EMDB-13455: Stacked stretched Dunaliella PSII

Basic information

Entry

Database: EMDB / ID: EMD-13455

• Title: Stacked stretched Dunaliella PSII

Sample

• Complex: Dunaliella salina Photosystem II complex
  • Protein or peptide: x 25 types
• Protein or peptide: x 2 types
• Ligand: x 30 types

Function / homology

Function:

oxygen evolving activity / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / electron transfer activity / membrane => GO:0016020 / protein stabilization / iron ion binding / heme binding / metal ion binding

Domain/homology:

Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.

Component:

Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II reaction center protein K / Photosystem II reaction center protein I / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein M / Cytochrome b559 subunit alpha / Photosystem II reaction center protein H / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II protein D1 / Photosystem II reaction center protein Psb30 / Cytochrome b559 subunit beta / Photosystem II reaction center protein L

• Biological species: Dunaliella salina (plant) / Green alga, Protococcus salinus
• Method: single particle reconstruction / cryo EM / Resolution: 4.0 Å
• Authors: Caspy I / Fadeeva M / Mazor Y / Nelson N

Funding support

Israel, 2 items

Organization	Grant number	Country
Israel Science Foundation	569/17	Israel
Israel Science Foundation	199/21	Israel

• Citation: Journal: Elife / Year: 2023; Title: Structure of photosystem II reveals conformational flexibility of stacked and unstacked supercomplexes.; Authors: Ido Caspy / Maria Fadeeva / Yuval Mazor / Nathan Nelson / ; Abstract: Photosystem II (PSII) generates an oxidant whose redox potential is high enough to enable water oxidation , a substrate so abundant that it assures a practically unlimited electron source for life on earth . Our knowledge on the mechanism of water photooxidation was greatly advanced by high-resolution structures of prokaryotic PSII . Here, we show high-resolution cryogenic electron microscopy (cryo-EM) structures of eukaryotic PSII from the green alga at two distinct conformations. The conformers are also present in stacked PSII, exhibiting flexibility that may be relevant to the grana formation in chloroplasts of the green lineage. CP29, one of PSII associated light-harvesting antennae, plays a major role in distinguishing the two conformations of the supercomplex. We also show that the stacked PSII dimer, a form suggested to support the organisation of thylakoid membranes , can appear in many different orientations providing a flexible stacking mechanism for the arrangement of grana stacks in thylakoids. Our findings provide a structural basis for the heterogenous nature of the eukaryotic PSII on multiple levels.

History

Deposition	Aug 23, 2021	-
Header (metadata) release	Aug 17, 2022	-
Map release	Aug 17, 2022	-
Update	Mar 1, 2023	-
Current status	Mar 1, 2023	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_13455.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 0.96 Å

Density

Contour Level	By AUTHOR: 0.0175
Minimum - Maximum	-0.03524484 - 0.06272602
Average (Standard dev.)	7.4657815e-05 (±0.0046893945)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 480 480 480 Spacing 480 480 480
Cell	A=B=C: 460.8 Å α=β=γ: 90.0 °

