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- EMDB-48266: Dunaliella tertiolecta PSI-LHCI supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-48266
TitleDunaliella tertiolecta PSI-LHCI supercomplex
Map dataGlobal EM map
Sample
  • Complex: Dunaliella tertiolecta PSI-LHCI supercomplex
    • Protein or peptide: x 18 types
  • Ligand: x 15 types
Keywordsiron homeostasis / membrane protein / photosystem I / Dunaliella / green alga / PSI-LHCI supercomplex / TIDI / thylakoid iron-deficiency induced protein / photosynthetic apparatus / photosynthesis / eukaryotes
Biological speciesDunaliella tertiolecta (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsLiu HW / Khera R / Iwai M / Merchant SS
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020627 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: A distinct LHCI arrangement is recruited to photosystem I in Fe-starved green algae.
Authors: Helen W Liu / Radhika Khera / Patricia Grob / Sean D Gallaher / Samuel O Purvine / Carrie D Nicora / Mary S Lipton / Krishna K Niyogi / Eva Nogales / Masakazu Iwai / Sabeeha S Merchant /
Abstract: Iron (Fe) availability limits photosynthesis at a global scale where Fe-rich photosystem (PS) I abundance is drastically reduced in Fe-poor environments. We used single-particle cryoelectron ...Iron (Fe) availability limits photosynthesis at a global scale where Fe-rich photosystem (PS) I abundance is drastically reduced in Fe-poor environments. We used single-particle cryoelectron microscopy to reveal a unique Fe starvation-dependent arrangement of light-harvesting chlorophyll (LHC) proteins where Fe starvation-induced TIDI1 is found in an additional tetramer of LHC proteins associated with PSI in and . These cosmopolitan green algae are resilient to poor Fe nutrition. TIDI1 is a distinct LHC protein that co-occurs in diverse algae with flavodoxin (an Fe-independent replacement for the Fe-containing ferredoxin). The antenna expansion in eukaryotic algae we describe here is reminiscent of the iron-starvation induced (encoding) antenna ring in cyanobacteria, which typically co-occurs with , encoding flavodoxin. Our work showcases the convergent strategies that evolved after the Great Oxidation Event to maintain PSI capacity.
History
DepositionDec 11, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48266.png

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Map

FileDownload / File: emd_48266.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal EM map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 480 pix.
= 504. Å		1.05 Å/pix.
x 480 pix.
= 504. Å		1.05 Å/pix.
x 480 pix.
= 504. Å

Surface

Projections

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0172
Minimum - Maximum-0.019219564 - 0.090866774
Average (Standard dev.)0.0000012478396 (±0.0017933687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 503.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48266_msk_1.map
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Half map: Half map 1

Fileemd_48266_half_map_1.map
AnnotationHalf map 1
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Half map: Half map 2

Fileemd_48266_half_map_2.map
AnnotationHalf map 2
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Sample components

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Entire : Dunaliella tertiolecta PSI-LHCI supercomplex

EntireName: Dunaliella tertiolecta PSI-LHCI supercomplex
Components
  • Complex: Dunaliella tertiolecta PSI-LHCI supercomplex
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: LHCA3
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: LHCA9
    • 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
    • Protein or peptide: PSAF1
    • Protein or peptide: PSAG1
    • Protein or peptide: PSAH1
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: PSI-K
    • Protein or peptide: PSAL1
    • Protein or peptide: LHCA2
  • 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: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium

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Supramolecule #1: Dunaliella tertiolecta PSI-LHCI supercomplex

SupramoleculeName: Dunaliella tertiolecta PSI-LHCI supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Dunaliella tertiolecta (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: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 24.763281 KDa
SequenceString: MQVMQRTFGA SPVAKQAVNR SVVRPSIRVQ AQRAGNFAPG SEPKEYLNDL PGNFNFDPLE LGKEKGTLQR YREAELIHCR WAMLGAAGC LAVEVLGLGN WYDAPLWAVT GDKPTWFGIE VPFDIATILG VEVVAMAVAE GLRNDNQDME KRLYPGGAFD P LGFSKDPK ...String:
MQVMQRTFGA SPVAKQAVNR SVVRPSIRVQ AQRAGNFAPG SEPKEYLNDL PGNFNFDPLE LGKEKGTLQR YREAELIHCR WAMLGAAGC LAVEVLGLGN WYDAPLWAVT GDKPTWFGIE VPFDIATILG VEVVAMAVAE GLRNDNQDME KRLYPGGAFD P LGFSKDPK SFEDKKLKEL KNGRLAMVAC LGFAGQHAAT GKPILEALGD HLSSPFFNNF ATNGVSVPGV

