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- EMDB-48262: Dunaliella salina PSI-LHCI-TIDI1 supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-48262
TitleDunaliella salina PSI-LHCI-TIDI1 supercomplex
Map dataGlobal map
Sample
  • Complex: Dunaliella salina PSI-LHCI-TIDI1 supercomplex
    • Protein or peptide: x 20 types
  • Ligand: x 18 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 salina (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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_48262.png

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Map

FileDownload / File: emd_48262.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal map
Projections & slices

Image control

Size
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Others
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)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0128
Minimum - Maximum-0.021735199 - 0.08272493
Average (Standard dev.)0.00030026774 (±0.0016796974)
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_48262_msk_1.map
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Additional map: Composite map with all the local refinements of subunits

Fileemd_48262_additional_1.map
AnnotationComposite map with all the local refinements of subunits
Projections & Slices
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Half map: Half map 1

Fileemd_48262_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_48262_half_map_2.map
AnnotationHalf map 2
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Sample components

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Entire : Dunaliella salina PSI-LHCI-TIDI1 supercomplex

EntireName: Dunaliella salina PSI-LHCI-TIDI1 supercomplex
Components
  • Complex: Dunaliella salina PSI-LHCI-TIDI1 supercomplex
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: LHCA2
    • Protein or peptide: LHCA3
    • Protein or peptide: LHCA7
    • Protein or peptide: LHCA8
    • 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: PSAD1
    • Protein or peptide: PSAE1
    • Protein or peptide: PSAF1
    • Protein or peptide: PSAG1
    • Protein or peptide: PSAH1
    • Protein or peptide: PSAI1
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: PSAK1
    • Protein or peptide: PSAL1
    • Protein or peptide: PSAO1
    • Protein or peptide: TIDI1
  • Ligand: CHLOROPHYLL A
  • Ligand: CHLOROPHYLL B
  • 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-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • 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
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Tripalmitoylglycerol
  • Ligand: water

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Supramolecule #1: Dunaliella salina PSI-LHCI-TIDI1 supercomplex

SupramoleculeName: Dunaliella salina PSI-LHCI-TIDI1 supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14, #18, #15, #19, #16-#17, #20
Source (natural)Organism: Dunaliella salina (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: 2 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 24.682316 KDa
SequenceString: MQVMQKTLGA SPVHKQAVNR SVVRPCVRVH ATRAGNFAPG SEPKDYLEGL PGNYNFDPLE LGKEKGTLQR YREAELIHCR WAMLGAAGC LAVEVLGLGN WYDAPLWAVT GDKPTWFGIE VPFDIATILG VEVVAMAVAE GLRNENQDME KRLYPGGAFD P LGFSKDPK ...String:
MQVMQKTLGA SPVHKQAVNR SVVRPCVRVH ATRAGNFAPG SEPKDYLEGL PGNYNFDPLE LGKEKGTLQR YREAELIHCR WAMLGAAGC LAVEVLGLGN WYDAPLWAVT GDKPTWFGIE VPFDIATILG VEVVAMAVAE GLRNENQDME KRLYPGGAFD P LGFSKDPK SFEDKKLKEL KNGRLAMVAC LGFAGQHAAT GKPILAALGD HLSSPFFNNF ATNGVSVPGL

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Macromolecule #2: LHCA2

MacromoleculeName: LHCA2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 28.730088 KDa
SequenceString: MSALLMNKGI AGASSCALKA GTRSVGRITP APARRNVAAQ AGREMWYPGA TPPPHLDGSM LGDYGFDPLR LGTNPDRLKW FREAELMNG RWAMAAVVGI LFTDLVGLPK WWEAGAQTYP IDNQTLLIIE IAVFSFLESK RYEGYKKTGG TGFAFFFPFD P MGMRSQDK ...String:
MSALLMNKGI AGASSCALKA GTRSVGRITP APARRNVAAQ AGREMWYPGA TPPPHLDGSM LGDYGFDPLR LGTNPDRLKW FREAELMNG RWAMAAVVGI LFTDLVGLPK WWEAGAQTYP IDNQTLLIIE IAVFSFLESK RYEGYKKTGG TGFAFFFPFD P MGMRSQDK ELKELKNGRL AMLAFLGFAS TAAVNGQGPI ESLQTHLADP AHNNIFTSSV GKESCVFVAV LSILPMLIEA NK ALGKGQE SVPLFPWNEE WEKVAK

