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- EMDB-35018: Cryo-EM structure of PpPSI-L -

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Basic information

Entry
Database: EMDB / ID: EMD-35018
TitleCryo-EM structure of PpPSI-L
Map dataCombining three focused refinement maps, smPSI, LHCII and outer LHCI plus Lhcb9
Sample
  • Complex: photosystem I from Physcomitrium patens
    • Protein or peptide: x 20 types
  • Ligand: x 13 types
KeywordsLhcb9 / PSI / PHOTOSYNTHESIS
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 / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaO / 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 PsaO / 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
Chlorophyll a-b binding protein, chloroplastic / Uncharacterized protein / Photosystem I reaction center subunit III / Photosystem I reaction center subunit V, chloroplastic / Photosystem I subunit O / Photosystem I reaction center subunit VI, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSI-K ...Chlorophyll a-b binding protein, chloroplastic / Uncharacterized protein / Photosystem I reaction center subunit III / Photosystem I reaction center subunit V, chloroplastic / Photosystem I subunit O / Photosystem I reaction center subunit VI, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSI-K / PSI subunit V / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / 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: 2.87 Å
AuthorsLi M / Pan XW / Sun HY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Plants / Year: 2023
Title: Structural insights into the assembly and energy transfer of the Lhcb9-dependent photosystem I from moss Physcomitrium patens.
Authors: Haiyu Sun / Hui Shang / Xiaowei Pan / Mei Li /
Abstract: In plants and green algae, light-harvesting complexes I and II (LHCI and LHCII) constitute the antennae of photosystem I (PSI), thus effectively increasing the cross-section of the PSI core. The moss ...In plants and green algae, light-harvesting complexes I and II (LHCI and LHCII) constitute the antennae of photosystem I (PSI), thus effectively increasing the cross-section of the PSI core. The moss Physcomitrium patens (P. patens) represents a well-studied primary land-dwelling photosynthetic autotroph branching from the common ancestor of green algae and land plants at the early stage of evolution. P. patens possesses at least three types of PSI with different antenna sizes. The largest PSI form (PpPSI-L) exhibits a unique organization found neither in flowering plants nor in algae. Its formation is mediated by the P. patens-specific LHC protein, Lhcb9. While previous studies have revealed the overall architecture of PpPSI-L, its assembly details and the relationship between different PpPSI types remain unclear. Here we report the high-resolution structure of PpPSI-L. We identified 14 PSI core subunits, one Lhcb9, one phosphorylated LHCII trimer and eight LHCI monomers arranged as two belts. Our structural analysis established the essential role of Lhcb9 and the phosphorylated LHCII in stabilizing the complex. In addition, our results suggest that PpPSI switches between different types, which share identical modules. This feature may contribute to the dynamic adjustment of the light-harvesting capability of PSI under different light conditions.
History
DepositionDec 21, 2022-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35018.png

Downloads & links

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Map

FileDownload / File: emd_35018.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombining three focused refinement maps, smPSI, LHCII and outer LHCI plus Lhcb9
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.0188
Minimum - Maximum-0.03939079 - 0.2498145
Average (Standard dev.)0.0005223833 (±0.0049055596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : photosystem I from Physcomitrium patens

EntireName: photosystem I from Physcomitrium patens
Components
  • Complex: photosystem I from Physcomitrium patens
    • 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: Chlorophyll a-b binding protein, chloroplastic
    • 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, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit IV, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit V, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit VI, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I subunit X
    • Protein or peptide: PSI subunit V
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Photosystem I subunit O
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: water

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Supramolecule #1: photosystem I from Physcomitrium patens

SupramoleculeName: photosystem I from Physcomitrium patens / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Physcomitrium patens (plant)

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Macromolecule #1: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 28.403947 KDa
SequenceString: MAAATAMHST TLAGQSLLKP VNELSRKVGS SEARVTMRR(TPO) VKSTSDSIWY GADRPKYLGP FSGETPSYLT GEFAGD YGW DTAGLSSDPE TFARNRELEV IHARWAMLGA LGCLTPELLA KSGVKFGEAV WFKAGAQIFS EGGLDYLGNP SLVHAQS IL AIWASQVVLM ...String:
MAAATAMHST TLAGQSLLKP VNELSRKVGS SEARVTMRR(TPO) VKSTSDSIWY GADRPKYLGP FSGETPSYLT GEFAGD YGW DTAGLSSDPE TFARNRELEV IHARWAMLGA LGCLTPELLA KSGVKFGEAV WFKAGAQIFS EGGLDYLGNP SLVHAQS IL AIWASQVVLM GAVEGYRVAG GPLGEITDPI YPGGSFDPLG LADDPDTFAE LKVKEIKNGR LAMFSMFGFF VQAIVTGK G PLENLNDHLA DPVANNAWAY ATNFVPGN

