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- EMDB-53120: Monomeric Photosystem I Cryo-EM structure at 1.8 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-53120
TitleMonomeric Photosystem I Cryo-EM structure at 1.8 A resolution
Map dataSharpened map from final non-uniform refinement in CryoSPARC. Sharpening B-factor from Guinier fit: -35.8.
Sample
  • Complex: Monomeric photosystem I
    • Protein or peptide: x 11 types
  • Ligand: x 11 types
KeywordsMonomeric Photosystem I / mPSI / photosynthesis
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / 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 psaG and psaK proteins signature. ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / 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 psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / 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 protein PsaC / Photosystem I PsaA / 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 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 4.8K protein
Similarity search - Component
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.74 Å
AuthorsGaullier G / Boyka J / Zouni A / Blikstad C
Funding support Germany, Sweden, 4 items
OrganizationGrant numberCountry
Germanys Excellence StrategyEXC 2008/1-390540038 Germany
German Research Foundation (DFG)SFB1078 - TP A5 Germany
Swedish Research Council2019-03700_VR Sweden
Formas2019-01171_Formas Sweden
CitationJournal: To Be Published
Title: Monomeric Photosystem I Cryo-EM structure at 1.8 A resolution
Authors: Boyka J / Gaullier G / Blikstad C / Zouni A
History
DepositionMar 12, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53120.png

Downloads & links

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Map

FileDownload / File: emd_53120.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from final non-uniform refinement in CryoSPARC. Sharpening B-factor from Guinier fit: -35.8.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 512 pix.
= 331.776 Å		0.65 Å/pix.
x 512 pix.
= 331.776 Å		0.65 Å/pix.
x 512 pix.
= 331.776 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.51073664 - 1.4683826
Average (Standard dev.)0.00011664033 (±0.016124183)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 331.776 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53120_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_53120_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unfiltered, unsharpened map from final non-uniform refinement in...

Fileemd_53120_additional_1.map
AnnotationUnfiltered, unsharpened map from final non-uniform refinement in CryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A from final non-uniform refinement in CryoSPARC.

Fileemd_53120_half_map_1.map
AnnotationHalf-map A from final non-uniform refinement in CryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B from final non-uniform refinement in CryoSPARC.

Fileemd_53120_half_map_2.map
AnnotationHalf-map B from final non-uniform refinement in CryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Monomeric photosystem I

EntireName: Monomeric photosystem I
Components
  • Complex: Monomeric photosystem I
    • 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 III
    • 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 XII
    • Protein or peptide: Photosystem I 4.8K protein
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: MAGNESIUM ION
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: water

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Supramolecule #1: Monomeric photosystem I

SupramoleculeName: Monomeric photosystem I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Details: Endogeneous photosystem I complex purified from its native source organism Thermosynechococcus vestitus BP-1.
Source (natural)Organism: Thermosynechococcus vestitus 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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
Molecular weightTheoretical: 17.716586 KDa
SequenceString:
MRRFLALLLV LTLWLGFTPL ASADVAGLVP CKDSPAFQKR AAAAVNTTAD PASGQKRFER YSQALCGEDG LPHLVVDGRL SRAGDFLIP SVLFLYIAGW IGWVGRAYLI AVRNSGEANE KEIIIDVPLA IKCMLTGFAW PLAALKELAS GELTAKDNEI T VSPR

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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
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 XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
Molecular weightTheoretical: 3.426115 KDa
SequenceString:
MALTDTQVYV ALVIALLPAV LAFRLSTELY K

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #11: Photosystem I 4.8K protein

MacromoleculeName: Photosystem I 4.8K protein / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
Molecular weightTheoretical: 4.424317 KDa
SequenceString:
MSTMATKSAK PTYAFRTFWA VLLLAINFLV AAYYFGILK

UniProtKB: Photosystem I 4.8K protein

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Macromolecule #12: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 12 / Number of copies: 16 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #13: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 13 / Number of copies: 90 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #14: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 14 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #15: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 15 / Number of copies: 19 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #16: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 16 / Number of copies: 5 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #17: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 17 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #18: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 18 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #19: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 19 / Number of copies: 1 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #20: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 20 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #21: 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: 21 / Number of copies: 1 / 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 #22: water

MacromoleculeName: water / type: ligand / ID: 22 / Number of copies: 1183 / 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

Concentration2.5 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMTricin
25.0 mMsodium chlorideNaCl
0.02 % w/vn-dodecyl-beta-D-maltoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.04 kPa
Details: Current 20 mA. Performed with a Pelco easiGlow device.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Delay time 30 s Blot time 2 s Blot force 0 Drain time 0 s.
DetailsConcentration is expressed in mM chlorophyll.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 22001 / Average electron dose: 40.0 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: 1.4000000000000001 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 1000224
Details: Topaz was trained with a manually picked set of 1010 particles.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5)
Details: Patch CTF estimation job in CryoSPARC, run with default settings.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Initial model computed from the particle images by an ab initio reconstruction job in CryoSPARC.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5)
Details: Resolution as reported by CryoSPARC, using its mask auto-tightening procedure.
Number images used: 712866
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

a405

chain_id: A, source_name: AlphaFold, initial_model_type: in silico model

a407

chain_id: B, source_name: AlphaFold, initial_model_type: in silico model

a415

chain_id: C, source_name: AlphaFold, initial_model_type: in silico model

a420

chain_id: D, source_name: AlphaFold, initial_model_type: in silico model

a423

chain_id: E, source_name: AlphaFold, initial_model_type: in silico model

a401

chain_id: F, source_name: AlphaFold, initial_model_type: in silico model

a427

chain_id: I, source_name: AlphaFold, initial_model_type: in silico model

a429

chain_id: J, source_name: AlphaFold, initial_model_type: in silico model

a425

chain_id: K, source_name: AlphaFold, initial_model_type: in silico model

a403

chain_id: M, source_name: AlphaFold, initial_model_type: in silico model

dkp6

chain_id: X, source_name: AlphaFold, initial_model_type: in silico model
DetailsAlphafold2 predictions fetched from AlphaFold-DB were placed into the map by rigid body fitting. Termini not supported by the map were trimmed. Every residue was visually inspected at least once, and its fit to density adjusted if necessary, using ISOLDE.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9qfp:
Monomeric Photosystem I Cryo-EM structure at 1.8 A resolution

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