[English] 日本語
Yorodumi
- EMDB-38455: Structure of inactive Photosystem II associated with CAC antenna ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38455
TitleStructure of inactive Photosystem II associated with CAC antenna from Rhodomonas Salina
Map dataComposite map of PSII-CAC supercomplex from Rhodomonas Salina
Sample
  • Complex: Inactive Photosystem II associated with chlorophyll a/c binding protein
    • Protein or peptide: x 23 types
  • Ligand: x 17 types
KeywordsPhotosystem II associated with CAC antenna from Rhodomonas Salina / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide / chlorophyll binding / photosynthetic electron transport in photosystem II / : ...photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide / chlorophyll binding / photosynthetic electron transport in photosystem II / : / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / electron transfer activity / oxidoreductase activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbX, type 1 subfamily / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL ...Photosystem II PsbX, type 1 subfamily / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / 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 cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / 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.
Similarity search - Domain/homology
Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 / Photosystem II reaction center protein X / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein I / Photosystem II reaction center protein Z ...Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 / Photosystem II reaction center protein X / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein I / Photosystem II reaction center protein Z / Photosystem II reaction center protein K / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein T / Photosystem II reaction center protein H
Similarity search - Component
Biological speciesRhodomonas salina (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsSi L / Li M
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for the distinct core-antenna assembly of cryptophyte photosystem II.
Authors: Long Si / Shumeng Zhang / Xiaodong Su / Mei Li /
Abstract: Photosystem II (PSII) catalyzes the light-driven charge separation and water oxidation reactions of photosynthesis. Eukaryotic PSII core is usually associated with membrane-embedded light-harvesting ...Photosystem II (PSII) catalyzes the light-driven charge separation and water oxidation reactions of photosynthesis. Eukaryotic PSII core is usually associated with membrane-embedded light-harvesting antennae, which greatly increase the absorbance cross-section of the core. The peripheral antennae in different phototrophs vary considerably in protein composition and arrangement. Photosynthetic cryptophytes possess chlorophyll a/c binding proteins (CACs) that serve as their antennae. How these CACs assemble with the PSII core remains unclear. Here, we report the 2.57-Å resolution structure of cryptophyte PSII-CAC purified from cells at nitrogen-limited stationary growth phase. We show that each monomer of the PSII homodimer contains a core complex, six chlorophyll a/c binding proteins (CACs) and a previously unseen chlorophyll-binding protein (termed CAL-II). Six CACs are arranged as a double-layered arc-shaped non-parallel belt, and two such belts attach to the dimeric core from opposite sides. The CAL-II simultaneously interacts with a number of core subunits and five CACs. The distinct organization of CACs and the presence of CAL-II may play a critical role in stabilizing the dimeric PSII-CAC complex under stress conditions. Our study provides mechanistic insights into the assembly and function of the PSII-CAC complex as well as the possible adaptation of cryptophytes in response to environmental stresses.
History
DepositionDec 26, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38455.png

Downloads & links

-
Map

FileDownload / File: emd_38455.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of PSII-CAC supercomplex from Rhodomonas Salina
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 416 pix.
= 432.653 Å		1.04 Å/pix.
x 416 pix.
= 432.653 Å		1.04 Å/pix.
x 416 pix.
= 432.653 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04003 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024
Minimum - Maximum0.0 - 0.25331298
Average (Standard dev.)0.0005058164 (±0.0043911315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 432.65326 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Inactive Photosystem II associated with chlorophyll a/c binding p...