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #2: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 25.931562 KDa
SequenceString: MASAMATAAA AQVSRVVTGV ATAQKSSFFA GSSSVSLLGC SNGSRVCMAE WLPGNPRPSY LDGSAPGDFG FDPLGLGEVP ENLERFKES ELIHARWAML AVPGVLIPEA LGYGNWVSAQ KWAATPGGQA TYLGNPVPWG NLPVILAIEF LAIAFAESQR N GEPDPEKR ...String:
MASAMATAAA AQVSRVVTGV ATAQKSSFFA GSSSVSLLGC SNGSRVCMAE WLPGNPRPSY LDGSAPGDFG FDPLGLGEVP ENLERFKES ELIHARWAML AVPGVLIPEA LGYGNWVSAQ KWAATPGGQA TYLGNPVPWG NLPVILAIEF LAIAFAESQR N GEPDPEKR KYPGGAFDPL GFSKGANLEE LKLKEIKNGR LALVAFLGFA VQAIAYPGTG PLENLKTHLA DPWHNTIAHV II PRSVL

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 29.036998 KDa
SequenceString: MASAVCASSN VAVVAGPSTS KVVNSAGPAR TSLLAGRVRR VTRIAASPQA EAPVPAQPSL PNNDRPLWFP GSQPPEWLDG SLPGDFGFD PLGLGSDPEL LKWFVQAELV HCRWAMLGAA GIFIPEALTK AGILNTPSWT VAGDQQYFTD ATTLFVIEII L FAWAEGRR ...String:
MASAVCASSN VAVVAGPSTS KVVNSAGPAR TSLLAGRVRR VTRIAASPQA EAPVPAQPSL PNNDRPLWFP GSQPPEWLDG SLPGDFGFD PLGLGSDPEL LKWFVQAELV HCRWAMLGAA GIFIPEALTK AGILNTPSWT VAGDQQYFTD ATTLFVIEII L FAWAEGRR WADIINPGCV NVDPVFPNNK LTGTDVGYPG GLWFDPLGWG QTGDAAKLKD LRTREIKNGR LAMLAVLGAV VQ ANYTHTG PIDNLLAHLA DPGHNTIFAL SNLVGK

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 34.673801 KDa
SequenceString: MRTFNLTHLS FPSIGVFLSP LSCIESRVAG VQVCSAMATR VAAGCAVSSF AAKVSPSAFE GKRSAVFGTN LPSTFYVVSK KASSSAKTV VTKAQLSPTG GSKRSLIFAS KQSLSYLDGT LPGDYGFDPL GLMDPEGAGG FIDPQWLPYA EIINGRFAML G AAGAIAPE ...String:
MRTFNLTHLS FPSIGVFLSP LSCIESRVAG VQVCSAMATR VAAGCAVSSF AAKVSPSAFE GKRSAVFGTN LPSTFYVVSK KASSSAKTV VTKAQLSPTG GSKRSLIFAS KQSLSYLDGT LPGDYGFDPL GLMDPEGAGG FIDPQWLPYA EIINGRFAML G AAGAIAPE VLGRIGLIPQ ETAIPWFQSG VIPPVGNYSY WADPYTLFVL EMALMGFAEH RRAQDYYKPG SMGKQYFLGL EK FLGGSGN PAYPGGPIFN FLGFGKNEKE LQELKVKEVK NGRLAMMAVL GYFTQAIFTG VGPFQNLLDH LADPVHNNVL TNL KIH

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 28.818881 KDa
SequenceString: MASAVCASSS VAAVAAPSTS KVVSNVGSAR TSFLAGRALR TTQVCGAAKG DMTVSATLTG NKTDRPLWLP GSEAPKWLDG SLPGDYGFD PLDLAAEPGR LNWMVQAELV HCRWAMLGAA GIFIPELLTK IGILNTPSWY KAGDATYFAD QGTLFIVELL L MAWAESRR ...String:
MASAVCASSS VAAVAAPSTS KVVSNVGSAR TSFLAGRALR TTQVCGAAKG DMTVSATLTG NKTDRPLWLP GSEAPKWLDG SLPGDYGFD PLDLAAEPGR LNWMVQAELV HCRWAMLGAA GIFIPELLTK IGILNTPSWY KAGDATYFAD QGTLFIVELL L MAWAESRR WADIARPGSV NTDPIFPNNK LTGTDVGYPG GLWFDPLGWG SGSEDKLKEI RTKEVKNGRL AMLAVLGAFV QA NVTHVGP IDNLFAHLAD PYHTTILQSL FGK

