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- EMDB-65883: Cryo-EM structure of PSI-CpcL -

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Basic information

Entry
Database: EMDB / ID: EMD-65883
TitleCryo-EM structure of PSI-CpcL
Map data
Sample
  • Complex: PSI-CpcL
    • Protein or peptide: x 13 types
  • Ligand: x 8 types
KeywordsPhotosystem I / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosystem I reaction center / phycobilisome / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / phycobilisome / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem I iron-sulfur center / Photosystem I-associated linker protein CpcL / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A2 1 / Photosystem I 4.8 kDa protein / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 ...Photosystem I iron-sulfur center / Photosystem I-associated linker protein CpcL / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A2 1 / Photosystem I 4.8 kDa protein / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsMao ZY / Li ZH / Han GY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural insight of a photosystem I-CpcL-phycobilisome supercomplex from a cyanobacterium sp. PCC 7120.
Authors: Zhiyuan Mao / Zhenhua Li / Xingyue Li / Liangliang Shen / Tingyun Kuang / Wenda Wang / Jian-Ren Shen / Guangye Han /
Abstract: Phycobilisomes (PBSs) are supramolecular pigment-protein complexes composed of phycobiliproteins and linker proteins, serving as the major light-harvesting complexes that capture and transfer light ...Phycobilisomes (PBSs) are supramolecular pigment-protein complexes composed of phycobiliproteins and linker proteins, serving as the major light-harvesting complexes that capture and transfer light energy to photosystem II (PSII) and photosystem I (PSI) in cyanobacteria and eukaryotic red algae. In cyanobacteria, a rod-type PBS that does not have a core is specifically connected to PSI by a linker protein CpcL to form a PSI-CpcL-PBS supercomplex. However, the mechanism of CpcL-PBS association to PSI remains unclear. Here, we report the cryoelectron microscopic structures of PSI-CpcL-PBS at 2.98 Å and CpcL-PBS at 2.93 Å resolution from a cyanobacterium sp. PCC 7120, respectively. CpcL-PBS is located on the stromal side of a PSI tetramer and exhibits a structure of three-layered PBS consisting of four linkers (CpcL, CpcC1, CpcC2, PecC) and 18 pairs of phycocyanin αβ monomers. The C-terminal transmembrane helix of CpcL inserts to the membrane and interacts with PsaA, PsaB, and PsaM of PSI at an interface I between two PSI monomers, enabling the formation of the PSI-CpcL-PBS supercomplex. The exact structure of protein subunits and arrangement of bilin and chlorophyll pigments are revealed, which provide a structural basis for the assembly of PSI-CpcL-PBS and possible excitation energy transfer pathways from antennas to PSI within this supercomplex, shedding light on the organization and attachment of CpcL-PBS in cyanobacterial thylakoids.
History
DepositionAug 18, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65883.png

Downloads & links

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Map

FileDownload / File: emd_65883.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 660 pix.
= 686.4 Å		1.04 Å/pix.
x 660 pix.
= 686.4 Å		1.04 Å/pix.
x 660 pix.
= 686.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.185
Minimum - Maximum-0.38888395 - 1.1264603
Average (Standard dev.)0.00017601135 (±0.022472747)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions660660660
Spacing660660660
CellA=B=C: 686.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65883_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65883_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : PSI-CpcL

EntireName: PSI-CpcL
Components
  • Complex: PSI-CpcL
    • Protein or peptide: Photosystem I-associated linker protein CpcL
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I 4.8 kDa protein
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2 1
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I reaction center subunit II
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit PsaK 1
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Supramolecule #1: PSI-CpcL

SupramoleculeName: PSI-CpcL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

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Macromolecule #1: Photosystem I-associated linker protein CpcL

MacromoleculeName: Photosystem I-associated linker protein CpcL / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 27.232633 KDa
SequenceString: MALPLLEYKP TTQNQRVQSF GTADVNEDTP YIYRLENANS PSEIEELIWA AYRQVFNEQE ILKFNRQIGL ETQLKNRSIT VKDFIRGLA KSERFYQLVV TPNNNYRLVE MSLKRLLGRS PYNEEEKIAW SIQIASKGWG GFVDALIDST EYEQAFGDNT V PYQRKRLT ...String:
MALPLLEYKP TTQNQRVQSF GTADVNEDTP YIYRLENANS PSEIEELIWA AYRQVFNEQE ILKFNRQIGL ETQLKNRSIT VKDFIRGLA KSERFYQLVV TPNNNYRLVE MSLKRLLGRS PYNEEEKIAW SIQIASKGWG GFVDALIDST EYEQAFGDNT V PYQRKRLT TDRPFSFTPR YGADYRDRAG IVRPGRMSNW NNSANQNYDG VAILGVLLAI SAGMTFLFVL NWLGISSSF