EntireName: Inactive Photosystem II associated with chlorophyll a/c binding protein
Components
  • Complex: Inactive Photosystem II associated with chlorophyll a/c binding protein
    • Protein or peptide: Photosystem II protein D1
    • Protein or peptide: Photosystem II CP47 reaction center protein
    • 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 K
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: Photosystem II protein M
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II protein W
    • Protein or peptide: Photosystem II reaction center X protein
    • Protein or peptide: Photosystem II reaction center protein Psb30
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: NCP
    • Protein or peptide: CAC2
    • Protein or peptide: CAC3
    • Protein or peptide: CAC4
    • Protein or peptide: CAC5
    • Protein or peptide: CAC6
    • Protein or peptide: CAC1
  • Ligand: FE (II) ION
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN A
  • Ligand: 1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • 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: BICARBONATE ION
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: CHLORIDE ION
  • Ligand: MANGANESE (II) ION
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: Chlorophyll c2
  • Ligand: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
  • Ligand: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
  • Ligand: water

+
Supramolecule #1: Inactive Photosystem II associated with chlorophyll a/c binding p...

SupramoleculeName: Inactive Photosystem II associated with chlorophyll a/c binding protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#23
Source (natural)Organism: Rhodomonas salina (eukaryote)

+
Macromolecule #1: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 36.342285 KDa
SequenceString: ESASLWERFC SWITSTDNRL YIGWFGVLMI PTLLTATTVY IIAFIAAPPV DIDGIREPVA GSLLYGNNII TGAVIPSSAS IGIHFYPIW EAASLDEWLY NGGPYQLIVD HFLLGVCGWI GREWEFSYRL GMRPWISVAF TAPVAAASAV FLVYPIGQGS F SDGMPLGI ...String:
ESASLWERFC SWITSTDNRL YIGWFGVLMI PTLLTATTVY IIAFIAAPPV DIDGIREPVA GSLLYGNNII TGAVIPSSAS IGIHFYPIW EAASLDEWLY NGGPYQLIVD HFLLGVCGWI GREWEFSYRL GMRPWISVAF TAPVAAASAV FLVYPIGQGS F SDGMPLGI SGTFNFMLVF QAEHNILMHP FHQLGVAGVF GGSLFSAMHG SLVTSSLIRE TTENESANYG YKFGQEEETY NI VAAHGYF GRLIFQYASF NNSRALHFFL GLWPVVGIWF TALGIMTMAF NLNGFNFNQS VVDSQGRVIN TWADILNRAN LGM EVMHER NA

UniProtKB: Photosystem II protein D1

+
Macromolecule #2: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 56.331055 KDa
SequenceString: MGLPWYRVHT VVLNDPGRLI AVHLMHTALV AGWAGSMALY ELAVFDPSDP VLNPMWRQGM FVMPFMARIG VTDSWGGWSI TGESVANPG FWSFEGVALA HIGLSGLLFL AAVWHWVYWD LELFRDPRTG NPALDLPKIF GIHLLLSGVL CFGFGAFHVT G AWGPGIWV ...String:
MGLPWYRVHT VVLNDPGRLI AVHLMHTALV AGWAGSMALY ELAVFDPSDP VLNPMWRQGM FVMPFMARIG VTDSWGGWSI TGESVANPG FWSFEGVALA HIGLSGLLFL AAVWHWVYWD LELFRDPRTG NPALDLPKIF GIHLLLSGVL CFGFGAFHVT G AWGPGIWV SDAYGITGKV QPVAPAWGPE GFNPFNPSGV ASHHIAAGIL GFAAGIFHIA VRPPQRLYRA LRMGNIETVL SS SIAAVFW SAFITTGTMW YGSATTPIEL FGPTRYQWDS GYFQQEIERR VENSLNEGLS LSEAWSRIPD KLAFYDYVGN NPA KGGLFR AGPMNKGDGI AEAWLGHPIF QDKEGRELTV RRMPAFFETF PVILVDKDGI IRADIPFRRA ESKYSIEQVG VTTS FYGGK LNGQVFTDAP TVKKYARKAQ LGEVMEFDRT TLESDGVFRS SPRGWYTFGH ANFALLFFLG HLWHGSRTLF RDVFS GIGA EVTEQVEFGA FQKLGDRSTK KQGAV