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Macromolecule #3: LHCA3

MacromoleculeName: LHCA3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 33.94773 KDa
SequenceString: MASLFSKQAA LQGLTAPKSL SRRQVVVRAE GEQQPPPAAP KVAPKAAAPE AKAAAPAAEA KAAPKAAPKA APKAAPKEQT SVAKIDRSK DFLYVGSDAA ALKYLDGTLP GDYGFDPLGL LDPSVSGGKG EGGFVNPRWL QYSEVIHARW AMLGAAGCIA P EILGKAGV ...String:
MASLFSKQAA LQGLTAPKSL SRRQVVVRAE GEQQPPPAAP KVAPKAAAPE AKAAAPAAEA KAAPKAAPKA APKAAPKEQT SVAKIDRSK DFLYVGSDAA ALKYLDGTLP GDYGFDPLGL LDPSVSGGKG EGGFVNPRWL QYSEVIHARW AMLGAAGCIA P EILGKAGV IPAETAVDWF RTGVIPPAGV YKNFWADPFT LFFIEVVAIQ FAELKRLQDY KNPGSQSRQY FLGLEGLFKG SD NPAYPGG PFFNFANFGK TEEEMKKLKL NEIKNGRLAM LAMFGYGAQA VITGDGPFDN LLAHLADPTG NNLITNLGGK FGQ

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Macromolecule #4: LHCA7

MacromoleculeName: LHCA7 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 27.723631 KDa
SequenceString: MSALMNKSVS LQAASKAPLA ARSIAPRSVA SRTRNVALRA GADRPLWSPG SEPPAWLDGS LAGDYGFDPL HLSEEPEMRK WMVQAELVH ARWAMLGVAG ILFTSIAAKT GAPFPDWYDA GKEAIKTSPA PLGSLIFTEL LLFGWVETKR LYDLRNPGSQ G DGSFLGIT ...String:
MSALMNKSVS LQAASKAPLA ARSIAPRSVA SRTRNVALRA GADRPLWSPG SEPPAWLDGS LAGDYGFDPL HLSEEPEMRK WMVQAELVH ARWAMLGVAG ILFTSIAAKT GAPFPDWYDA GKEAIKTSPA PLGSLIFTEL LLFGWVETKR LYDLRNPGSQ G DGSFLGIT DGLKGKENGY PGGLFDPMGM SKNEASYKEA KVKEIKNGRL AMLAFVGFIA QHHATHKSPI DNLLDHVADP FH VTFATNG VSIPHFTEF

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Macromolecule #5: LHCA8

MacromoleculeName: LHCA8 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 27.496387 KDa
SequenceString: MQVTQKQMMR ASGVKAPLSR RGVTVKASMQ GNWLPGSQTP AHLKDLKMAG NFGFDPLNLG AEPQALRWYQ QAELVHSRTA MMGVAGILI PGIFTKLGAL NVPQWYEAGK VYIEGEGAIP FGTLLMTTLF SYAFVEGKRW QDFRKPGSQA EPGTFFGLES Q FKGTENGY ...String:
MQVTQKQMMR ASGVKAPLSR RGVTVKASMQ GNWLPGSQTP AHLKDLKMAG NFGFDPLNLG AEPQALRWYQ QAELVHSRTA MMGVAGILI PGIFTKLGAL NVPQWYEAGK VYIEGEGAIP FGTLLMTTLF SYAFVEGKRW QDFRKPGSQA EPGTFFGLES Q FKGTENGY PGGIFDPLGY SKTSPEKLDE LKLKEIKNGR LAMVAFLGFA GQYGATGKGP IDNLADHLAD PWHNTFAENG IS VPGLSAV EQAAANL

