVDPA APGPNVITRF LFKDRPVRRS DPSLSEVDR EATMRTVYRN VMGNAYVMEE ERAELATLES QFLVGAISTR DFVRGVAKSA TYKKRFFESV SQFRFIELNF K HFMGRAPL DMAEMSKHYE IFAAGGYDAE VDSYFDSEEY LDVFGLDTVP YMRFRGTYAP NSTFNLQCRL QGGWARSDKK LP MMSMLPL NNKAAIMPHQ IVDGLPVIPN SEHPSQKYNV PKVSREKLQR ELLIAQGKAN ALQIELDAAY TSLASSRAFL APF AAMAAD MDIRPLYGKN PQVFAGQFLG VGAGQWGKTG ADTVRGRSRR VAADIGVKEF QLERVKQLVV DLQRALALED AEAD APATS LLQAYQAKVY VKPPVIAKKK GPEPVNEDEI TIGQGDKKIK VTVLRNLGDR TEKLREKPEK EEEEGPRTFK DLYET AKPM KGFPGDGSEM NVGG

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Macromolecule #17: Allophycocyanin alpha subunit

Macromolecule	Name: Allophycocyanin alpha subunit / type: protein_or_peptide / ID: 17 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 17.639123 KDa
Sequence	String: MSIVTKSIVN ADAEARYLSP GELDRIKSFV LSGQRRLRIA QTLTENRERI VKQGGQQLFQ RRPDVVSPGG NAYGEEMTAT CLRDLDYYL RLVTYGIIAG DVTPIEEIGL VGVKEMYSAL GTPISGVAEG IRCMKDVACS LLSGEDAAEV GFYFDYTLAA M Q

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Macromolecule #18: Allophycocyanin beta subunit

Macromolecule	Name: Allophycocyanin beta subunit / type: protein_or_peptide / ID: 18 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 17.415797 KDa
Sequence	String: MQDAITSVIN AADVQGKYLD ANSVEKLRGY FQTGELRVRA AATIAANAAT IIKEAVAKSL LYSDITRPGG (MEN)MYTTR RYA ACIRDLDYYL RYATYGMLAG DPSILDERVL NGLKETYNSL GVPIGATIQA IQAMKEVTGS LVGSDAGKEM GLYFDYI CS GLS

+
Macromolecule #19: Allophycocyanin gamma subunit

Macromolecule	Name: Allophycocyanin gamma subunit / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 18.126934 KDa
Sequence	String: MSLVTQVILS ADDELRYPTA GELETISSYL KTGEYRIRLI SILQGKEQEI IRLASKKIFQ LHPEYIAPGG NASGARQRAL CLRDYGWYL RLITYAILAG DKEPLEKIGI IGVREMYNSL GVPIIGMIDA IKCLKEATVE VISQEEEDFV APYYDYIIQG M S

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Macromolecule #20: Allophycocyanin beta 18 subunit

Macromolecule	Name: Allophycocyanin beta 18 subunit / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 19.77874 KDa
Sequence	String: MQDIITSVIN QYDLSGRYLD IKGINQINNY FDTGLKRLMI AKLINKEATN LIKEASELLF IEQPELLRPC GNAFIGNAYT TRRYAACIR DIEYYLRYSA YSIIAGNNSI LDERVLDGLK ETYNSLLVPI GPTIRVIQLL KEIIQKKFST ENIENAIIAE P FDYLAINL SDKNL

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Macromolecule #21: LC

Macromolecule	Name: LC / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 10.428983 KDa
Sequence	String: MAYDMDGTGA GSLEPRGIKS SAVEKDSRCF KVTFVLPSQS RLYTFRELQN VYTTKMVPFS SWYAEQQRIQ KMGGKILKVE LVAGGQMRS VGNQ

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Macromolecule #22: Phycobilisome linker polypeptide