UniProtKB: Photosystem II CP47 reaction center protein

+
Macromolecule #3: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 53.609383 KDa
SequenceString: MKVFALGWLL KISLMKTLYS LRRFYHVETP FNSNLGIAGR DIESTGFAWW SGNSRLINVS GKLLGAHVAH AGLMVFWCGA MTLFEVAHY IPEKPLYEQG LILLPHLATL GWGVGPGGEI VDIYPYFVVG ILHIISSAVL GFGGVYHSLI GPDTLEESFP A FGYDWRDK ...String:
MKVFALGWLL KISLMKTLYS LRRFYHVETP FNSNLGIAGR DIESTGFAWW SGNSRLINVS GKLLGAHVAH AGLMVFWCGA MTLFEVAHY IPEKPLYEQG LILLPHLATL GWGVGPGGEI VDIYPYFVVG ILHIISSAVL GFGGVYHSLI GPDTLEESFP A FGYDWRDK NKITTILGIH LVILGFGALL LVVKAMYVGG LYDTWAPGGG DVRIIDNPTL NPVVIIGYVL KSPWGGDGWI VS VNNMEDI VGGHIWIGFT CIAGGFWHIL TKPFAWARRA YVWSGEAYLS YSLVAVSLMG FIASQYSWYN NTAYPSEFYG PTG PEASQS QAFTFLVRDQ RLGASVASAQ GPTGLGKYLM RSPSGEIILG GETQRFWDLR APWIEPLRGP NGLDLNKIKN DIQP WQERR AAEYMTHAPL GSLNSVGGVA TEINSVNFVS PRSWLTCAHF LLGFVFYIGH LWHAGRARAA AAGFEKGINR ENEPT LSLR PID

UniProtKB: Photosystem II CP43 reaction center protein

+
Macromolecule #4: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 39.220824 KDa
SequenceString: MTIAIGQEEG RGWFDLMDDW LKRDRFVFVG WSGLLLFPTS YLSIGGWFTG TTFVTSWYTH GLASSYLEGC NFFTAAVSTP ANSMGHSLL LLWGPEAQGD FTRWCQIGGL WAFCALHGSF GLIGFCLRQF EIARLVGIRP YNAIAFSGPI AIFVSVFLMY P LGQASWFF ...String:
MTIAIGQEEG RGWFDLMDDW LKRDRFVFVG WSGLLLFPTS YLSIGGWFTG TTFVTSWYTH GLASSYLEGC NFFTAAVSTP ANSMGHSLL LLWGPEAQGD FTRWCQIGGL WAFCALHGSF GLIGFCLRQF EIARLVGIRP YNAIAFSGPI AIFVSVFLMY P LGQASWFF APSLGVAAIF RFLLFIQGFH NFTLNPFHMM GVAGILGAAL LCAIHGATVQ NTIFEDGDAA NTFRAFTPTQ AE ETYSMVT ANRFWSQIFG VAFSNKRWLH FFMLFVPLAG LWTSAIGIVG LALNLRAYDF VSQELRAAED PEFETFYTKN ILL NEGIRS WMAAQDQPHE NFIFPEEVLP RGNAL

UniProtKB: Photosystem II D2 protein

+
Macromolecule #5: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 9.50372 KDa
SequenceString:
MSGGSTGERP FSDIITSIRY WIIHSITIPA LFVAGWLFVS TGLAYDIFGT PRPNEYFTQE RQQVPLVNDR FSAKQELEDL TKGL

UniProtKB: Cytochrome b559 subunit alpha

+
Macromolecule #6: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 4.860847 KDa
SequenceString:
MSKIKQPISY PIFTFRWLAI HGLAVPTVFF LGAITSMQFI QR

UniProtKB: Cytochrome b559 subunit beta

+
Macromolecule #7: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 7.429764 KDa
SequenceString:
MALRTRLGEL LRPLNSEYGK VAPGWGTTPI MGFVMLLFAV FLLIILQIYN SSLIIENVDV DWASLGS

UniProtKB: Photosystem II reaction center protein H

+
Macromolecule #8: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 4.390065 KDa
SequenceString:
MFTLKIVVYT TVTLFVSLFT FGFLSNDASR NPNRKDLE

