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- EMDB-31605: Cryo-EM structure of cyanobacterial photosystem I in the presence... -

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Basic information

Entry
Database: EMDB / ID: EMD-31605
TitleCryo-EM structure of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6
Map data3D refined map in C3 symmetry, which was used for model building and refinement.
Sample
  • Complex: Cryo-EM map of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6
    • Complex: Photosystem I trimer
      • Protein or peptide: x 10 types
    • Complex: Ga-Substituted Ferredoxin
      • Protein or peptide: x 3 types
  • Ligand: x 11 types
KeywordsPhotosystem I / Ferredoxin / Cytochrome c6 / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Ferredoxin [2Fe-2S], plant / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Ferredoxin [2Fe-2S], plant / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / 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 PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / 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 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Electron transport accessory-like domain superfamily / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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
Ferredoxin-1 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit VIII ...Ferredoxin-1 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI / Photosystem I 4.8K protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria) / Thermosynechococcus vestitus BP-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.97 Å
AuthorsLi J / Kurisu G
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2022
Title: Structure of cyanobacterial photosystem I complexed with ferredoxin at 1.97 Å resolution.
Authors: Jiannan Li / Noriyuki Hamaoka / Fumiaki Makino / Akihiro Kawamoto / Yuxi Lin / Matthias Rögner / Marc M Nowaczyk / Young-Ho Lee / Keiichi Namba / Christoph Gerle / Genji Kurisu /
Abstract: Photosystem I (PSI) is a light driven electron pump transferring electrons from Cytochrome c (Cyt c) to Ferredoxin (Fd). An understanding of this electron transfer process is hampered by a paucity of ...Photosystem I (PSI) is a light driven electron pump transferring electrons from Cytochrome c (Cyt c) to Ferredoxin (Fd). An understanding of this electron transfer process is hampered by a paucity of structural detail concerning PSI:Fd interface and the possible binding sites of Cyt c. Here we describe the high resolution cryo-EM structure of Thermosynechococcus elongatus BP-1 PSI in complex with Fd and a loosely bound Cyt c. Side chain interactions at the PSI:Fd interface including bridging water molecules are visualized in detail. The structure explains the properties of mutants of PsaE and PsaC that affect kinetics of Fd binding and suggests a molecular switch for the dissociation of Fd upon reduction. Calorimetry-based thermodynamic analyses confirms a single binding site for Fd and demonstrates that PSI:Fd complexation is purely driven by entropy. A possible reaction cycle for the efficient transfer of electrons from Cyt c to Fd via PSI is proposed.
History
DepositionAug 1, 2021-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31605.png

Downloads & links

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Map

FileDownload / File: emd_31605.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D refined map in C3 symmetry, which was used for model building and refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 400 pix.
= 322.4 Å		0.81 Å/pix.
x 400 pix.
= 322.4 Å		0.81 Å/pix.
x 400 pix.
= 322.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.806 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.024400305 - 0.089562714
Average (Standard dev.)-0.00020721252 (±0.002811805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 322.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_31605_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Post-process map in C3 symmetry. (Resolution: 1.97 A)

Fileemd_31605_additional_1.map
AnnotationPost-process map in C3 symmetry. (Resolution: 1.97 A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Post-process map in C1 symmetry. (Resolution: 2.08 A)

Fileemd_31605_additional_2.map
AnnotationPost-process map in C1 symmetry. (Resolution: 2.08 A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of 3D refine.

Fileemd_31605_half_map_1.map
AnnotationHalf map of 3D refine.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of 3D refine.

Fileemd_31605_half_map_2.map
AnnotationHalf map of 3D refine.
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : Cryo-EM map of cyanobacterial photosystem I in the presence of fe...

EntireName: Cryo-EM map of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6
Components
  • Complex: Cryo-EM map of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6
    • Complex: Photosystem I trimer
      • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
      • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
      • 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 VIII
      • Protein or peptide: Photosystem I reaction center subunit IX
      • Protein or peptide: Photosystem I reaction center subunit PsaK
      • Protein or peptide: Photosystem I reaction center subunit XI
      • Protein or peptide: Photosystem I reaction center subunit XII
    • Complex: Ga-Substituted Ferredoxin
      • Protein or peptide: Photosystem I reaction center subunit III
      • Protein or peptide: Ferredoxin-1
      • Protein or peptide: Photosystem I 4.8K protein
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: UNKNOWN LIGAND
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: CALCIUM ION
  • Ligand: [2Ga-2S] cluster
  • Ligand: water

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Supramolecule #1: Cryo-EM map of cyanobacterial photosystem I in the presence of fe...