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Macromolecule #6: LHCA9

MacromoleculeName: LHCA9 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 24.326207 KDa
SequenceString: MAVLTSKMST KLTSSGVRPV KPTTRASRMV MKASNRPLWL PDVIPPPHLN GTLPGDSGFD PLGLGLNEER LKWYVEAEKM NGRWAMMAV TGIMGQELLG VPVKWFEAGA AEYDLPVQAQ VPILFLVMGF LETKRFQGFR ETGTSGFINS YPFDPVGLNS P KHAVNEVK ...String:
MAVLTSKMST KLTSSGVRPV KPTTRASRMV MKASNRPLWL PDVIPPPHLN GTLPGDSGFD PLGLGLNEER LKWYVEAEKM NGRWAMMAV TGIMGQELLG VPVKWFEAGA AEYDLPVQAQ VPILFLVMGF LETKRFQGFR ETGTSGFINS YPFDPVGLNS P KHAVNEVK NGRLAMVAFV GFAVQALVTR TQPIEGLQKH LADPFGKNIT YYLTHTPEVI AGTA

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Macromolecule #7: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 82.978586 KDa
SequenceString: TISSPEREAK KVKIAVDRNP VETNFEKWAK PGHFSRALAK GPNTTTWIWN LHADAHDFDN HTSDLEEISR KVFSAHFGQL GIILIWLSG MYFHGARFSN YEGWLSDPTH IKPSAQVVWP IVGQEILNGD VGGGFQGIQI TSGFFQLWRA SGITSELQLY S TAIGGLVL ...String:
TISSPEREAK KVKIAVDRNP VETNFEKWAK PGHFSRALAK GPNTTTWIWN LHADAHDFDN HTSDLEEISR KVFSAHFGQL GIILIWLSG MYFHGARFSN YEGWLSDPTH IKPSAQVVWP IVGQEILNGD VGGGFQGIQI TSGFFQLWRA SGITSELQLY S TAIGGLVL AAACFFAGWF HYHKAAPKLE WFQNVESMLN HHLAGLLGLG SLAWAGHQIH VSLPVNKLLD AGVDPKEIPL PH EFLLNQS IIADLYPSFS KGLAPFFTLN WAEYSDFLTF KGGLNPVTGG LWLSDTAHHH LAIAVLFLVA GHQYRTNWGI GHS IKDILE SHKGPFTGNG HAGLYEILTT SWHAQLAINL ALFGSLSIIV AHHMYAMPPY PYLATDYGTQ LSLFTHHMWI GGFC VVGAG AHAAIFMVRD YDPTNNYNNL LDRVIRHRDA IISHLNWVSI FLGFHSFGLY IHNDTMSALG RPQDMFSDTA IQLQP VFAQ WIQNTHFTAP QLTAPNALAA TSLTWGGDVV AVGGKVAMMP IALGTSDFLV HHIHAFTIHV TVLILLKGVL FARSSR LIP DKANLGFRFP CDGPGRGGTC QVSAWDHVFL GLFWMYNSLS IVIFHFSWKM QSDVWGTVTD SGVSHITGGN FAQSANT IN GWLRDFLWAQ SSQVIQSYGS ALSAYGLMFL GAHFVWAFSL MFLFSGRGYW QELIESIVWA HNKLRVAPSI QPRALSIT Q GRAVGVAHYL LGGIATTWSF FLARIIAVG

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Macromolecule #8: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 81.873703 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 HLAGLFGVSS 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 PAYSAGQSLW 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 YAAFLIASTA GRFG

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Macromolecule #9: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 8.848286 KDa
SequenceString:
MAHVVKIYDT CIGCTQCVRA CPLDVLEMVP WDGCKAAQMA SSPRTEDCVG CKRCETACPT DFLSVRVYLG NESTRSLGLA Y