UniProtKB: Photosystem II reaction center protein I

+
Macromolecule #9: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 5.025104 KDa
SequenceString:
MEGIFLLAKL PEAYAVFKPI IDVAPVIPVF FLLLAFVWQA AVGFR

UniProtKB: Photosystem II reaction center protein K

+
Macromolecule #10: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 4.363087 KDa
SequenceString:
MSGPNPNKQP VELNRTSLFW GLLLIFVLAV LFSSYFFN

UniProtKB: Photosystem II reaction center protein L

+
Macromolecule #11: Photosystem II protein M

MacromoleculeName: Photosystem II protein M / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 4.300023 KDa
SequenceString:
MNVSVAAYLA VLLGTFIPVV FLITLFIQSE ARKAAESGQE

+
Macromolecule #12: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 3.7085 KDa
SequenceString:
METLVYTFLL IGTLGVLFFA VFFRDPPRIA KK

UniProtKB: Photosystem II reaction center protein T

+
Macromolecule #13: Photosystem II protein W

MacromoleculeName: Photosystem II protein W / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 7.864871 KDa
SequenceString:
MNANVAKALA PAVAAFSVAA PAFAEGTGEA LGVDDGRLLV PLVLIPVFIA ILFSNFASTQ DNEDFFDTYD QRRK

+
Macromolecule #14: Photosystem II reaction center X protein

MacromoleculeName: Photosystem II reaction center X protein / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 4.192965 KDa
SequenceString:
MTPSFSAFIN SLLAGLFIVI IPIGTALLIV SQSDRLTRN

UniProtKB: Photosystem II reaction center protein X

+
Macromolecule #15: Photosystem II reaction center protein Psb30

MacromoleculeName: Photosystem II reaction center protein Psb30 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 3.662478 KDa
SequenceString:
MPNLQTVAQL ISLFLILTSG PAIIVLIALR RGNL

UniProtKB: Photosystem II reaction center protein Psb30

+
Macromolecule #16: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 6.656092 KDa
SequenceString:
MVAILQLLVS MLILLSFALV VSVPVILVSP GEWEKSKGLV YTGAGLWFGL VIMTAAFNSF VI

UniProtKB: Photosystem II reaction center protein Z

+
Macromolecule #17: NCP

MacromoleculeName: NCP / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 30.760855 KDa
SequenceString: RTVLVLACSL LLFAPSSHAF APAGVARVGM PLRGKSVSAR SARVTPAKMA MDPSQLSHIA DGAQTFLSTL DTVPFIDEVT GEPQGFTSP KNHFASVIGL WVLFALPVWS AAYKQAGCTT PDWFGVSQVA EDAPGVGLLA KAAPEYNGPS FREGLEYVFS F VWKPPILI ...String:
RTVLVLACSL LLFAPSSHAF APAGVARVGM PLRGKSVSAR SARVTPAKMA MDPSQLSHIA DGAQTFLSTL DTVPFIDEVT GEPQGFTSP KNHFASVIGL WVLFALPVWS AAYKQAGCTT PDWFGVSQVA EDAPGVGLLA KAAPEYNGPS FREGLEYVFS F VWKPPILI AWKPRADLDR DAMDPARDTV VSSLYKGLGG ALDKTAVYDE EDQLLILSDI VTFEETDLGR RREAIAEASG WY TGNPSFG RSLIEYSEQT RKGKRDQGTV TISTEELAKL RAEAAKK