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Macromolecule #2: LHCA3

MacromoleculeName: LHCA3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 30.707969 KDa
SequenceString: MASLFAKTQA LQGLTTKAPK SLRRQVVVRA EGEQQPPAPA AEAKQTSVAK VDRSKDVLYV GSDAAALKYL DGTLPGDYGF DPLGLLDPT VSNGQGAGGF VNPRWLQYSE VIHARWAMLG AAGCIAPEIL GKAGVIPAET AVDWFRTGVI PPAGVYKDFW A DPFTLFFI ...String:
MASLFAKTQA LQGLTTKAPK SLRRQVVVRA EGEQQPPAPA AEAKQTSVAK VDRSKDVLYV GSDAAALKYL DGTLPGDYGF DPLGLLDPT VSNGQGAGGF VNPRWLQYSE VIHARWAMLG AAGCIAPEIL GKAGVIPAET AVDWFRTGVI PPAGVYKDFW A DPFTLFFI EVVAIQFAEL KRLQDYKNPG SQSRQYFLGL EGLFKGSDNP AYPGGPFFNF ANFGKTEAEM KKLKLNEIKN GR LAMLAMF GYGAQAVITG DGPFDNLLAH LADPTGANLI TNLGGKFGQ

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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: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 27.611418 KDa
SequenceString: MSMLLNKSVS LQTSAKASQA ARSVAPRSVA SRRNVAARAG ADRPLWSPGS QPPAWLDGSL AGDYGFDPLH LSEEPEMRKW MVQAELVHA RWAMLGVAGI LFTSIAAKNG APFPDWYDAG KEAIKTSPAP LGSLIFTELL LFGWVETKRL YDLRNPGSQG D GSFLGITD ...String:
MSMLLNKSVS LQTSAKASQA ARSVAPRSVA SRRNVAARAG ADRPLWSPGS QPPAWLDGSL AGDYGFDPLH LSEEPEMRKW MVQAELVHA RWAMLGVAGI LFTSIAAKNG APFPDWYDAG KEAIKTSPAP LGSLIFTELL LFGWVETKRL YDLRNPGSQG D GSFLGITD GLKGKENGYP GGLFDPMGMS KNEASFKEAK VKEIKNGRLA MLAFVGFIAQ HHATHKSPID NLVDHVADPF HV TFATNGV SVPHFTEF

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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: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 27.475346 KDa
SequenceString: MQVMQKQCMR ASGVKAPLSR RSVTVKANMN GNWLPGSQTP AHLKDLKMAG NFGFDPLNLG AEPEALRWYQ QAELVHSRTA MMAVAGILI PGLFTKLGAL NVPQWYEAGK VYIEGEGAIP FGTLLMSTLF SYAFVEGKRW QDFRNPGSQA EPGTFFGLEG M FKGTDNGY ...String:
MQVMQKQCMR ASGVKAPLSR RSVTVKANMN GNWLPGSQTP AHLKDLKMAG NFGFDPLNLG AEPEALRWYQ QAELVHSRTA MMAVAGILI PGLFTKLGAL NVPQWYEAGK VYIEGEGAIP FGTLLMSTLF SYAFVEGKRW QDFRNPGSQA EPGTFFGLEG M FKGTDNGY PGGIFDPLGY SKTSPEKLDE LKLKEIKNGR LAMVAFLGFA GQYSATGKGP IDNLADHLAD PWHNTFAENG VS VPGLSAV EQAAASL