Macromolecule	Name: Phycobilisome linker polypeptide / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 99.468367 KDa
Sequence	String: MVTKASGGSP VVKPQLYKTA SMLTIAQAEQ QDRFLELGEL NQLVSFLNTG NIRLEIADLL TKNANIIVAR AADRIFVGGS AISYLERPQ ASIIEANSAD IASIRQMSGD SQSNFLENLT SVFQGNNATP TGFKPISVVR YGPSRMKKSL RDLDWFLRYL T YAIVAGDP ...String: MVTKASGGSP VVKPQLYKTA SMLTIAQAEQ QDRFLELGEL NQLVSFLNTG NIRLEIADLL TKNANIIVAR AADRIFVGGS AISYLERPQ ASIIEANSAD IASIRQMSGD SQSNFLENLT SVFQGNNATP TGFKPISVVR YGPSRMKKSL RDLDWFLRYL T YAIVAGDP NILFVNIRGL REIIENACSS AATIVALKEM KKTSLSLFPE NSIQKEIIEE YFNVVVDEFI NPALTDTIRK RT SNDLQGL RLPQIYAKAG ISRQKFVMKP GLSTDEKQSV ISACYRQVFE RDISKAYGFS FSVLESQVKN GQISIKEFVR SLG KSSVYQ KQFYQPYVNS RVVELAFRHF LGRNLSSLAE FQKFFAILSK KGLTGLVDSL INSREYSDYF NEETVPYIRG FGEE PQECR NWGTQIDLFQ YSAPFRKVPQ SITLFSDYLK ALPDQHPYGR GNDPLLIQFG AIFPIGTKNL KQNPAPFGKD TRRLL IRRG PGIYNQVGNP STRSVSVGSL GPKVFKSEGI NSNAQRTNNE SILQASYLAV FGRMIYQNER IGLKGIDNKF LDNNLS VKE LIRSLAISDT FRSLYWTPLY VCKSIEWIHY RLLGRPTYGR QEINQYFNVA YKKGFVGVIN SIIDSVEYNE CFGDNIV PY ERYLTANSVS QRQLKLGNII KSANLKPQNI EKFVQLGQSQ TNQNLYSIKY KVKQGVSKLR DQQKIFETKG SLSKDAYL S IFQAACRQIF ERDISTFVIG NEIENIKIQF IKGQISVKEM INALGKSSVY LKEFYNPYPN IKVIELGTKH FLGRAPNNQ AEIRFYNQIL ASCGLQAFID MLTNSQEYAE IFGEVRVPFR RFPTLPAANF PNTNTLFDKQ TKQNSVVIVP SFKAITGNQ

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Macromolecule #23: LRC4

Macromolecule	Name: LRC4 / type: protein_or_peptide / ID: 23 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 16.91526 KDa
Sequence	String: MAFVACGPLR AGEGGARLGA RKAACSMQLA PPGIPPGEDA RNNQSLRQYV ARPVETYQKR SFATPLPLTW TGETETVGAF DVVVPPQEK DLPVSGEATS AFVKYSDMVR AERKAALQAL LSASAAGEGR PTCGAEGRKF VSNANPVLVN GVKCVEYWRK

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Macromolecule #24: LRC5

Macromolecule	Name: LRC5 / type: protein_or_peptide / ID: 24 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 30.272959 KDa
Sequence	String: MAFVSGAGVA VPAGAKASAP LCALRMSGYG DYSYSTDRTK GHVNQYYVDK ARSRSDWGNR NVLPASEGDA VLGRTAKGAV AVPEFGIPQ LDDPVLGFGP DSMVDPRIAE ADGAVWRWDA GFVDESMTLA SCADISDEAV ADEAFAKFRG SVLAERGAMI T KAESATAS ...String: MAFVSGAGVA VPAGAKASAP LCALRMSGYG DYSYSTDRTK GHVNQYYVDK ARSRSDWGNR NVLPASEGDA VLGRTAKGAV AVPEFGIPQ LDDPVLGFGP DSMVDPRIAE ADGAVWRWDA GFVDESMTLA SCADISDEAV ADEAFAKFRG SVLAERGAMI T KAESATAS VITSLRDGLY SGEAQLLTAS GQRLANVAGQ EKIATISGYT WDGQPQTEIP GKPFVKSIGA MDYMDGVEGG DV VAAKVGA FWKPKAPKEV PYKRPMGANT PELPYNTVPR LVQAAGLAVQ E