+
Macromolecule #18: CAC2

MacromoleculeName: CAC2 / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 23.912699 KDa
SequenceString: MLRTALIAAC VASASAFVPA SGFAPMAMKS RTSAVSSMRM QEGDFSAAVP FLKRPSNLDG AYIGDVGFDP LGFSDVFDLR VLREAELKH GRFAMLAVLG FIVQELYTFP FFPKMAPVDA HDYFVKQGGG SQIIFWISFV ELFGVVALFE TLQGKREPGD F AFDPLGLA ...String:
MLRTALIAAC VASASAFVPA SGFAPMAMKS RTSAVSSMRM QEGDFSAAVP FLKRPSNLDG AYIGDVGFDP LGFSDVFDLR VLREAELKH GRFAMLAVLG FIVQELYTFP FFPKMAPVDA HDYFVKQGGG SQIIFWISFV ELFGVVALFE TLQGKREPGD F AFDPLGLA KDEATLERYR LAEVKHARLA MIAIGGFIHQ YWVTKQTVLE QLGNFKSLA

+
Macromolecule #19: CAC3

MacromoleculeName: CAC3 / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 23.723541 KDa
SequenceString: MAVLALACVA AASAFSSPAL LGGVTRATRA SAISGMKMQD RSYSMPFLSR PPALDGTMAG DVGFDPLGFS NYFDLKWLRE AELKHGRIC MLGCLGFITQ EKIQLPLPGF DNKVATEAFF SVPAGGLWQI FFTLGAIEIL SNGGKLAPAD MFAEGRAPGD L GFDPLNLS ...String:
MAVLALACVA AASAFSSPAL LGGVTRATRA SAISGMKMQD RSYSMPFLSR PPALDGTMAG DVGFDPLGFS NYFDLKWLRE AELKHGRIC MLGCLGFITQ EKIQLPLPGF DNKVATEAFF SVPAGGLWQI FFTLGAIEIL SNGGKLAPAD MFAEGRAPGD L GFDPLNLS GDDAALRRFE LAELKHARLA MIGLGGMLHQ MLITKQAPLE QLANFQPIQY YGL

+
Macromolecule #20: CAC4

MacromoleculeName: CAC4 / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 23.11185 KDa
SequenceString: MAVVASASAF APAGVLPRAA TRAAAKSSAP TMQLYQEGIL QGITVNAIPK AERPPGLDGT YVGDIGFDPL GFSSIIDMRW LREAELKHG RVCMLAATGM IVQDVYQFPG VTKSFGDAKM TTLHDVAVKQ GSMQQLLVWL GFLEIFGFVA IVQMLQGSDR Q PGDFGFDP ...String:
MAVVASASAF APAGVLPRAA TRAAAKSSAP TMQLYQEGIL QGITVNAIPK AERPPGLDGT YVGDIGFDPL GFSSIIDMRW LREAELKHG RVCMLAATGM IVQDVYQFPG VTKSFGDAKM TTLHDVAVKQ GSMQQLLVWL GFLEIFGFVA IVQMLQGSDR Q PGDFGFDP LNCAANPDAL ARRQLVELKN GRLAMIATAG MLHHFFITGK GPIQLITG

+
Macromolecule #21: CAC5

MacromoleculeName: CAC5 / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 24.738434 KDa
SequenceString: MLRTTLALAA VAGAAAFAPS PAFAPKAATT RAVATQGPRM AVFGGDFSES VPFLKTPTNL DGSLPGDVGF DPLGFSEVFD IRVLREAEL KHGRIAMLAT LGYLVQEAYV LPFFEKVPPI QAHDALVKSG GMSQILLWTS FLEIFGGIAL FSTIQGRRYP G DFSFDPLG ...String:
MLRTTLALAA VAGAAAFAPS PAFAPKAATT RAVATQGPRM AVFGGDFSES VPFLKTPTNL DGSLPGDVGF DPLGFSEVFD IRVLREAEL KHGRIAMLAT LGYLVQEAYV LPFFEKVPPI QAHDALVKSG GMSQILLWTS FLEIFGGIAL FSTIQGRRYP G DFSFDPLG LSQGKNADKL EQYQLAEIKH SRLAMLAFSG FVHQGFITKQ GVLEQLGNFR PIPGFPEATF F