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Macromolecule #5: LHCA9

MacromoleculeName: LHCA9 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 24.23701 KDa
SequenceString: MAALTSKMST KLTTSGVRPA KPTRASRMVM KASNNRPLWL PDVIPPPHLN GTLPGDSGFD PLGLGLNEER LKWYVEAEKT NGRWAMMAV TGILGQELLG VPAKWYEAGA AEYDLPVQAQ VPILFLVMGF LETKRFQGFR ETGTSGFINS FPFDPVGLNS P KHAVNEVK ...String:
MAALTSKMST KLTTSGVRPA KPTRASRMVM KASNNRPLWL PDVIPPPHLN GTLPGDSGFD PLGLGLNEER LKWYVEAEKT NGRWAMMAV TGILGQELLG VPAKWYEAGA AEYDLPVQAQ VPILFLVMGF LETKRFQGFR ETGTSGFINS FPFDPVGLNS P KHAVNEVK NGRLAMVAFI GFAMQALVSR TQPIEGLQKH LADPFGKNIT YFLTHTPEVI AGTA

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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: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 83.109773 KDa
SequenceString: MTISSPEREA KKVKIAVDRN PVETNFEKWA KPGHFSRALA KGPNTTTWIW NLHADAHDFD NHTSDLEEIS RKVFSAHFGQ LGIILIWLS GMYFHGARFS NYEGWLSDPT HIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELQL Y STAIGGLV ...String:
MTISSPEREA KKVKIAVDRN PVETNFEKWA KPGHFSRALA KGPNTTTWIW NLHADAHDFD NHTSDLEEIS RKVFSAHFGQ LGIILIWLS GMYFHGARFS NYEGWLSDPT HIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELQL Y STAIGGLV LAAACFFAGW FHYHKAAPKL EWFQNVESML NHHLAGLLGL GSLAWAGHQI HVSLPVNKLL DAGVDPKEIP LP HEFLLNQ SIIADLYPSF SKGLAPFFTL NWAEYSDFLT FKGGLNPVTG GLWLSDTAHH HLAIAVLFLV AGHQYRTNWG IGH SIKDIL ESHKGPFTGN GHAGLYEILT TSWHAQLAIN LALFGSLSII VAHHMYAMPP YPYLATDYGT QLSLFTHHMW IGGF CVVGA GAHAAIFMVR DYDPTNNYNN LLDRVIRHRD AIISHLNWVS IFLGFHSFGL YIHNDTMSAL GRPQDMFSDT AIQLQ PVFA QWIQNTHFTA PQLTAPNALA ATSLTWGGDV VAVGGKVAMM PIALGTSDFL VHHIHAFTIH VTVLILLKGV LFARSS RLI PDKANLGFRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSL SIVIFHFSWK MQSDVWGTVT DSGVSHITGG NFAQSAN TI NGWLRDFLWA QSSQVIQSYG SALSAYGLMF LGAHFVWAFS LMFLFSGRGY WQELIESIVW AHNKLRVAPS IQPRALSI T QGRAVGVAHY LLGGIATTWS FFLARIIAVG

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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: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 81.895672 KDa
SequenceString: MATKLFPKFS QGLAQDPSTR RIWYGLATAH DFESHDGMTE ENLYQKIFAS HFGQLAIIFL WTSGNLFHVA WQGNFEQWVT DPIHVRPIA HAIWDPHFGQ PAVEAFTRGG ASGPVNIATS GVYQWWYTIG LRSNQELYVS SVFLALVSAV FLFAGWLHLQ P NFQPSLSW ...String:
MATKLFPKFS QGLAQDPSTR RIWYGLATAH DFESHDGMTE ENLYQKIFAS HFGQLAIIFL WTSGNLFHVA WQGNFEQWVT DPIHVRPIA HAIWDPHFGQ PAVEAFTRGG ASGPVNIATS GVYQWWYTIG LRSNQELYVS SVFLALVSAV FLFAGWLHLQ P NFQPSLSW FKDAESRLNH HLSGLFGVSS LAWTGHLVHV AIPESRGQHV GWDNFLSVLP HPQGLTPFWS GNWAAYAQNP DT ASHAFGT ADGSGTAILT FLGGFHPQTQ SLWLSDMAHH HLAIAVLFIV AGHMYRTNFG IGHRLEAILE AHTPPAGGLG AGH KGLFHT VNNSLHFQLG LALASVGTIT SLVAQHMYSL PPYAYLAVDF TTQASLYTHH QYIAGFIMCG AFAHGAIFFI RDYD PEQNK GNVLARVLDH KEAIISHLSW VSLFLGFHTL GLYVHNDVVQ AFGTPEKQIL IEPVFAQWIQ AAQGKSLYGF DLLLA SSSS SAYSAGQSLW LPGWLEAINN NQNSLFLTIG PGDFLVHHAI ALGLHTTTLI LVKGALDARG SKLMPDKKDF GYSFPC DGP GRGGTCDISA YDAFYLAVFW MLNTIGWVTF YWHWKHLTLW QGNVSQFDES STYLMGWLRD YLWLNSSQLI NGYNPFG MN SLSVWAWTFL FGHLVYATGF MFLISWRGYW QELIETLVWA HEKTPLANLV YWKDKPVALS IVQARLVGLA HFSVGYIF T YAAFLIASTS GRFG