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Macromolecule #10: PSAD1

MacromoleculeName: PSAD1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 22.024441 KDa
SequenceString: MQALRSTSAA SRVSCRPGRE ARRSVLVRAE AAPPAAGAPP EPKAAGAPPA APKKKAPPPP WKQPELDPDT PSPIFGGSTG GLLRKAQVE EFYVTTWESP KEQIFEMPTG GAAIMRKGPN LLKLARKEHC LALTTQLRTK FRMSPCFYRV YADGKVEYLH P KDGVYPEK ...String:
MQALRSTSAA SRVSCRPGRE ARRSVLVRAE AAPPAAGAPP EPKAAGAPPA APKKKAPPPP WKQPELDPDT PSPIFGGSTG GLLRKAQVE EFYVTTWESP KEQIFEMPTG GAAIMRKGPN LLKLARKEHC LALTTQLRTK FRMSPCFYRV YADGKVEYLH P KDGVYPEK VNAGRVGVNQ NMRSIGKNVD PIKVKFTGSE PFEI

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Macromolecule #11: PSAE1

MacromoleculeName: PSAE1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 13.525501 KDa
SequenceString:
MAMLSASRIS CRPSVSAKPQ RTRLIVRAEG EAPPAAPKQA PAEAKAAPKG EAKAAPKKKE IGPKRGSLVK VLRPESYWYN QVGKVVSVD QSGIRYPVVV RFENQNYAGV STNNYALDEV TDPPSK

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Macromolecule #12: PSAF1

MacromoleculeName: PSAF1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 25.280117 KDa
SequenceString: MASLTQMNLR SAPVARAPAA RPVARRTATV ARAHQQEQPA QNLGAVACAT ALALTMGLTA DVQPASADIA GLTPCSESKA YNKLERKEL KVLDKRLKKY EPGSAPYLAL QATKERTENR FKTYAKQGLL CGNDGLPHLI SDPGLALRFN HAGEVFIPTF G FLYVAGYI ...String:
MASLTQMNLR SAPVARAPAA RPVARRTATV ARAHQQEQPA QNLGAVACAT ALALTMGLTA DVQPASADIA GLTPCSESKA YNKLERKEL KVLDKRLKKY EPGSAPYLAL QATKERTENR FKTYAKQGLL CGNDGLPHLI SDPGLALRFN HAGEVFIPTF G FLYVAGYI GHVGRQYIIL SKEDAKPTDK EIILDVPLAL KLAFQGWAWP LASIQELRNG SLLEKDENIT VSPR

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Macromolecule #13: PSAG1

MacromoleculeName: PSAG1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 15.118331 KDa
SequenceString:
MALSSKANIQ QFSRQATQSR AVVSRPASRQ AVKTNALIAA PVAIGGSTAA LLALGRFVFL PYQRRRTDME VGPGRLGPKT TGDTFFDRL QKPASFVETK SKDPSGFGLI DVLGWGALGH VFGYFLLACS SLQDAGIEPF PR

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Macromolecule #14: PSAH1

MacromoleculeName: PSAH1 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 14.769955 KDa
SequenceString:
MALLAKTGAQ TLASRRPAAC RAPAPVRRNV KVCAKYGEQS KYFDLQDLEN TTGAWDLYGV DEKKRYPGLQ EEFFQRATDA VSRREALNG FVALTGVASI ALFGLKGAST LELPITKGPR MEKTENGKGG ILRSRI

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

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Macromolecule #16: PSAL1

MacromoleculeName: PSAL1 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 21.413055 KDa
SequenceString: MMMLQKNVAL QKSAVRSSVK PAGLPKFSRT PRGLTIRAAN EEKKPQQVIQ PINGDPFVGM LETPVTSAPI VANYLSNLPA YRTGVAPNL RGVEIGLAHG FLLAGPFIKL GPLRDVPGTA EVVGCMSAAG LVLILALCLS LYGNAAFQNQ PSMGKKTLSG R PLPQDPLM ...String:
MMMLQKNVAL QKSAVRSSVK PAGLPKFSRT PRGLTIRAAN EEKKPQQVIQ PINGDPFVGM LETPVTSAPI VANYLSNLPA YRTGVAPNL RGVEIGLAHG FLLAGPFIKL GPLRDVPGTA EVVGCMSAAG LVLILALCLS LYGNAAFQNQ PSMGKKTLSG R PLPQDPLM SEEGWAKFAA GFTVGGLSGV AWAYILTQIL PYYS