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #6: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 83.226508 KDa
SequenceString: MTIRSPEPEV KIMVEKDPVK TSFEKWAKPG HFSRTLAKGP NTTTWIWNLH ADAHDFDSHT NDLEEISRKV FSAHFGQLAV IFIWLSGMY FHGARFSNYE AWLSDPTHIK PSAQVVWPIV GQKILNGDVG GGFQGIQITS GFFQLWRASG ITSELQLYTT A IGGLIFAA ...String:
MTIRSPEPEV KIMVEKDPVK TSFEKWAKPG HFSRTLAKGP NTTTWIWNLH ADAHDFDSHT NDLEEISRKV FSAHFGQLAV IFIWLSGMY FHGARFSNYE AWLSDPTHIK PSAQVVWPIV GQKILNGDVG GGFQGIQITS GFFQLWRASG ITSELQLYTT A IGGLIFAA LMLFAGWFHY HKAAPKLAWF QNVESMLNHH LAGLLGLGSL AWAGHQVHVS LPINRLLDAG VDPKEIPLPH EF ILNRDLL AQLYPSFSKG LTPFFTLNWS EYSDFLTFRG GLNPVTGGLW LTDTAHHHLA IAVLFLVAGH MYRTNFGIGH SMK EILEAH KGPFTGEGHK GLYEILTTSW HAQLAINLAM LGSLTIIVAH HMYAMPPYPY LATDYATQLS LFTHHMWIGG FLVV GAAAH AAIFMVRDYD PTTQYNNLLD RVLRHRDAII SHLNWVCIFL GFHSFGLYIH NDTMSALGRP QDMFSDTAIQ LQPVF AQWI QNTHALAPSL TAPNATASTS LTWGGGDLVA VGGKVALLPI PLGTADFLVH HIHAFTIHVT VLILLKGVLF ARSSRL IPD KANLGFRFPC DGPGRGGTCQ VSAWDHVFLG LFWMYNAISV VIFHFSWKMQ SDVWGSISDQ GVVTHITGGN FAQSSIT IN GWLRDFLWAQ ASQVIQSYGS SLSAYGLLFL GAHFVWAFSL MFLFSGRGYW QELIESIVWA HNKLKVAPAI QPRALSIV Q GRAVGVAHYL LGGIATTWAF FLARIISVG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #7: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 82.44775 KDa
SequenceString: MASRFPKFSR GLSQDPTTRR IWFGIATAHD FESHDDMTEE RLYQKIFASH FGQLAIIFLW TSGNLFHVAW QGNFEAWGQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA SGPVNIAYSG VYQWWYTIGL RTNQDLYGGS IFLLFVSALF LIAGWLHLQP K WKPSVSWF ...String:
MASRFPKFSR GLSQDPTTRR IWFGIATAHD FESHDDMTEE RLYQKIFASH FGQLAIIFLW TSGNLFHVAW QGNFEAWGQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA SGPVNIAYSG VYQWWYTIGL RTNQDLYGGS IFLLFVSALF LIAGWLHLQP K WKPSVSWF KNAESRLNHH LSGLFGVSSL AWTGHLVHVA IPESRGEHVR WNNLLTALPH PQGLGPFFAG QWNVYAQNPD SN SHLFGTS EGAGTAILTF LGGFHPQTQS LWLTDMAHHH LAIAVIFIIA GHMYRTNFGI GHSMKEILEA HTPPGGRLGR GHK GLYDTI NNSLHFQLGL ALASLGVITS LVAQHMYSLP PYAFLAQDFT TQAALYTHHQ YIAGFIMTGA FAHGAIFFIR DYNP EQNKD NVLARMLEHK EAIISHLSWA SLFLGFHTLG LYVHNDVMLA FGTPEKQILI EPVFAQWIQS AHGKALYGFD VLLSS ADSP AFNAGQTLWL PGWLDAINNN SNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKEFG YSFPCD GPG RGGTCDISAW DAFYLAVFWM LNTIGWVTFY WHWKHITLWQ GNVAQFNESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LSVWAWMFLF GHLVWATGFM FLISWRGYWQ ELIETLAWAH ERTPLANLVR WKDKPVALSI VQARLVGLAH FSVGYIFT Y AAFLIASTSG KFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #8: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 8.781153 KDa
SequenceString:
MAHSVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKASQIA SAPRTEDCVG CKRCESACPT DFLSVRVYLG AETTRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #9: Photosystem I reaction center subunit II, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit II, chloroplastic
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 22.183309 KDa
SequenceString: MAALAATSAA SIALAIPQAS SGASTSRSVN LRLSGIQGQK LAAVCNGSRV VAKAAGAAPD ATAEAPKGFT PPTLNADTPA PIFGGSTGG LLRKAQVEEF YVITWESPKE QIFEMPTGGA AIMRSGPNLL KLARKEQCLA LGARLRTKFK IQYQFYRVFP N GEVQYLHP ...String:
MAALAATSAA SIALAIPQAS SGASTSRSVN LRLSGIQGQK LAAVCNGSRV VAKAAGAAPD ATAEAPKGFT PPTLNADTPA PIFGGSTGG LLRKAQVEEF YVITWESPKE QIFEMPTGGA AIMRSGPNLL KLARKEQCLA LGARLRTKFK IQYQFYRVFP N GEVQYLHP KDGVYPEKVN AGRTAVGVNN RSIGQNANPA ELKFAHKQAY DL