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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: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 8.848286 KDa
SequenceString:
MAHVVKIYDT CIGCTQCVRA CPLDVLEMVP WDGCKAAQMA SSPRTEDCVG CKRCETACPT DFLSVRVYLG NESTRSLGLA Y

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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: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 21.171371 KDa
SequenceString: MQALRSTSAA SRASCRPSYE GRRAAFVVRA EAAPAAGAPP AAPKKKAPPP PWKQPELDPD TPSPIFGGST GGLLRKAQVE EFYVTTWES PKEQIFEMPT GGAAIMRKGP NLLKFARKEQ CLALTTQLRT KFKMTPCFYR VYADGKVEYL HPKDGVYPEK V NAGRVGVN ...String:
MQALRSTSAA SRASCRPSYE GRRAAFVVRA EAAPAAGAPP AAPKKKAPPP PWKQPELDPD TPSPIFGGST GGLLRKAQVE EFYVTTWES PKEQIFEMPT GGAAIMRKGP NLLKFARKEQ CLALTTQLRT KFKMTPCFYR VYADGKVEYL HPKDGVYPEK V NAGRVGVN QNMRSIGENV DPIKVKFTGS QPFTI

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Macromolecule #10: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 12.209986 KDa
SequenceString:
MATLSASRVS CRPSFAAKPQ RTCRLMVRAQ DAAPPAEPKA APKKKEVGPK RGSLVKVLRP ESYWYNQVGK VVSVDQSGIR YPVVVRFEN QNYAGVSTNN YALDEVTDPP AK

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Macromolecule #11: PSAF1

MacromoleculeName: PSAF1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 24.645479 KDa
SequenceString: MASLAQMNLR SAPLARAPAA RPVARRSAIV AKAQEQNMGA VACATALALT MGLTADVQPA SADVAGLTPC SESKAYNKLE RKELKTLEK RLKKYEPGSA PYLALQATKE RTQNRFKNYA KAGLLCGNDG LPHLISDPGL ALRFNHAGEV FIPTFGFLYV A GYIGHVGR ...String:
MASLAQMNLR SAPLARAPAA RPVARRSAIV AKAQEQNMGA VACATALALT MGLTADVQPA SADVAGLTPC SESKAYNKLE RKELKTLEK RLKKYEPGSA PYLALQATKE RTQNRFKNYA KAGLLCGNDG LPHLISDPGL ALRFNHAGEV FIPTFGFLYV A GYIGHVGR QYIIKSKEDA KPTDKEIILD VPLALQLAFQ GWAWPLAAIQ ELRNGSLLEK DENITVSPR

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Macromolecule #12: PSAG1

MacromoleculeName: PSAG1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 15.154409 KDa
SequenceString:
MALSSKASIQ QFSRQASQSR AVARPASSRQ PLKTRAMIEA PVAIGGSTVA LLGLGRFVFL PYQRRRTDME VGPGKLGPKT TGDTFFDRL QKPASFVETK SKDPSGFGII DVLGWGALGH VFGYFLLACS SLQDAGIDAF PR

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Macromolecule #13: PSAH1

MacromoleculeName: PSAH1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 14.549641 KDa
SequenceString:
MALIAKTGAQ TLASRRPAAK ATAPVRRSVK VCAKYGEQSK YFDLQDLENT TGAWDMYGVD EKKRYPGMQE EFFQRATDAV SRRESLNGF VALSGIAAIA LFGLKGASTL ELPITKGPRD GKTENGKGGI LRSRV

