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- EMDB-23040: The Structure of the moss PSI-LHCI reveals the evolution of the L... -

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Basic information

Entry
Database: EMDB / ID: EMD-23040
TitleThe Structure of the moss PSI-LHCI reveals the evolution of the LHCI antenna
Map data
Sample
  • Complex: PSI
    • Protein or peptide: x 17 types
  • Ligand: x 12 types
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane ...photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / 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 PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / 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 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 PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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 / Chlorophyll a-b binding protein, chloroplastic / Photosystem I subunit X / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSI subunit V / Photosystem I reaction center subunit V, chloroplastic / Predicted protein / Chlorophyll a-b binding protein, chloroplastic / Predicted protein ...Photosystem I reaction center subunit III / Chlorophyll a-b binding protein, chloroplastic / Photosystem I subunit X / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSI subunit V / Photosystem I reaction center subunit V, chloroplastic / Predicted protein / Chlorophyll a-b binding protein, chloroplastic / Predicted protein / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1
Similarity search - Component
Biological speciesPhyscomitrium patens (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRiddle R / Gorski C / Toporik H / Dobson Z / Da Z / Williams D / Mazor Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Plants / Year: 2022
Title: The structure of the Physcomitrium patens photosystem I reveals a unique Lhca2 paralogue replacing Lhca4.
Authors: C Gorski / R Riddle / H Toporik / Z Da / Z Dobson / D Williams / Y Mazor /
Abstract: The moss Physcomitrium patens diverged from green algae shortly after the colonization of land by ancient plants. This colonization posed new environmental challenges, which drove evolutionary ...The moss Physcomitrium patens diverged from green algae shortly after the colonization of land by ancient plants. This colonization posed new environmental challenges, which drove evolutionary processes. The photosynthetic machinery of modern flowering plants is adapted to the high light conditions on land. Red-shifted Lhca4 antennae are present in the photosystem I light-harvesting complex of many green-lineage plants but absent in P. patens. The cryo-EM structure of the P. patens photosystem I light-harvesting complex I supercomplex (PSI-LHCI) at 2.8 Å reveals that Lhca4 is replaced by a unique Lhca2 paralogue in moss. This PSI-LHCI supercomplex also retains the PsaM subunit, present in Cyanobacteria and several algal species but lost in vascular plants, and the PsaO subunit responsible for binding light-harvesting complex II. The blue-shifted Lhca2 paralogue and chlorophyll b enrichment relative to flowering plants make the P. patens PSI-LHCI spectroscopically unique among other green-lineage supercomplexes. Overall, the structure represents an evolutionary intermediate PSI with the crescent-shaped LHCI common in vascular plants, and contains a unique Lhca2 paralogue that facilitates the moss's adaptation to low-light niches.
History
DepositionNov 25, 2020-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_23040.png

Downloads & links

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Map

FileDownload / File: emd_23040.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy EMDB: 0.5
Minimum - Maximum-3.4054306 - 4.882017
Average (Standard dev.)-1.6681953e-11 (±0.14418158)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 291.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : PSI

EntireName: PSI
Components
  • Complex: PSI
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: PsaD
    • Protein or peptide: PsaE
    • Protein or peptide: PSI-F
    • Protein or peptide: PSI-G
    • Protein or peptide: PsaH
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: PsaK
    • Protein or peptide: PSI subunit V
    • Protein or peptide: Photosystem I reaction center subunit XII
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: CHLOROPHYLL B
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: water

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Supramolecule #1: PSI

SupramoleculeName: PSI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Physcomitrium patens (plant)