UniProtKB: Photosystem I-associated linker protein CpcL

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 83.28968 KDa
SequenceString: MTISPPEREE KKARVIVDKD PVPTSFEKWA QPGHFDRTLA RGPKTTTWIW NLHALAHDFD THTSDLEDIS RKIFAAHFGH LAVVTIWLS GMIFHGAKFS NYEAWLSDPL NVRPSAQVVW PIVGQDILNG DVGGGFHGIQ ITSGLFQVWR GWGITNSFQL Y CTAIGGLV ...String:
MTISPPEREE KKARVIVDKD PVPTSFEKWA QPGHFDRTLA RGPKTTTWIW NLHALAHDFD THTSDLEDIS RKIFAAHFGH LAVVTIWLS GMIFHGAKFS NYEAWLSDPL NVRPSAQVVW PIVGQDILNG DVGGGFHGIQ ITSGLFQVWR GWGITNSFQL Y CTAIGGLV LAGLFLFAGW FHYHKRAPKL EWFQNVESML NHHLQVLLGC GSLGWAGHLI HVSAPINKLM DAGVAVKDIP LP HEFILNK SLLIDLFPGF AAGLTPFFTL NWGQYADFLT FKGGLNPVTG GLWMTDIAHH HLAIAVVFII AGHQYRTNWG IGH SIKEIL ENHKGPFTGE GHKGLYENLT TSWHAQLATN LAFLGSLTII IAHHMYAMPP YPYLATDYAT QLCIFTHHIW IGGF LIVGG AAHAAIFMVR DYDPVVNQNN VLDRVIRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMRAL GRPQDMFSDT AIQLQ PVFA QWVQNLHTLA PGGTAPNALE PVSYAFGGGV LAVGGKVAMM PIALGTADFL IHHIHAFTIH VTVLILLKGV LFARSS RLI PDKANLGFRF PCDGPGRGGT CQVSGWDHVF LGLFWMYNSL SIVIFHFSWK MQSDVWGTVD AAGNVSHITG GNFAQSA IT INGWLRDFLW AQASQVINSY GSALSAYGLM FLGAHFVWAF SLMFLFSGRG YWQELIESIV WAHNKLKVAP AIQPRALS I TQGRAVGVAH YLLGGIATTW AFFHAHILSV G

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #3: Photosystem I 4.8 kDa protein

MacromoleculeName: Photosystem I 4.8 kDa protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 4.872792 KDa
SequenceString:
MAKAKISPVA NTGAKPPYTF RTGWALLLLA VNFLVAAYYF HIIQ

UniProtKB: Photosystem I 4.8 kDa protein

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Macromolecule #4: Photosystem I P700 chlorophyll a apoprotein A2 1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 1 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 83.457016 KDa
SequenceString: MATKFPKFSQ DLAQDPTTRR IWYAMAMGND FESHDGMTEE NLYQKIFATH FGHLAIIFLW ASSLLFHVAW QGNFEQWIKD PLHVRPIAH AIWDPHFGKP AIEAFTQAGA NGPVNIAYSG VYHWWYTIGM RTNTELYTGS VFLLLFASLF LFAGWLHLQP K FRPSLAWF ...String:
MATKFPKFSQ DLAQDPTTRR IWYAMAMGND FESHDGMTEE NLYQKIFATH FGHLAIIFLW ASSLLFHVAW QGNFEQWIKD PLHVRPIAH AIWDPHFGKP AIEAFTQAGA NGPVNIAYSG VYHWWYTIGM RTNTELYTGS VFLLLFASLF LFAGWLHLQP K FRPSLAWF KSAESRLNHH LAGLFGVSSL AWAGHLIHVA IPESRGQHVG WDNFLSTAPH PAGLQPFFTG NWGVYAQNPD TA GHIFSTS QGAGTAILTF LGGFHPQTES LWLTDMAHHH LAIAVLFIVA GHMYRTNFGI GHSIKEMMNA KTFFGKPVEG PFN MPHQGI YDTYNNSLHF QLGWHLACLG VVTSWVAQHM YSLPSYAFIA KDYTTQAALY THHQYIAIFL MVGAFAHGAI FLVR DYDPE QNKGNVLERV LQHKEAIISH LSWVSLFLGF HTLGLYVHND VVVAFGTPEK QILIEPVFAQ FIQAAHGKVL YGLDT LLSN PDSVAYTAYP NYANVWLPGW LDAINSGTNS LFLTIGPGDF LVHHAIALGL HTTTLILVKG ALDARGSKLM PDKKDF GYA FPCDGPGRGG TCDISAWDSF YLSLFWALNT VGWVTFYWHW KHLGIWQGNV AQFNENSTYL MGWFRDYLWA NSAQLIN GY NPYGVNNLSV WAWMFLFGHL VWATGFMFLI SWRGYWQELI ETLVWAHERT PIANLVRWKD KPVALSIVQA RVVGLAHF T VGYVLTYAAF LIASTAGKFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2 1