UniProtKB: Photosystem I reaction center subunit II, chloroplastic

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Macromolecule #10: Photosystem I reaction center subunit IV, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit IV, chloroplastic
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 13.919796 KDa
SequenceString:
MSTAVSSFVG VASNAVAATG AATSSMFSTK VPCRPLSMVV SGRNSARLVV RAEEAAAAPP AKKEAQPVIG PKRGSIVKVL RRESYWFND TGKVVAVDQA PGVRYPVVVR FDKVNYAGVS TNNYSPDELE QSA

UniProtKB: Uncharacterized protein

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Macromolecule #11: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 26.112318 KDa
SequenceString: MASVTMAAIA PAGLVAPLCK DVSSRTAISG ARASVFVKSS KARIVCSTSA DETSTVAETA GKFATALALA AVVGSSDFVV PDARADVAG LTPCKESKGF AKRQKQEIKK LEGRLKLYAP DSAPALAINA TIEKTKRRFE FYGNQGLLCG TDGLPHLIVD G DQAHLGEF ...String:
MASVTMAAIA PAGLVAPLCK DVSSRTAISG ARASVFVKSS KARIVCSTSA DETSTVAETA GKFATALALA AVVGSSDFVV PDARADVAG LTPCKESKGF AKRQKQEIKK LEGRLKLYAP DSAPALAINA TIEKTKRRFE FYGNQGLLCG TDGLPHLIVD G DQAHLGEF VYPGLVFLYI AGWIGWVGRA YLIDVRTSKK PTEKEIIIDV PLALRIMSKG LTWPVAAIGE LRSGKLVEKS SN ITVSPR

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #12: Photosystem I reaction center subunit V, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit V, chloroplastic
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 16.231396 KDa
SequenceString:
MASCAASMTG VAASSLSLKA NFSGLRRGTK VDSIAMSRSS SFASKTAIAK SSGKVTCEAN TALTITLSTG ALLFLGRFVF LPFQRDNVS RQGLPVQNGV THFDAGDSRA QEVTSFLKTN DPAGFTIVDV LAWGALGHAV GFFILATINN GYNPQF

UniProtKB: Photosystem I reaction center subunit V, chloroplastic

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Macromolecule #13: Photosystem I reaction center subunit VI, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit VI, chloroplastic
type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 14.506459 KDa
SequenceString:
MAAASATMAV SGLAGSSLAG QKFAIAPAKS VSVRSPSKVG AISAKYGEKS VYFDLGEIDN TTGNWDLYGN DDPNRYNGFQ NKFFETFAG AFTKRGLLLK FLVLGGATTI GYLGSTSSGD LLAIKNGPKQ APIMGPRGRK

UniProtKB: Photosystem I reaction center subunit VI, chloroplastic

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Macromolecule #14: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 4.017787 KDa
SequenceString:
MTASYLPSIF VPLIGLVFPA ITMASLFIYI EQDEII

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #15: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 4.59746 KDa
SequenceString:
MQDVKTYLST APVLATLWFG FLAGLLIEIN RFFPDALVLP L