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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: Physcomitrium patens (plant)
Molecular weightTheoretical: 82.313422 KDa
SequenceString: EVKIMVEKDP VKTSFEKWAK PGHFSRTLAK GPNTTTWIWN LHADAHDFDS HTNDLEEISR KVFSAHFGQL AVIFIWLSGM YFHGARFSN YEAWLSDPTH IKPSAQVVWP IVGQKILNGD VGGGFQGIQI TSGFFQLWRA SGITSELQLY TTAIGGLIFA A LMLFAGWF ...String:
EVKIMVEKDP VKTSFEKWAK PGHFSRTLAK GPNTTTWIWN LHADAHDFDS HTNDLEEISR KVFSAHFGQL AVIFIWLSGM YFHGARFSN YEAWLSDPTH IKPSAQVVWP IVGQKILNGD VGGGFQGIQI TSGFFQLWRA SGITSELQLY TTAIGGLIFA A LMLFAGWF HYHKAAPKLA WFQNVESMLN HHLAGLLGLG SLAWAGHQVH VSLPINRLLD AGVDPKEIPL PHEFILNRDL LA QLYPSFS KGLTPFFTLN WSEYSDFLTF RGGLNPVTGG LWLTDTAHHH LAIAVLFLVA GHMYRTNFGI GHSMKEILEA HKG PFTGEG HKGLYEILTT SWHAQLAINL AMLGSLTIIV AHHMYAMPPY PYLATDYATQ LSLFTHHMWI GGFLVVGAAA HAAI FMVRD YDPTTQYNNL LDRVLRHRDA IISHLNWVCI FLGFHSFGLY IHNDTMSALG RPQDMFSDTA IQLQPVFAQW IQNTH ALAP SLTAPNATAS TSLTWGGGDL VAVGGKVALL PIPLGTADFL VHHIHAFTIH VTVLILLKGV LFARSSRLIP DKANLG FRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNAI SVVIFHFSWK MQSDVWGSIS DQGVVTHITG GNFAQSSITI NGWLRDF LW AQASQVIQSY GSSLSAYGLL FLGAHFVWAF SLMFLFSGRG YWQELIESIV WAHNKLKVAP AIQPRALSIV QGRAVGVA H YLLGGIATTW AFFLARIISV G

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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: Physcomitrium patens (plant)
Molecular weightTheoretical: 82.245477 KDa
SequenceString: SRFPKFSRGL SQDPTTRRIW FGIATAHDFE SHDDMTEERL YQKIFASHFG QLAIIFLWTS GNLFHVAWQG NFEAWGQDPL HVRPIAHAI WDPHFGQPAV EAFTRGGASG PVNIAYSGVY QWWYTIGLRT NQDLYGGSIF LLFVSALFLI AGWLHLQPKW K PSVSWFKN ...String:
SRFPKFSRGL SQDPTTRRIW FGIATAHDFE SHDDMTEERL YQKIFASHFG QLAIIFLWTS GNLFHVAWQG NFEAWGQDPL HVRPIAHAI WDPHFGQPAV EAFTRGGASG PVNIAYSGVY QWWYTIGLRT NQDLYGGSIF LLFVSALFLI AGWLHLQPKW K PSVSWFKN AESRLNHHLS GLFGVSSLAW TGHLVHVAIP ESRGEHVRWN NLLTALPHPQ GLGPFFAGQW NVYAQNPDSN SH LFGTSEG AGTAILTFLG GFHPQTQSLW LTDMAHHHLA IAVIFIIAGH MYRTNFGIGH SMKEILEAHT PPGGRLGRGH KGL YDTINN SLHFQLGLAL ASLGVITSLV AQHMYSLPPY AFLAQDFTTQ AALYTHHQYI AGFIMTGAFA HGAIFFIRDY NPEQ NKDNV LARMLEHKEA IISHLSWASL FLGFHTLGLY VHNDVMLAFG TPEKQILIEP VFAQWIQSAH GKALYGFDVL LSSAD SPAF NAGQTLWLPG WLDAINNNSN SLFLTIGPGD FLVHHAIALG LHTTTLILVK GALDARGSKL MPDKKEFGYS FPCDGP GRG GTCDISAWDA FYLAVFWMLN TIGWVTFYWH WKHITLWQGN VAQFNESSTY LMGWLRDYLW LNSSQLINGY NPFGMNS LS VWAWMFLFGH LVWATGFMFL ISWRGYWQEL IETLAWAHER TPLANLVRWK DKPVALSIVQ ARLVGLAHFS VGYIFTYA A FLIASTSGKF G