+
Macromolecule #25: LRC6

Macromolecule	Name: LRC6 / type: protein_or_peptide / ID: 25 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)	Organism: Red alga (eukaryote)
Molecular weight	Theoretical: 26.620727 KDa
Sequence	String: MAGFVASTGA VLRKQQVDAA PVCERASSRA RAVAPLSMAR TAYPYTGSGY GSAGVPYGQD TYGYKATTAK SITETAAQAG VFNTFVKLL NESGVEKLVE QAGPYTVFAP TDDAFAALLE PHSFNKLATL LRPENNDALR KVLMHHVIPG AFTSASLMDR A VTVKSLAG ...String: MAGFVASTGA VLRKQQVDAA PVCERASSRA RAVAPLSMAR TAYPYTGSGY GSAGVPYGQD TYGYKATTAK SITETAAQAG VFNTFVKLL NESGVEKLVE QAGPYTVFAP TDDAFAALLE PHSFNKLATL LRPENNDALR KVLMHHVIPG AFTSASLMDR A VTVKSLAG EPISIMGLNK LVTAGTAKVV RADVPCANGC IIHAVSSVII PPNYVPVPQP TKPVFPRSVI AEIAKLPTPR QA LGLDPAP SKIVKY

+
Macromolecule #26: PHYCOERYTHROBILIN

Macromolecule	Name: PHYCOERYTHROBILIN / type: ligand / ID: 26 / Number of copies: 1430 / Formula: PEB
Molecular weight	Theoretical: 588.694 Da
Chemical component information	ChemComp-PEB: PHYCOERYTHROBILIN / Phycoerythrobilin

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Macromolecule #27: PHYCOUROBILIN

Macromolecule	Name: PHYCOUROBILIN / type: ligand / ID: 27 / Number of copies: 48 / Formula: PUB
Molecular weight	Theoretical: 590.71 Da
Chemical component information	ChemComp-CYB: PHYCOUROBILIN / Phycourobilin

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Macromolecule #28: PHYCOCYANOBILIN

Macromolecule	Name: PHYCOCYANOBILIN / type: ligand / ID: 28 / Number of copies: 120 / Formula: CYC
Molecular weight	Theoretical: 588.694 Da
Chemical component information	ChemComp-CYC: PHYCOCYANOBILIN / Phycocyanobilin

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Experimental details

-
Structure determination

Method	cryo EM
Processing	single particle reconstruction
Aggregation state	particle

-
Sample preparation

Concentration

1.5 mg/mL

Buffer

pH: 7
Component:

Concentration	Formula
750.0 mmol.L-1	Na₂HPO₃
750.0 mmol.L-1	KH₂PO₃

Sugar embedding

Material: ice

Vitrification

Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy

Microscope	FEI TITAN KRIOS
Electron beam	Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics	C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.001 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Specialist optics	Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stage	Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recording	Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Number real images: 16218 / Average exposure time: 5.6 sec. / Average electron dose: 48.0 e/Å²
Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selection	Number selected: 686369
CTF correction	Software - Name: CTFFIND
Startup model	Type of model: PDB ENTRY PDB model - PDB ID: 5y6p
Initial angle assignment	Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classification	Software - Name: RELION
Final angle assignment	Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstruction	Applied 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 / Number images used: 191825

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-Sample components

+Entire : Complex of phycobilisome from red alga P.purpureum.

+Supramolecule #1: Complex of phycobilisome from red alga P.purpureum.

+Macromolecule #1: Phycoerythrin alpha subunit

+Macromolecule #2: B-phycoerythrin beta chain

+Macromolecule #3: LR7

+Macromolecule #4: LR2_Hb

+Macromolecule #5: LR9

+Macromolecule #6: LR1

+Macromolecule #7: LR4

+Macromolecule #8: Phycobilisome rod-core linker polypeptide

+Macromolecule #9: C-phycocyanin alpha subunit

+Macromolecule #10: C-phycocyanin beta subunit

+Macromolecule #11: LR2

+Macromolecule #12: LRC2

+Macromolecule #13: LR5

+Macromolecule #14: LR8

+Macromolecule #15: LR3

+Macromolecule #16: LRC3

+Macromolecule #17: Allophycocyanin alpha subunit

+Macromolecule #18: Allophycocyanin beta subunit

+Macromolecule #19: Allophycocyanin gamma subunit

+Macromolecule #20: Allophycocyanin beta 18 subunit

+Macromolecule #21: LC

+Macromolecule #22: Phycobilisome linker polypeptide

+Macromolecule #23: LRC4

+Macromolecule #24: LRC5

+Macromolecule #25: LRC6

+Macromolecule #26: PHYCOERYTHROBILIN

+Macromolecule #27: PHYCOUROBILIN

+Macromolecule #28: PHYCOCYANOBILIN

-Experimental details

-Structure determination

-Sample preparation

-Electron microscopy

-Image processing

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