+
Macromolecule #22: CAC6

MacromoleculeName: CAC6 / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 24.792469 KDa
SequenceString: MDKHADIETE KSCIPGRIPR SRRCTLISIP RRVSDGCTLC SAAAIARGPT MQDNAMPFLE RPPKLDGSLA GDVGFDPVGF SNYFDLRWL RESELKHGRV CMLGVTGLLV QEAVCLPQFS NGKTPVDDFF VVPAAGLWQV FFAIGAVEFF SHGFKLTPGD M FSEGREAG ...String:
MDKHADIETE KSCIPGRIPR SRRCTLISIP RRVSDGCTLC SAAAIARGPT MQDNAMPFLE RPPKLDGSLA GDVGFDPVGF SNYFDLRWL RESELKHGRV CMLGVTGLLV QEAVCLPQFS NGKTPVDDFF VVPAAGLWQV FFAIGAVEFF SHGFKLTPGD M FSEGREAG DFGFDPLNLS GNPDALARRR LVEVKNGRLA MIAFGGLLHQ QLLTGQGTFE QLANFKAIA

+
Macromolecule #23: CAC1

MacromoleculeName: CAC1 / type: protein_or_peptide / ID: 23 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas salina (eukaryote)
Molecular weightTheoretical: 25.265215 KDa
SequenceString: MRFAFAALCA SASAFTASPA LFTRQSTRAA VSRGPSMQLY QEGVLQGLGV DAIPGTDRPK NLDGTLVGDI GFDPLGFSNW LDLRWAREA EIKHGRVAML AATGMIVQDV YKFPGVQQTF GDASMMKLHN VAVGQGAMQQ LFLWITVLET LTGIPAIIQT L KGSERQPG ...String:
MRFAFAALCA SASAFTASPA LFTRQSTRAA VSRGPSMQLY QEGVLQGLGV DAIPGTDRPK NLDGTLVGDI GFDPLGFSNW LDLRWAREA EIKHGRVAML AATGMIVQDV YKFPGVQQTF GDASMMKLHN VAVGQGAMQQ LFLWITVLET LTGIPAIIQT L KGSERQPG DFGFDPLGCG SNPEQLARRQ LVELKNGRLA MIAVGGMVHH YLLVGRGPIE FIKNIPNFKN PLPPF

+
Macromolecule #24: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 24 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #25: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 25 / Number of copies: 194 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #26: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 26 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

+
Macromolecule #27: 1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tet...

MacromoleculeName: 1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene
type: ligand / ID: 27 / Number of copies: 24 / Formula: WVN
Molecular weightTheoretical: 536.873 Da

+
Macromolecule #28: 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: 28 / Number of copies: 4 / 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

+
Macromolecule #29: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...

MacromoleculeName: 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: 29 / Number of copies: 4 / Formula: PL9
Molecular weightTheoretical: 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

+
Macromolecule #30: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 30 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

+
Macromolecule #31: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 31 / Number of copies: 20 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #32: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 32 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

+
Macromolecule #33: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 33 / Number of copies: 4 / Formula: MN
Molecular weightTheoretical: 54.938 Da

+
Macromolecule #34: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 34 / Number of copies: 22 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #35: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 35 / Number of copies: 4 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #36: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 36 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #37: Chlorophyll c2

MacromoleculeName: Chlorophyll c2 / type: ligand / ID: 37 / Number of copies: 24 / Formula: KC2
Molecular weightTheoretical: 608.926 Da
Chemical component information

ChemComp-KC2:
Chlorophyll c2

+
Macromolecule #38: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...

MacromoleculeName: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17- ...Name: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
type: ligand / ID: 38 / Number of copies: 48 / Formula: II0
Molecular weightTheoretical: 564.84 Da
Chemical component information

ChemComp-II0:
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol

+
Macromolecule #39: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...

MacromoleculeName: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
type: ligand / ID: 39 / Number of copies: 8 / Formula: IHT
Molecular weightTheoretical: 550.856 Da
Chemical component information

ChemComp-IHT:
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol

+
Macromolecule #40: water

MacromoleculeName: water / type: ligand / ID: 40 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6jlu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112613
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more