SupramoleculeName: Cryo-EM map of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Details: Cytochrome C6 was not be built in model because of limited resolution
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 1.08 MDa

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Supramolecule #2: Photosystem I trimer

SupramoleculeName: Photosystem I trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5, #7-#11
Details: 12 subunits with 10x his-tag on N-ter of PsaF in each monomer.

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Supramolecule #3: Ga-Substituted Ferredoxin

SupramoleculeName: Ga-Substituted Ferredoxin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6, #12-#13
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 83.267773 KDa
SequenceString: MTISPPEREP KVRVVVDNDP VPTSFEKWAK PGHFDRTLAR GPQTTTWIWN LHALAHDFDT HTSDLEDISR KIFSAHFGHL AVVFIWLSG MYFHGAKFSN YEAWLADPTG IKPSAQVVWP IVGQGILNGD VGGGFHGIQI TSGLFQLWRA SGITNEFQLY C TAIGGLVM ...String:
MTISPPEREP KVRVVVDNDP VPTSFEKWAK PGHFDRTLAR GPQTTTWIWN LHALAHDFDT HTSDLEDISR KIFSAHFGHL AVVFIWLSG MYFHGAKFSN YEAWLADPTG IKPSAQVVWP IVGQGILNGD VGGGFHGIQI TSGLFQLWRA SGITNEFQLY C TAIGGLVM AGLMLFAGWF HYHKRAPKLE WFQNVESMLN HHLAGLLGLG SLAWAGHQIH VSLPINKLLD AGVAAKDIPL PH EFILNPS LMAELYPKVD WGFFSGVIPF FTFNWAAYSD FLTFNGGLNP VTGGLWLSDT AHHHLAIAVL FIIAGHMYRT NWG IGHSLK EILEAHKGPF TGAGHKGLYE VLTTSWHAQL AINLAMMGSL SIIVAQHMYA MPPYPYLATD YPTQLSLFTH HMWI GGFLV VGGAAHGAIF MVRDYDPAMN QNNVLDRVLR HRDAIISHLN WVCIFLGFHS FGLYVHNDTM RAFGRPQDMF SDTGI QLQP VFAQWVQNLH TLAPGGTAPN AAATASVAFG GDVVAVGGKV AMMPIVLGTA DFMVHHIHAF TIHVTVLILL KGVLFA RSS RLIPDKANLG FRFPCDGPGR GGTCQVSGWD HVFLGLFWMY NCISVVIFHF SWKMQSDVWG TVAPDGTVSH ITGGNFA QS AITINGWLRD FLWAQASQVI GSYGSALSAY GLLFLGAHFI WAFSLMFLFS GRGYWQELIE SIVWAHNKLK VAPAIQPR A LSIIQGRAVG VAHYLLGGIA TTWAFFLARI ISVG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 83.123648 KDa
SequenceString: MATKFPKFSQ DLAQDPTTRR IWYAIAMAHD FESHDGMTEE NLYQKIFASH FGHLAIIFLW VSGSLFHVAW QGNFEQWVQD PVNTRPIAH AIWDPQFGKA AVDAFTQAGA SNPVDIAYSG VYHWWYTIGM RTNGDLYQGA IFLLILASLA LFAGWLHLQP K FRPSLSWF ...String:
MATKFPKFSQ DLAQDPTTRR IWYAIAMAHD FESHDGMTEE NLYQKIFASH FGHLAIIFLW VSGSLFHVAW QGNFEQWVQD PVNTRPIAH AIWDPQFGKA AVDAFTQAGA SNPVDIAYSG VYHWWYTIGM RTNGDLYQGA IFLLILASLA LFAGWLHLQP K FRPSLSWF KNAESRLNHH LAGLFGVSSL AWAGHLIHVA IPESRGQHVG WDNFLSTMPH PAGLAPFFTG NWGVYAQNPD TA SHVFGTA QGAGTAILTF LGGFHPQTES LWLTDMAHHH LAIAVLFIVA GHMYRTQFGI GHSIKEMMDA KDFFGTKVEG PFN MPHQGI YETYNNSLHF QLGWHLACLG VITSLVAQHM YSLPPYAFIA QDHTTMAALY THHQYIAGFL MVGAFAHGAI FLVR DYDPA QNKGNVLDRV LQHKEAIISH LSWVSLFLGF HTLGLYVHND VVVAFGTPEK QILIEPVFAQ FIQAAHGKLL YGFDT LLSN PDSIASTAWP NYGNVWLPGW LDAINSGTNS LFLTIGPGDF LVHHAIALGL HTTTLILVKG ALDARGSKLM PDKKDF GYA FPCDGPGRGG TCDISAWDAF YLAMFWMLNT IGWVTFYWHW KHLGVWEGNV AQFNESSTYL MGWLRDYLWL NSSQLIN GY NPFGTNNLSV WAWMFLFGHL VWATGFMFLI SWRGYWQELI ETLVWAHERT PLANLVRWKD KPVALSIVQA RLVGLAHF S VGYILTYAAF LIASTAAKFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 8.809207 KDa
SequenceString:
MAHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKAGQIA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #4: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 15.389494 KDa
SequenceString:
MTTLTGQPPL YGGSTGGLLS AADTEEKYAI TWTSPKEQVF EMPTAGAAVM REGENLVYFA RKEQCLALAA QQLRPRKIND YKIYRIFPD GETVLIHPKD GVFPEKVNKG REAVNSVPRS IGQNPNPSQL KFTGKKPYDP