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Macromolecule #3: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 20.761584 KDa
SequenceString: EWLPGNPRPS YLDGSAPGDF GFDPLGLGEV PENLERFKES ELIHARWAML AVPGVLIPEA LGYGNWVSAQ KWAATPGGQA TYLGNPVPW GNLPVILAIE FLAIAFAESQ RNGEPDPEKR KYPGGAFDPL GFSKGANLEE LKLKEIKNGR LALVAFLGFA V QAIAYPGT ...String:
EWLPGNPRPS YLDGSAPGDF GFDPLGLGEV PENLERFKES ELIHARWAML AVPGVLIPEA LGYGNWVSAQ KWAATPGGQA TYLGNPVPW GNLPVILAIE FLAIAFAESQ RNGEPDPEKR KYPGGAFDPL GFSKGANLEE LKLKEIKNGR LALVAFLGFA V QAIAYPGT GPLENLKTHL ADPWHNTIAH VIIP

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Macromolecule #4: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 22.124145 KDa
SequenceString: RPLWFPGSQP PEWLDGSLPG DFGFDPLGLG SDPELLKWFV QAELVHCRWA MLGAAGIFIP EALTKAGILN TPSWTVAGDQ QYFTDATTL FVIEIILFAW AEGRRWADII NPGCVNVDPV FPNNKLTGTD VGYPGGLWFD PLGWGQTGDA AKLKDLRTRE I KNGRLAML ...String:
RPLWFPGSQP PEWLDGSLPG DFGFDPLGLG SDPELLKWFV QAELVHCRWA MLGAAGIFIP EALTKAGILN TPSWTVAGDQ QYFTDATTL FVIEIILFAW AEGRRWADII NPGCVNVDPV FPNNKLTGTD VGYPGGLWFD PLGWGQTGDA AKLKDLRTRE I KNGRLAML AVLGAVVQAN YTHTGPIDNL LAHLADPGHN TIFAL

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Macromolecule #5: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 23.834248 KDa
SequenceString: RSLIFASKQS LSYLDGTLPG DYGFDPLGLM DPEGAGGFID PQWLPYAEII NGRFAMLGAA GAIAPEVLGR IGLIPQETAI PWFQSGVIP PVGNYSYWAD PYTLFVLEMA LMGFAEHRRA QDYYKPGSMG KQYFLGLEKF LGGSGNPAYP GGPIFNFLGF G KNEKELQE ...String:
RSLIFASKQS LSYLDGTLPG DYGFDPLGLM DPEGAGGFID PQWLPYAEII NGRFAMLGAA GAIAPEVLGR IGLIPQETAI PWFQSGVIP PVGNYSYWAD PYTLFVLEMA LMGFAEHRRA QDYYKPGSMG KQYFLGLEKF LGGSGNPAYP GGPIFNFLGF G KNEKELQE LKVKEVKNGR LAMMAVLGYF TQAIFTGVGP FQNLLDHLAD PVHNNVLTNL

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Macromolecule #6: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 22.305465 KDa
SequenceString: RPLWLPGSEA PKWLDGSLPG DYGFDPLDLA AEPGRLNWMV QAELVHCRWA MLGAAGIFIP ELLTKIGILN TPSWYKAGDA TYFADQGTL FIVELLLMAW AESRRWADIA RPGSVNTDPI FPNNKLTGTD VGYPGGLWFD PLGWGSGSED KLKEIRTKEV K NGRLAMLA ...String:
RPLWLPGSEA PKWLDGSLPG DYGFDPLDLA AEPGRLNWMV QAELVHCRWA MLGAAGIFIP ELLTKIGILN TPSWYKAGDA TYFADQGTL FIVELLLMAW AESRRWADIA RPGSVNTDPI FPNNKLTGTD VGYPGGLWFD PLGWGSGSED KLKEIRTKEV K NGRLAMLA VLGAFVQANV THVGPIDNLF AHLADPYHTT ILQSL