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Macromolecule #17: PSAO1

MacromoleculeName: PSAO1 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 14.118299 KDa
SequenceString:
MMLAQKSLLT AKSATVARPA LPARPARTSV RVAASSQGFD RNWLRVDPIV PAISFVGWTL PSNIGTSALN GQSLFGAFYE SIGQNLAHW PTGPALDDKF WLYMVTWHTG LFIVMLLGQV GVQGKKQGYW

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Macromolecule #18: PSAI1

MacromoleculeName: PSAI1 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 11.271324 KDa
SequenceString:
MLAQKNIVAK PCVRAAKPTA MPVKPMAMQK KQQAAGKVAL SAGAVGLASA FAAAPVEAAN IVANVASATE GYPFVPPDWA PALFVPLTG LVLPAVGMAW AFTYIQKERQ

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Macromolecule #19: PSAK1

MacromoleculeName: PSAK1 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 12.71403 KDa
SequenceString:
MALSLTRAPK VLPTRTQRAA PCPKVQQPRS RKAMVCKADA SFIGSPTNLI MVSSIGACLF ASRFGLAPSV RKVAQPLKLS DREVLQTTG DPAGFTATDV LAMGAAGHAI GVGIVLGLKG IGQL

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Macromolecule #20: TIDI1

MacromoleculeName: TIDI1 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 39.288672 KDa
SequenceString: MPPLRPKESA LARTGAPRTS ILIKPFKITR LHAHEGGSDA PAPGPAPPKE QVASPPPAAA QAATEPPKPQ VTSPPPAAAD AAAEPPKPQ AAAAASEAPP APEPRKGSAF KGYVQQNLVQ PGRTLQQLAG RKIYPGSDER ALSYLTGSLP GDFGWDPLHL A DTNDQDRL ...String:
MPPLRPKESA LARTGAPRTS ILIKPFKITR LHAHEGGSDA PAPGPAPPKE QVASPPPAAA QAATEPPKPQ VTSPPPAAAD AAAEPPKPQ AAAAASEAPP APEPRKGSAF KGYVQQNLVQ PGRTLQQLAG RKIYPGSDER ALSYLTGSLP GDFGWDPLHL A DTNDQDRL NNAMSMEWLS YAEVIHGRWA MLGAVGALSP EILGKAGVIP EETGLTWFQA GGLDSTSNLI AVPFTGPIPF QY WTDKYVL LYTMLVAMGF AETRRWQEYK QPGSVQKQFF LGLEKLTPPS QQPAYPGGAF FNFAGLGTKD EKKMFELKVK EIR NGRLAM LAFLGFMVQA EVTHVGPFQN LLDHINSPGA QNLLSRLTS

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Macromolecule #21: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 21 / Number of copies: 218 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #22: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 22 / Number of copies: 23 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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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: 14 / 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 #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: 10 / 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 #25: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 25 / Number of copies: 35 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #26: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 26 / Number of copies: 6 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #27: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 27 / Number of copies: 4 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #28: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 28 / Number of copies: 21 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #29: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 29 / Number of copies: 15 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #30: 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: 30 / Number of copies: 2 / 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 #31: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 31 / Number of copies: 2 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Macromolecule #32: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 32 / Number of copies: 4 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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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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Macromolecule #34: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 34 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #35: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 35 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #36: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 36 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #37: Tripalmitoylglycerol

MacromoleculeName: Tripalmitoylglycerol / type: ligand / ID: 37 / Number of copies: 1 / Formula: 4RF
Molecular weightTheoretical: 807.32 Da
Chemical component information

ChemComp-4RF:
Tripalmitoylglycerol

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Macromolecule #38: water

MacromoleculeName: water / type: ligand / ID: 38 / Number of copies: 5 / 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

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: 6270 / 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: 1138207
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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 120321
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-9mgw:
Dunaliella salina PSI-LHCI-TIDI1 supercomplex

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