Supplemental data

Sample components

Entire : Dunaliella salina Photosystem II complex

• Entire: Name: Dunaliella salina Photosystem II complex

Components

• Complex: Dunaliella salina Photosystem II complex
  • Protein or peptide: Photosystem II protein D1
  • Protein or peptide: Photosystem II CP47 reaction center protein
  • Protein or peptide: Photosystem II reaction center protein Ycf12
  • Protein or peptide: Photosystem II CP43 reaction center protein
  • Protein or peptide: Photosystem II D2 protein
  • Protein or peptide: Cytochrome b559 subunit alpha
  • Protein or peptide: Cytochrome b559 subunit beta
  • Protein or peptide: Photosystem II reaction center protein H
  • Protein or peptide: Photosystem II reaction center protein I
  • Protein or peptide: Photosystem II reaction center protein J
  • Protein or peptide: Photosystem II reaction center protein K
  • Protein or peptide: Photosystem II reaction center protein L
  • Protein or peptide: Photosystem II reaction center protein M
  • Protein or peptide: PsbO
  • Protein or peptide: PsbP
  • Protein or peptide: Photosystem II reaction center protein T
  • Protein or peptide: PsbW
  • Protein or peptide: PsbX
  • Protein or peptide: PsbZ
  • Protein or peptide: LHCII M3
  • Protein or peptide: LHCII M2
  • Protein or peptide: CP29
  • Protein or peptide: CP26
  • Protein or peptide: LHCII M1
  • Protein or peptide: PsbU
• Protein or peptide: Photosystem II reaction center protein M
• Protein or peptide: CP29
• Ligand: CA-MN4-O5 CLUSTER
• Ligand: FE (II) ION
• Ligand: CHLORIDE IONChloride
• Ligand: CHLOROPHYLL A
• Ligand: PHEOPHYTIN APheophytin
• Ligand: BETA-CAROTENEΒ-Carotene
• Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
• Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
• Ligand: SODIUM IONSodium
• Ligand: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
• Ligand: DIACYL GLYCEROLDiglyceride
• Ligand: GLYCEROL
• Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
• Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
• 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: BICARBONATE IONBicarbonate
• Ligand: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
• Ligand: PROTOPORPHYRIN IX CONTAINING FE
• Ligand: (3R)-beta,beta-caroten-3-ol
• 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: (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: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
• Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
• Ligand: SPHINGOSINE
• Ligand: Tripalmitoylglycerol
• Ligand: DODECYL-BETA-D-MALTOSIDE
• Ligand: ERGOSTEROL
• Ligand: PHOSPHATIDYLETHANOLAMINE

Supramolecule #1: Dunaliella salina Photosystem II complex

• Supramolecule: Name: Dunaliella salina Photosystem II complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#25
• Source (natural): Organism: Dunaliella salina (plant)

Macromolecule #1: Photosystem II protein D1

• Macromolecule: Name: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem II
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 37.291488 KDa

Sequence

String:

ENTSLWARFC EWITSTENRL YIGWFGVIMI PTLLTAISVY IIAFIAAPPV DIDGIREPVS GSLLYGNNII TGAVVPTSNA IGLHFYPIW EAASLDEWLY NGGPYQLVVC HFFLGVCCYM GREWELSYRL GMRPWIAVAY SAPVAAATAV FIIYPIGQGS F SDGMPLGI SGTFNFMIVF QAEHNILMHP FHMFGVAGVF GGSLFSAMHG SLVTSSLIRE TTENESANAG YKFGQEEETY NI VAAHGYF GRLIFQYASF NNSRSLHFFL AVWPVVCIWL TALGISTMAF NLNGFNFNQS VVDSNGRVLN TWADIINRAN LGM EVMHER NAHNFPLDLA

Macromolecule #2: Photosystem II CP47 reaction center protein

• Macromolecule: Name: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 53.289516 KDa

Sequence

String:

GLPWYRVHTV VINDPGRLIS VHLMHTALVA GWAGAMTLFE IAVFDPSDPV LNPMWRQGMF VLPFLTRLGV TQSWGGWTIS GETSSNPGI WSYEGAAASH IVLSGLLFLA SVWHWVYWDL ELFRDPRTGK TALDLPKIFG IHLFLAGLLC FGFGAFHVTG V FGPGIWVS DPYGLTGSVQ PVAPSWGAEG FDPYNPGGVP AHHIAAGILG VLAGLFHLCV RPSIRLYFGL SMGSIESVLS SS IAAVFWA AFVVAGTMWY GSAATPIELF GPTRYQWDQG FFQQEIQKRV AQSTSEGLSV SEAWAKIPEK LAFYDYIGNN PAK GGLFRT GAMNSGDGIA VGWLGHASFK DQEGRELFVR RMPTFFETFP VVLIDKDGVV RADVPFRKAE SKYSIEQVGV SVTF YGGEL NGLTFTDPST VKKYARKAQL GEIFEFDRST LQSDGVFRSS PRGWFTFGHL SFALLFFFGH IWHGSRTIFR DVFAG IDED