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Macromolecule #5: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 8.825206 KDa
SequenceString:
MSHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKAAQVA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #6: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 15.17624 KDa
SequenceString:
MAETLSGKTP LFAGSTGGLL TKAVEEEKYA ITWTSPKAQV FELPTGGAAT MHEGENLLYI ARKEYGIALG GQLRKFKITN YKIYRILPS GETTFIHPAD GVFPEKVNAG REKVRFNARS IGENPNPSQV KFSGKATYDA

UniProtKB: Photosystem I reaction center subunit II

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Macromolecule #7: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 7.897051 KDa
SequenceString:
MVQRGSKVRI LRPESYWFQD VGTVASVDQS GIKYPVIVRF DKVNYAGINT NNFAVDELIE VEAPKAKAKK

UniProtKB: Photosystem I reaction center subunit IV

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Macromolecule #8: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 17.850568 KDa
SequenceString:
MRRLFALILV ICLSFSFAPP AKALGADLTP CAENPAFQAL AKNARNTTAD PQSGQKRFER YSQALCGPEG YPHLIVDGRL DRAGDFLIP SILFLYIAGW IGWVGRAYLQ AIKKDSDTEQ KEIQLDLGIA LPIIATGFAW PAAAVKELLS GELTAKDSEI T VSPR

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #9: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 9 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 5.499422 KDa
SequenceString:
MADKADQSSY LIKFISTAPV AATIWLTITA GILIEFNRFF PDLLFHPLP

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #10: Photosystem I reaction center subunit PsaK 1

MacromoleculeName: Photosystem I reaction center subunit PsaK 1 / type: protein_or_peptide / ID: 10 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 8.852457 KDa
SequenceString:
MLTSTLLAAA TTPLEWSPTV GIIMVIANVI AITFGRQTIK YPSAEPALPS AKFFGGFGAP ALLATTAFGH ILGVGLVLGL HNLGRI

UniProtKB: Photosystem I reaction center subunit PsaK 1

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Macromolecule #11: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 11 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 5.066925 KDa
SequenceString:
MATAFLPSIL ADASFLSSIF VPVIGWVVPI ATFSFLFLYI EREDVA

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #12: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 12 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 18.130725 KDa
SequenceString:
MAQAVDASKN LPSDPRNREV VFPAGRDPQW GNLETPVNAS PLVKWFINNL PAYRPGLTPF RRGLEVGMAH GYFLFGPFAK LGPLRDAAN ANLAGLLGAI GLVVLFTLAL SLYANSNPPT ALASVTVPNP PDAFQSKEGW NNFASAFLIG GIGGAVVAYF L TSNLALIQ GLVG

UniProtKB: Photosystem I reaction center subunit XI

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Macromolecule #13: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 13 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 3.538204 KDa
SequenceString:
MSSISDTQVY IALVVALIPG LLAWRLATEL YK

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #14: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 14 / Number of copies: 376 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #15: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 15 / Number of copies: 8 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #16: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 16 / Number of copies: 12 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #17: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 17 / Number of copies: 92 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #18: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 18 / Number of copies: 12 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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Macromolecule #19: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 19 / Number of copies: 4 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #20: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 20 / Number of copies: 8 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

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Macromolecule #21: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 21 / Number of copies: 6 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 120345
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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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

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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

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