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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: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 11.159255 KDa
SequenceString:
MLAQKNVVAK PCVKAAKPVA RPVKPVAMQK KQQAAAKVAS AGIVGIASAA IAAAPVEAAN IVANVASATE GYPFVPPAWA PSLFVPLTG LVLPAIGMAW AFTYIQKEKQ

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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: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 4.614362 KDa
SequenceString:
MKDFTTYLST APVVGLGWAI FTSGLLIEIN RFFPDPLVFS F

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Macromolecule #16: PSI-K

MacromoleculeName: PSI-K / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 12.429592 KDa
SequenceString:
MALSSRVSAA PKALQASRVS AAPKVQQPRS RKAMVCKADA GFIGSPTNLI MVASTGACLF ASRFGLAPSV RKVAQPLKLA DREVIQTTG DPAGFTATDV LAMGAAGHAI GVGIVLGLKG IGQL

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Macromolecule #17: PSAL1

MacromoleculeName: PSAL1 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 20.694154 KDa
SequenceString: MMMLQKNAAL QKSAVRSASK PAAFSRVPRG LTIRAANEDK RAQVIQPLNG DPFVGMLETP VTSAPIVANY LSNLPAYRTG VAPNLRGVE IGLAHGFLLA GPFIKLGPLR NVPGAAEVVG CMSAAGLVLI LALCLSLYGN AAFQSTPSMG KKTLSGRPLA Q DPLMSSEG ...String:
MMMLQKNAAL QKSAVRSASK PAAFSRVPRG LTIRAANEDK RAQVIQPLNG DPFVGMLETP VTSAPIVANY LSNLPAYRTG VAPNLRGVE IGLAHGFLLA GPFIKLGPLR NVPGAAEVVG CMSAAGLVLI LALCLSLYGN AAFQSTPSMG KKTLSGRPLA Q DPLMSSEG WAKFAGGFTV GGLSGVAWAY VLTQVLPYYS

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Macromolecule #18: LHCA2

MacromoleculeName: LHCA2 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella tertiolecta (plant)
Molecular weightTheoretical: 28.445744 KDa
SequenceString: MSALLMNKSV ASGASLKAST RSVGRITPAP ARRSVAAQAA REMWYPGATP PAHLDGSMLG DYGFDPLRLG TNPDRMKWFR EAELTNGRW AMAAVVGILF TDLVGLPKWW EAGAQTYPID NQTLAIIEIA VFAFLEAKRY EGYKKTGGTG FAFFFPFDPM G MRSPEKEL ...String:
MSALLMNKSV ASGASLKAST RSVGRITPAP ARRSVAAQAA REMWYPGATP PAHLDGSMLG DYGFDPLRLG TNPDRMKWFR EAELTNGRW AMAAVVGILF TDLVGLPKWW EAGAQTYPID NQTLAIIEIA VFAFLEAKRY EGYKKTGGTG FAFFFPFDPM G MRSPEKEL KELKNGRLAM LAFLGFASTA AVNGQGPIES LQTHLADPAH NNIFTSSVGK ESCVFVAVLS VLPIIIEATK TL GKGKESV PLFPWNEEWE KVAK

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Macromolecule #19: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 19 / Number of copies: 13 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #20: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 20 / Number of copies: 167 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #21: (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: 21 / Number of copies: 7 / 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

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Macromolecule #22: (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: 22 / Number of copies: 6 / 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

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Macromolecule #23: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 23 / Number of copies: 29 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #24: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 24 / Number of copies: 16 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #25: 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: 25 / Number of copies: 6 / 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 #26: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 26 / Number of copies: 6 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #27: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 27 / Number of copies: 5 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #28: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 28 / Number of copies: 2 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #29: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 29 / Number of copies: 6 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMU:
DODECYL-ALPHA-D-MALTOSIDE / detergent*YM

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Macromolecule #30: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 30 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #31: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 31 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #32: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 32 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #33: trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S...

MacromoleculeName: trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium
type: ligand / ID: 33 / Number of copies: 1 / Formula: LMK
Molecular weightTheoretical: 773.241 Da
Chemical component information

ChemComp-LMK:
trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium

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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: 6.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5044 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 81000
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: 1330556
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6sl5

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 126839
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 3 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6sl5


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9mh1:
Dunaliella tertiolecta PSI-LHCI supercomplex

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