Macromolecule #3: Photosystem II reaction center protein Ycf12

• Macromolecule: Name: Photosystem II reaction center protein Ycf12 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 3.217949 KDa

Sequence

String:

SLTLILQLVA LFAVVAAGPL VVVLLSVRGG NL

Macromolecule #4: Photosystem II CP43 reaction center protein

• Macromolecule: Name: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 49.128992 KDa

Sequence

String:

GRDQETTGFA WWAGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVSH FVPEKPMYEQ GLILLPHIAT LGYGVGPGGE VLDTFPYFV SGVLHLISSA VLGFGGVYHS LIGPETLEES YPFFGYVWKD KNKMTNILGY HLIILGCGAW LLVLKALYFG G VYDTWAPG GGDVRIISNP TTNAAIIFGY IVKSPFGGDG WIVSVDNLED IIGGHIWIGT LCILGGIWHI YTTPWPWARR AF VWSGEAY LSYSLAAVSL MGFTACCFAW FNNTAYPSEF YGPTGPEASQ AQAFTFLVRD QRLGANVASA QGPTGLGKYL MRS PTGEII FGGETMRFWD FRGPWVEPLR GPSGLDLVKL KNDIQPWQER RAAEYMTHAP LGSLNSVGGV ATEINAVNFV SPRS WLATS HFCLGFFFFV GHLWHAGRAR AAAAGFEKGI DRVDEPVLSM RPLD

Macromolecule #5: Photosystem II D2 protein

• Macromolecule: Name: Photosystem II D2 protein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem II
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 38.965383 KDa

Sequence

String:

IGTYQEKRTW FDDADDWLRQ DRFVFVGWSG LLLLPCAYFA VGGWLTGCTF VTSWYTHGLA SSYIEGCNFL TAAVSTPANS LGHSLLFVW GPEAQGDLTR WFQLGGLWAF VALHGAFGLI GFMLRQFEIA RSVNLRPYNA IAFSAPIAVF VSVFLIYPLG Q SGWFFAPS FGVASIFRFI LFFQGFHNWT LNPFHMMGVA GVLGAALLCA IHGATVENTL FEDGDGANTF RAFNPTQAEE TY SMVTANR FWSQIFGVAF SNKRWLHFFM LFVPVTGLWM SALGVVGLAL NLRAYDFVSQ EIRAAEDPEF ETFYTKNILL NEG IRAWMA AQDQPHEKLT LPEEVLPRGN AL

Macromolecule #6: Cytochrome b559 subunit alpha

• Macromolecule: Name: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 8.743847 KDa

Sequence

String:

ERPFSDILTS IRYWVIHSIT VPSLFIAGWL FVSTGLAYDV FGSPRPNEYF TEDRQDAPLI TDRFNALEQV KKLSAQ

Macromolecule #7: Cytochrome b559 subunit beta

• Macromolecule: Name: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 3.549299 KDa

Sequence

String:

IFTVRWLAIH AIAVPTIFFL GAITAMQFIQ R

Macromolecule #8: Photosystem II reaction center protein H

• Macromolecule: Name: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 7.124381 KDa

Sequence

String:

EPGIVTPLGT LLRPLNSEAG KVLPGWGTTV LMAVAILLFA VFLLIILEIY NSSLILDGVT NSWESLA

Macromolecule #9: Photosystem II reaction center protein I

• Macromolecule: Name: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 9 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 3.929648 KDa

Sequence

String:

MLTLKIFVYT VVTFFVGLFI FGFLSNDPSR NPGKG

Macromolecule #10: Photosystem II reaction center protein J

• Macromolecule: Name: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 10 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 3.7375 KDa

Sequence

String:

IGRIPLWLVG TVVGLLAIGL LAIFFYGSYV GLGSSL

Macromolecule #11: Photosystem II reaction center protein K

• Macromolecule: Name: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 11 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 4.159991 KDa

Sequence

String:

KLPEAYAPFS PIVDVLPIIP VLFILLAFVW QASVSFR

Macromolecule #12: Photosystem II reaction center protein L

• Macromolecule: Name: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 4.417203 KDa

Sequence

String:

MARPNPNKQV VELNRSSLYW GLLLIFVLAV LFSSYIFN

Macromolecule #13: Photosystem II reaction center protein M

• Macromolecule: Name: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 3.437093 KDa

Sequence

String:

EVNILGLTAT ALFIIIPTSF LLILYVKTAA SE

Macromolecule #14: PsbO

• Macromolecule: Name: PsbO / type: protein_or_peptide / ID: 14 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Dunaliella salina (plant)
• Molecular weight: Theoretical: 25.874908 KDa

Sequence

String:

LTYDELQGLT YLQVKGTGIA NTCPVVEQGT SNVRELKPGD YKLEKFCMEP TSFTVKEEDA KGREEFVKTK LLTRLTYGLD GMNGSMKIN NDGSVEFRED EGLDYAATTV KLPGGEYVPF LFTIKEFDGK GTLDSFSGDF LVPSYRGSTF LDPKGRGGAT G YDNAIALP AKADADEIQR LNNKSYTPGK GSAVFSVAKV DTETGEIAGV FESIQPSDTE MGAHPAKDIK ITGLWYGQLT

Macromolecule #15: PsbP

• Macromolecule: Name: PsbP / type: protein_or_peptide / ID: 15 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Dunaliella salina (plant)
• Molecular weight: Theoretical: 20.425707 KDa

Sequence

String:

AYGEGANVFG RVTNKSGFVP YAGDSFALLL PSKWNPSDEK EVDSIVLRYA DNFDAVNNVY VIAQDTDKSS IQDYGSPEEF ISQFGYLLG RQAWAGQTVS EGGFDANKVS SAALLGVATE KDKKGKTYYK FEILSRTADG NEGGRHQLVK ATVSNGKLYL L KVQAGDKR WFKGTDKECL GVLDSFTVV

Macromolecule #16: Photosystem II reaction center protein T

• Macromolecule: Name: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 16 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 3.478194 KDa

Sequence

String:

MEALVYTFLL IGTLGIIFFS IFFREPPRIA

Macromolecule #17: PsbW

• Macromolecule: Name: PsbW / type: protein_or_peptide / ID: 17 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Dunaliella salina (plant)
• Molecular weight: Theoretical: 4.698315 KDa

Sequence

String:

LVDDRMNGDG TGLPFGVNDG ILGWVIAGTL GTIWAIYFVS QKDL

Macromolecule #18: PsbX

• Macromolecule: Name: PsbX / type: protein_or_peptide / ID: 18 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Dunaliella salina (plant)
• Molecular weight: Theoretical: 2.854407 KDa

Sequence

String:

SVTPSLKNFL LSLVAGAVVL AAIAGAVTAV

Macromolecule #19: PsbZ

• Macromolecule: Name: PsbZ / type: protein_or_peptide / ID: 19 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Dunaliella salina (plant)
• Molecular weight: Theoretical: 6.430616 KDa

Sequence

String:

MTSILQIALL GLVLVSFALV VGVPVVFASP NGWTENKGVV FSGLSVWFLL VFAVGVFNSF A

Macromolecule #20: LHCII M3

• Macromolecule: Name: LHCII M3 / type: protein_or_peptide / ID: 20 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Dunaliella salina (plant)
• Molecular weight: Theoretical: 24.075082 KDa

Sequence

String:

TINQFYGPDR NKWLGPYSTN TPPYLTGEFP GDYGWDTAGL SADPETFKRY RELELIHARW ALLGALGMVT PELLQDDDGI MFGESAIWF KAGAAIFQEG GLNYLGNPSL IHAQNIVATL AVQVVLMGLV EGYRVNGGPA GEGLDPLYPG EAFDPLGLAD D PEAFAELK VKEIKNGRLA MFACLGFFVQ AIVTGKGPIE NLTDHLANPA ENNAFAYATK FTPQ