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Macromolecule #7: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 8.649957 KDa
SequenceString:
AHSVKIYDTC IGCTQCVRAC PTDVLEMVPW DGCKASQIAS APRTEDCVGC KRCESACPTD FLSVRVYLGA ETTRSMGLAY

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Macromolecule #8: PsaD

MacromoleculeName: PsaD / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 15.789038 KDa
SequenceString:
FTPPTLNADT PAPIFGGSTG GLLRKAQVEE FYVITWESPK EQIFEMPTGG AAIMRSGPNL LKLARKEQCL ALGARLRTKF KIQYQFYRV FPNGEVQYLH PKDGVYPEKV NAGRTAVGVN NRSIGQNANP AELKFAHKQA YDL

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Macromolecule #9: PsaE

MacromoleculeName: PsaE / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 7.081935 KDa
SequenceString:
IGPKRGSIVK VLRRESYWFN DTGKVVAVDQ APGVRYPVVV RFDKVNYAGV STNNYSPDEL EQS

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Macromolecule #10: PSI-F

MacromoleculeName: PSI-F / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 17.646625 KDa
SequenceString:
VAGLTPCKES KGFAKRQKQE IKKLEGRLKL YAPDSAPALA INATIEKTKR RFEFYGNQGL LCGTDGLPHL IVDGDQAHLG EFVYPGLVF LYIAGWIGWV GRAYLIDVRT SKKPTEKEII IDVPLALRIM SKGLTWPVAA IGELRSGKLV EKSSNITVSP R

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Macromolecule #11: PSI-G

MacromoleculeName: PSI-G / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 9.72897 KDa
SequenceString:
ANTALTITLS TGALLFLGRF VFLPFQRDNV SRQGLPVQNG VTHFDAGDSR AQEVTSFLKT NDPAGFTIVD VLAWGALGHA VGFFILATI NN

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Macromolecule #12: PsaH

MacromoleculeName: PsaH / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 9.491607 KDa
SequenceString:
YFDLGEIDNT TGNWDLYGND DPNRYNGFQN KFFETFAGAF TKRGLLLKFL VLGGATTIGY LGSTSSGDLL AIKNGPKQAP IMGPRGR

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Macromolecule #13: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 3.791472 KDa
SequenceString:
MTASYLPSIF VPLIGLVFPA ITMASLFIYI EQDE

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Macromolecule #14: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 4.59746 KDa
SequenceString:
MQDVKTYLST APVLATLWFG FLAGLLIEIN RFFPDALVLP L

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Macromolecule #15: PsaK

MacromoleculeName: PsaK / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 8.106365 KDa
SequenceString:
YIGSSTNLIM VASTTLMLFA GRFGLAPSAN RKSTAGLKLV DRDSGLQTGD PAGFTATDTL ACGAMGHVIG VGIVLGLKAT A

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Macromolecule #16: PSI subunit V

MacromoleculeName: PSI subunit V / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 16.692316 KDa
SequenceString:
QVIEPLNGDP FIGGLETPVT SSPLIAWYLS NLPAYRTAVA PLLRGVEIGL AHGYLLVGPF VLAGPLRNSA VRGEAGSLAA AGLVAILTM CLTIYGIASF KEGEASKAPS LTLTGRQKAA DKLQTAEGWA GFTGGFFFGG LSGVAWAYIL LYVLNLPYPV K

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Macromolecule #17: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 3.179751 KDa
SequenceString:
SISDSQIIVA LVSAFITGIL ALRLGKSLYQ

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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 / Chlorophyll a

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Macromolecule #19: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 19 / Number of copies: 141 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #20: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 20 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

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Macromolecule #21: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 21 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #22: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 22 / Number of copies: 26 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #23: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 23 / Number of copies: 7 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #24: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 24 / Number of copies: 4 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #25: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 25 / Number of copies: 6 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #26: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 26 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #27: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 27 / Number of copies: 14 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

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Macromolecule #28: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 28 / Number of copies: 10 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / Lutein

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Macromolecule #29: water

MacromoleculeName: water / type: ligand / ID: 29 / Number of copies: 45 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5l8r

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114608

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