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #16: Photosystem I subunit X

MacromoleculeName: Photosystem I subunit X / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 13.278444 KDa
SequenceString:
MAAMATTMSV ATVRQFEGLK ATTSSFSKPL PSLALRKTAG KGALGARCDY IGSSTNLIMV ASTTLMLFAG RFGLAPSANR KSTAGLKLV DRDSGLQTGD PAGFTATDTL ACGALGHVIG VGIVLGLKAT AGL

UniProtKB: PSI-K

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Macromolecule #17: PSI subunit V

MacromoleculeName: PSI subunit V / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 23.530299 KDa
SequenceString: MAAAAMTRAG GLLAMERVQR VSKTTGAVSN RTFLGNVRGL RATSAPQALR VKVMAVRAGA EKYQVIEPLN GDPFIGGFET PVTSSPLIA WYLSNLPAYR TAVAPLLRGV EIGLAHGYLL VGPFVLAGPL RNSAVRGEAG SLAAAGLVTI LTMCLTIYGI A SFKEGEAS ...String:
MAAAAMTRAG GLLAMERVQR VSKTTGAVSN RTFLGNVRGL RATSAPQALR VKVMAVRAGA EKYQVIEPLN GDPFIGGFET PVTSSPLIA WYLSNLPAYR TAVAPLLRGV EIGLAHGYLL VGPFVLAGPL RNSAVRGEAG SLAAAGLVTI LTMCLTIYGI A SFKEGEAS KAPSLTLTGR QKEADKLQTA EGWASFTGGW FFGGLSGVAW AYFLLYVINL PYPVK

UniProtKB: PSI subunit V

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Macromolecule #18: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 3.412051 KDa
SequenceString:
MTSISDSQII VALVSAFITG ILALRLGKSL YQ

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #19: Photosystem I subunit O

MacromoleculeName: Photosystem I subunit O / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 15.393113 KDa
SequenceString:
MAMTATSMAM PAVAGLGSSS ILARRSPKLQ LTSAFVGGAI KVNKPLCMSR VTCFNRDWLR KDLSVIGFGL IGWLAPSSLP VINGNSLTG LFLGSIGPEL AHFPTGPALT SPFWLWMITW HVGLFIVLTL GQIGFKGRQD GYWN

UniProtKB: Photosystem I subunit O

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Macromolecule #20: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 33.175734 KDa
SequenceString: MASMAIQGVV APAVGAFGSS KCFQKKPSSI SSSSWTCQAV SKGEGTADAP TVSLEGVINA VQQAPSADPA PEALLAESTS NGSTATMTG IAEWYKVYGK SVAPDQDARA PYYGPNRPLW KGPFTKPKDV PEYLKGEYPG DYGCDIFKLA RLPANYARLR T QELMNGRW ...String:
MASMAIQGVV APAVGAFGSS KCFQKKPSSI SSSSWTCQAV SKGEGTADAP TVSLEGVINA VQQAPSADPA PEALLAESTS NGSTATMTG IAEWYKVYGK SVAPDQDARA PYYGPNRPLW KGPFTKPKDV PEYLKGEYPG DYGCDIFKLA RLPANYARLR T QELMNGRW AMLGITGCLT PELINSNSTP GFEPVWFNTG AQIFSDAGID YLGVPGFINA HSLFAVIVVQ ALLMGLAEYA RI KFVPEGA DPFYPGGKTF DPLGFSSDPE ILAELKVKEI KNGRLAMMAM AGLFAQGAVT GVSPLQNLHD WLHL

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #21: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 21 / Number of copies: 49 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

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Macromolecule #22: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 22 / Number of copies: 221 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #23: (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: 23 / Number of copies: 17 / 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

+
Macromolecule #24: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 24 / Number of copies: 11 / Formula: XAT
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-XAT:
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / Violaxanthin

+
Macromolecule #25: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

MacromoleculeName: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
type: ligand / ID: 25 / Number of copies: 4 / Formula: NEX
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-NEX:
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL

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Macromolecule #26: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 26 / Number of copies: 15 / 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 #27: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 27 / Number of copies: 33 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #28: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 28 / Number of copies: 6 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #29: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 29 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

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Macromolecule #30: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 30 / 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 #31: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 31 / Number of copies: 4 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #32: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 32 / 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 #33: water

MacromoleculeName: water / type: ligand / ID: 33 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

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

7ksq


Details: 5ZJI 7D0J
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144586

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