Macromolecule #21: LHCII M2

• Macromolecule: Name: LHCII M2 / type: protein_or_peptide / ID: 21 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Dunaliella salina (plant)
• Molecular weight: Theoretical: 23.719543 KDa

Sequence

String:

EFYGPDRAKF LGPFSENDTP EYLTGEFPGD YGWDTAGLSA DPQTFARYRE IELIHARWAL LGALGILTPE LLSQYAGVQF GEPVWFKAG AQIFAAGGLN YLGNESLIHA QSIIATLAVQ VVLMGLAEAY RANGGSEGFL DDLDTLYPGG AFDPLGLADD P DTFAELKV KEIKNGRLAM FSCLGFFVQA IVTGKGPVQN LTDHLADPTV NNAFASATKF TPG

Macromolecule #22: CP29

• Macromolecule: Name: CP29 / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Dunaliella salina (plant)
• Molecular weight: Theoretical: 21.748461 KDa

Sequence

String:

SLSYLDGHLP GDMGFDPLHL SSPTVSLQIG VDEEDQNQAQ NKKGDVEAIF RPEVFGLARF RETEVIHGRW AMLGTLGAIV GEAATGVSW VDAGKVELDG AQYLGQSLPF SISQLIWIEA ILVGGVEVLR NNELDLEKRI YPGGAFDPLN LADEEDEEKS F RLKTAEIK HGRLAMVAFL GFGIQAAATG EGALGSLAKF TSSL

Macromolecule #23: CP26

• Macromolecule: Name: CP26 / type: protein_or_peptide / ID: 23 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Dunaliella salina (plant)
• Molecular weight: Theoretical: 26.233607 KDa

Sequence

String:

PDLEKWYGPD RKLFLPGGLL DRDDVPEYLN GELAGDYGYD PLGLGKDEEQ VEKYRANELL HARWAMLAAA GIIIPEGLQA NGADIKGGT WFETGAEMLN GGTLNYFAVP FGVVQNPLPL AAVTLIEIVL LGAVEKFRVD GTGPAGFSPG VGKFDSDIFD G LDKLYPGG PFDPLNLADD PEVFAELQVK EIKNGRLAMI AVLAFAIQSY VTGEGPYANI TKHLSDPFGY NLLTVLQGDD RV PTL

Macromolecule #24: LHCII M1

• Macromolecule: Name: LHCII M1 / type: protein_or_peptide / ID: 24 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Dunaliella salina (plant)
• Molecular weight: Theoretical: 23.537566 KDa

Sequence

String:

SAWYGPDRPL FLGSLSGEPP SYLTGEFPGD YGWDTAGLSA DPTTFARYRT IELIHARWAL LGALGIITPE LLAKNGVPFS EDGAIWFKA GAEIFKEGGL NYLGNENLIH AQSILATLAV QVIVMGAAEG FRANGEAPGV EGLDPLYPGG PFDPLGLADD P EAFAELKV KEIKNGRLAM FSCLGFFVQA IVTGKGPIQN LQDHLADPGV NNAFASATKF VPTP

Macromolecule #25: PsbU

• Macromolecule: Name: PsbU / type: protein_or_peptide / ID: 25 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Dunaliella salina (plant)
• Molecular weight: Theoretical: 3.219625 KDa

Sequence

String:

QRVRTVLDMD DPAKEETVKE LRKDINN

Macromolecule #26: Photosystem II reaction center protein M

• Macromolecule: Name: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 26 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Green alga, Protococcus salinus
• Molecular weight: Theoretical: 3.307979 KDa

Sequence

String:

VNILGLTATA LFIIIPTSFL LILYVKTAAS E

Macromolecule #27: CP29

• Macromolecule: Name: CP29 / type: protein_or_peptide / ID: 27 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Dunaliella salina (plant)
• Molecular weight: Theoretical: 21.828438 KDa

Sequence

String:

SLSYLDGHLP GDMGFDPLHL SSPTV(SEP)LQIG VDEEDQNQAQ NKKGDVEAIF RPEVFGLARF RETEVIHGRW AMLGTL GAI VGEAATGVSW VDAGKVELDG AQYLGQSLPF SISQLIWIEA ILVGGVEVLR NNELDLEKRI YPGGAFDPLN LADEEDE EK SFRLKTAEIK HGRLAMVAFL GFGIQAAATG EGALGSLAKF TSSL

Macromolecule #28: CA-MN4-O5 CLUSTER

• Macromolecule: Name: CA-MN4-O5 CLUSTER / type: ligand / ID: 28 / Number of copies: 4 / Formula: OEX
• Molecular weight: Theoretical: 339.827 Da

Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

Macromolecule #29: FE (II) ION

• Macromolecule: Name: FE (II) ION / type: ligand / ID: 29 / Number of copies: 4 / Formula: FE2
• Molecular weight: Theoretical: 55.845 Da

Macromolecule #30: CHLORIDE ION

• Macromolecule: Name: CHLORIDE ION / type: ligand / ID: 30 / Number of copies: 8 / Formula: CL
• Molecular weight: Theoretical: 35.453 Da

Macromolecule #31: CHLOROPHYLL A

• Macromolecule: Name: CHLOROPHYLL A / type: ligand / ID: 31 / Number of copies: 316 / Formula: CLA
• Molecular weight: Theoretical: 893.489 Da

Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

Macromolecule #32: PHEOPHYTIN A

• Macromolecule: Name: PHEOPHYTIN A / type: ligand / ID: 32 / Number of copies: 8 / Formula: PHO
• Molecular weight: Theoretical: 871.2 Da

Chemical component information

ChemComp-PHO:
PHEOPHYTIN A / Pheophytin

Macromolecule #33: BETA-CAROTENE

• Macromolecule: Name: BETA-CAROTENE / type: ligand / ID: 33 / Number of copies: 32 / Formula: BCR
• Molecular weight: Theoretical: 536.873 Da

Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

Macromolecule #34: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

• Macromolecule: Name: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL; type: ligand / ID: 34 / Number of copies: 16 / Formula: SQD
• Molecular weight: Theoretical: 795.116 Da

Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

Macromolecule #35: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

• Macromolecule: Name: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 35 / Number of copies: 26 / Formula: LMG
• Molecular weight: Theoretical: 787.158 Da

Chemical component information

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

Macromolecule #36: SODIUM ION

• Macromolecule: Name: SODIUM ION / type: ligand / ID: 36 / Number of copies: 4
• Molecular weight: Theoretical: 22.99 Da

Macromolecule #37: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},...

• Macromolecule: Name: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol; type: ligand / ID: 37 / Number of copies: 4 / Formula: C7Z
• Molecular weight: Theoretical: 568.871 Da

Chemical component information

ChemComp-C7Z:
(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol

Macromolecule #38: DIACYL GLYCEROL

• Macromolecule: Name: DIACYL GLYCEROL / type: ligand / ID: 38 / Number of copies: 10 / Formula: DGA
• Molecular weight: Theoretical: 625.018 Da

Chemical component information

ChemComp-DGA:
DIACYL GLYCEROL / Diglyceride

Macromolecule #39: GLYCEROL

• Macromolecule: Name: GLYCEROL / type: ligand / ID: 39 / Number of copies: 5 / Formula: GOL
• Molecular weight: Theoretical: 92.094 Da

Chemical component information

ChemComp-GOL:
GLYCEROL / Glycerol

Macromolecule #40: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

• Macromolecule: Name: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 40 / Number of copies: 16 / Formula: DGD
• Molecular weight: Theoretical: 949.299 Da

Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

Macromolecule #41: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

• Macromolecule: Name: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 41 / Number of copies: 35 / Formula: LHG
• Molecular weight: Theoretical: 722.97 Da

Chemical component information

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

Macromolecule #42: trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S...

• Macromolecule: Name: 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: 42 / Number of copies: 4 / Formula: LMK
• Molecular weight: Theoretical: 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

Macromolecule #43: BICARBONATE ION

• Macromolecule: Name: BICARBONATE ION / type: ligand / ID: 43 / Number of copies: 4 / Formula: BCT
• Molecular weight: Theoretical: 61.017 Da

Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM / Bicarbonate

Macromolecule #44: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...