UniProtKB: Photosystem I reaction center subunit II

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Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 8.399485 KDa
SequenceString:
MVQRGSKVKI LRPESYWYNE VGTVASVDQT PGVKYPVIVR FDKVNYTGYS GSASGVNTNN FALHEVQEVA PPKKGK

UniProtKB: Photosystem I reaction center subunit IV

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Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 19.098062 KDa
Recombinant expressionOrganism: Thermosynechococcus vestitus BP-1 (bacteria)
SequenceString:
HHHHHHHHHH MRRFLALLLV LTLWLGFTPL ASADVAGLVP CKDSPAFQKR AAAAVNTTAD PASGQKRFER YSQALCGEDG LPHLVVDGR LSRAGDFLIP SVLFLYIAGW IGWVGRAYLI AVRNSGEANE KEIIIDVPLA IKCMLTGFAW PLAALKELAS G ELTAKDNE ITVSPR

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #7: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 4.297234 KDa
SequenceString:
MMGSYAASFL PWIFIPVVCW LMPTVVMGLL FLYIEGEA

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 4.770698 KDa
SequenceString:
MKHFLTYLST APVLAAIWMT ITAGILIEFN RFYPDLLFHP L

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #9: Photosystem I reaction center subunit PsaK

MacromoleculeName: Photosystem I reaction center subunit PsaK / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 8.483983 KDa
SequenceString:
MVLATLPDTT WTPSVGLVVI LCNLFAIALG RYAIQSRGKG PGLPIALPAL FEGFGLPELL ATTSFGHLLA AGVVSGLQYA GAL

UniProtKB: Photosystem I reaction center subunit PsaK

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Macromolecule #10: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 16.261685 KDa
SequenceString:
MAEELVKPYN GDPFVGHLST PISDSGLVKT FIGNLPAYRQ GLSPILRGLE VGMAHGYFLI GPWVKLGPLR DSDVANLGGL ISGIALILV ATACLAAYGL VSFQKGGSSS DPLKTSEGWS QFTAGFFVGA MGSAFVAFFL LENFSVVDGI MTGLFN

UniProtKB: Photosystem I reaction center subunit XI

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Macromolecule #11: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 11 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 3.426115 KDa
SequenceString:
MALTDTQVYV ALVIALLPAV LAFRLSTELY K

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #12: Ferredoxin-1

MacromoleculeName: Ferredoxin-1 / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 10.853959 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MATYKVTLVR PDGSETTIDV PEDEYILDVA EEQGLDLPFS CRAGACSTCA GKLLEGEVDQ SDQSFLDDDQ IEKGFVLTCV AYPRSDCKI LTNQEEELY

UniProtKB: Ferredoxin-1

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Macromolecule #13: Photosystem I 4.8K protein

MacromoleculeName: Photosystem I 4.8K protein / type: protein_or_peptide / ID: 13 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 4.424317 KDa
Recombinant expressionOrganism: Thermosynechococcus vestitus BP-1 (bacteria)
SequenceString:
MSTMATKSAK PTYAFRTFWA VLLLAINFLV AAYYFGILK

UniProtKB: Photosystem I 4.8K protein

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Macromolecule #14: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 14 / Number of copies: 3 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #15: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 15 / Number of copies: 285 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #16: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 16 / Number of copies: 6 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #17: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 17 / Number of copies: 9 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #18: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 18 / Number of copies: 72 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #19: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 19 / Number of copies: 9 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #20: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 20 / Number of copies: 51 / Formula: UNL
Molecular weightTheoretical: 40.078 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #21: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 21 / Number of copies: 3 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #22: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 22 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #23: [2Ga-2S] cluster

MacromoleculeName: [2Ga-2S] cluster / type: ligand / ID: 23 / Number of copies: 3 / Formula: GAK
Molecular weightTheoretical: 203.576 Da
Chemical component information

ChemComp-GAK:
[2Ga-2S] cluster

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Macromolecule #24: water

MacromoleculeName: water / type: ligand / ID: 24 / Number of copies: 348 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration30 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 1.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207142
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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