• Macromolecule: Name: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE; type: ligand / ID: 44 / Number of copies: 4 / Formula: PL9
• Molecular weight: Theoretical: 749.201 Da

Chemical component information

ChemComp-PL9:
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / Plastoquinone

Macromolecule #45: PROTOPORPHYRIN IX CONTAINING FE

• Macromolecule: Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 45 / Number of copies: 4 / Formula: HEM
• Molecular weight: Theoretical: 616.487 Da

Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

Macromolecule #46: (3R)-beta,beta-caroten-3-ol

• Macromolecule: Name: (3R)-beta,beta-caroten-3-ol / type: ligand / ID: 46 / Number of copies: 4 / Formula: RRX
• Molecular weight: Theoretical: 552.872 Da

Chemical component information

ChemComp-RRX:
(3R)-beta,beta-caroten-3-ol / Β-Cryptoxanthin

Macromolecule #47: CHLOROPHYLL B

• Macromolecule: Name: CHLOROPHYLL B / type: ligand / ID: 47 / Number of copies: 92 / Formula: CHL
• Molecular weight: Theoretical: 907.472 Da

Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

Macromolecule #48: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

• Macromolecule: Name: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL; type: ligand / ID: 48 / Number of copies: 36 / Formula: LUT
• Molecular weight: Theoretical: 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 #49: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

• Macromolecule: Name: (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: 49 / Number of copies: 16 / Formula: XAT
• Molecular weight: Theoretical: 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 #50: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

• Macromolecule: Name: (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: 50 / Number of copies: 20 / Formula: NEX
• Molecular weight: Theoretical: 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

Macromolecule #51: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypro...

• Macromolecule: Name: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate; type: ligand / ID: 51 / Number of copies: 4 / Formula: LPX
• Molecular weight: Theoretical: 453.55 Da

Chemical component information

ChemComp-LPX:
(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate

Macromolecule #52: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

• Macromolecule: Name: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 52 / Number of copies: 9 / Formula: 3PH
• Molecular weight: Theoretical: 704.998 Da

Chemical component information

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

Macromolecule #53: SPHINGOSINE

• Macromolecule: Name: SPHINGOSINE / type: ligand / ID: 53 / Number of copies: 6 / Formula: SPH
• Molecular weight: Theoretical: 299.492 Da

Chemical component information

ChemComp-SPH:
SPHINGOSINE / Sphingosine

Macromolecule #54: Tripalmitoylglycerol

• Macromolecule: Name: Tripalmitoylglycerol / type: ligand / ID: 54 / Number of copies: 4 / Formula: 4RF
• Molecular weight: Theoretical: 807.32 Da

Chemical component information

ChemComp-4RF:
Tripalmitoylglycerol / Tripalmitin

Macromolecule #55: DODECYL-BETA-D-MALTOSIDE

• Macromolecule: Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 55 / Number of copies: 2 / Formula: LMT
• Molecular weight: Theoretical: 510.615 Da

Chemical component information

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

Macromolecule #56: ERGOSTEROL

• Macromolecule: Name: ERGOSTEROL / type: ligand / ID: 56 / Number of copies: 2 / Formula: ERG
• Molecular weight: Theoretical: 396.648 Da

Chemical component information

ChemComp-ERG:
ERGOSTEROL / Ergosterol

Macromolecule #57: PHOSPHATIDYLETHANOLAMINE

• Macromolecule: Name: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 57 / Number of copies: 4 / Formula: PTY
• Molecular weight: Theoretical: 734.039 Da

Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 6.5
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 13586 / Average electron dose: 51.81 e/Ų
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 401467
• Initial angle assignment: Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
• Final angle assignment: Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 14307

Atomic model buiding 1

Initial model

PDB ID:

6kac

• Refinement: Protocol: AB INITIO MODEL

Output model

PDB-7piw:
Stacked stretched Dunaliella PSII