[English] 日本語
Yorodumi
- EMDB-66925: In situ structure of the PSI-LHCI supercomplex from Oryza sativa -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66925
TitleIn situ structure of the PSI-LHCI supercomplex from Oryza sativa
Map data
Sample
  • Complex: In situ structure of the PSI-LHCI supercomplex from Oryza sativa
    • Protein or peptide: x 2 types
  • Protein or peptide: x 16 types
  • Ligand: x 11 types
KeywordsPhotosystem I / PSI-LHCI / in situ / Oryza sativa / chloroplast / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid / chlorophyll binding ...photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein domain specific binding / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaO / PsaO transmembrane domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant ...Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaO / PsaO transmembrane domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / : / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit N, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Chlorophyll a-b binding protein, chloroplastic ...Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit N, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit IV / Chlorophyll a-b binding protein, chloroplastic / Os04g0414700 protein / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit III / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice) / Oryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsLi J / Elias E / Zhang K / Croce R / Zhu J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2026
Title: In situ structures of plant photosystem supercomplexes.
Authors: Jiao Li / Eduard Elias / Kai Zhang / Roberta Croce / Jiapeng Zhu /
Abstract: Photosynthesis sustains life on Earth by converting light to chemical energy through the coordinated action of photosystem I (PSI) and photosystem II (PSII) within thylakoid membranes. Although ...Photosynthesis sustains life on Earth by converting light to chemical energy through the coordinated action of photosystem I (PSI) and photosystem II (PSII) within thylakoid membranes. Although structures of isolated photosystems are available, their native organization in chloroplasts remains unknown. Here, using in situ cryo-electron microscopy, we directly imaged Oryza sativa (rice) chloroplasts and determined structures of photosystem supercomplexes in their native membrane environment. We resolved a CSML-type PSII-light harvesting complex II (LHCII) supercomplex, including four LHCII antenna trimers that were not retained in purified preparations. Excitation energy transfer calculations based on this architecture closely reproduce in vivo measurements, indicating its physiological relevance. We also resolved asymmetric PSII-LHCII dimers, including side-by-side, trans-lumenal and trans-stromal architectures, and higher-order assemblies of trimers and tetramers. On the basis of these observations, we propose that PSII forms a trans-lumenal and trans-stromal 'skeleton' that shapes thylakoid morphology and supports grana stacking. In addition, we obtained high-resolution structures of PSI-LHCI-LHCII and PSI-LHCI supercomplexes. Together, these structures reveal extensive networks of lipids, pigments and cofactors, providing the first molecular framework for understanding how the native architecture of plant photosystem supports the exceptional photon-to-electron efficiency of photosynthesis.
History
DepositionNov 4, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_66925.png

Downloads & links

-
Map

FileDownload / File: emd_66925.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.97050434 - 1.7859771
Average (Standard dev.)0.00019770447 (±0.045623627)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_66925_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66925_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : In situ structure of the PSI-LHCI supercomplex from Oryza sativa

EntireName: In situ structure of the PSI-LHCI supercomplex from Oryza sativa
Components
  • Complex: In situ structure of the PSI-LHCI supercomplex from Oryza sativa
    • Protein or peptide: Photosystem I reaction center subunit II, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit IV
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
  • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
  • Protein or peptide: Photosystem I iron-sulfur center
  • Protein or peptide: Photosystem I reaction center subunit III
  • Protein or peptide: Photosystem I reaction center subunit V, chloroplastic
  • Protein or peptide: Photosystem I reaction center subunit VI, chloroplastic
  • Protein or peptide: Photosystem I reaction center subunit VIII
  • Protein or peptide: Photosystem I reaction center subunit IX
  • Protein or peptide: Photosystem I reaction center subunit psaK, chloroplastic
  • Protein or peptide: Photosystem I reaction center subunit XI, chloroplastic
  • Protein or peptide: Photosystem I reaction center subunit N, chloroplastic
  • Protein or peptide: Os04g0414700 protein
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Supramolecule #1: In situ structure of the PSI-LHCI supercomplex from Oryza sativa

SupramoleculeName: In situ structure of the PSI-LHCI supercomplex from Oryza sativa
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #8-#9
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)

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

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 22.068029 KDa
SequenceString: SAEWMPGQPR PAHLDGSSPG DFGFDPLGLA TVPENFERFK ESEVYHCRWA MLAVPGVLVP EALGLGNWVQ AQEWAAEPGG QATYLGNPV PWGTLPTILV IEFVAIAFAE HQRTMEKDPE KKKYPGGAFD PLGFSKDPVK FEEYKLKEIK NGRLAMLAFV G FCVQQSAY ...String:
SAEWMPGQPR PAHLDGSSPG DFGFDPLGLA TVPENFERFK ESEVYHCRWA MLAVPGVLVP EALGLGNWVQ AQEWAAEPGG QATYLGNPV PWGTLPTILV IEFVAIAFAE HQRTMEKDPE KKKYPGGAFD PLGFSKDPVK FEEYKLKEIK NGRLAMLAFV G FCVQQSAY PGTGPLENLA SHLSDPWHNN IGDIIIPRTI YP

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 22.836908 KDa
SequenceString: AAAPDRPIWF PGSTPPPWLD GSLPGDFGFD PLGLGSDPES LRWNVQAELV HCRWAMLGAA GIFIPEFLTK IGILNTPSWY TAGEQQYFT DTTTLFIIEL ILIGWAEGRR WADIIKPGCV NTDPIFPNNK LTGTDVGYPG GLWFDPLGWG TGSPEKIKEL R TKEIKNGR ...String:
AAAPDRPIWF PGSTPPPWLD GSLPGDFGFD PLGLGSDPES LRWNVQAELV HCRWAMLGAA GIFIPEFLTK IGILNTPSWY TAGEQQYFT DTTTLFIIEL ILIGWAEGRR WADIIKPGCV NTDPIFPNNK LTGTDVGYPG GLWFDPLGWG TGSPEKIKEL R TKEIKNGR LAMLAVMGAW FQAEYTGTGP IDNLFAHLAD PGHATIFQAF

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #3: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 24.450938 KDa
SequenceString: DRQLWFASKQ SLSYLDGTLP GDFGFDPLGL SDPEGTGGFI EPRWLAYGEV FNGRTAMMGV VGMVAPELLG KLGLVPAETA IPWFQTGVI PPAGTYTYWA DPYTLFVFEL ALVGFAEHRR FQDWYTPGSM GKQYFLGLEK YLAGSGEPAY PGGPLFNPLG F GTKSEAEM ...String:
DRQLWFASKQ SLSYLDGTLP GDFGFDPLGL SDPEGTGGFI EPRWLAYGEV FNGRTAMMGV VGMVAPELLG KLGLVPAETA IPWFQTGVI PPAGTYTYWA DPYTLFVFEL ALVGFAEHRR FQDWYTPGSM GKQYFLGLEK YLAGSGEPAY PGGPLFNPLG F GTKSEAEM KELKLKEIKN GRLAMLAFLG FSVQALFTGV GPVQNLLDHL ADPVHNNILT SLKFH

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #4: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 22.188219 KDa
SequenceString: KGEWLPGLPS PTYLNGSLPG DNGFDPLGLA EDPENLRWFV QAELVNGRWA MLGVAGMLLP EVLTKIGLID APQWYDAGKA TYFASSSTL FVIEFILFHY VEIRRWQDIK NPGCVNQDPI FKSYSLPPHE CGYPGSVFNP LNFEPTLEAK EKELANGRLA M LAFLGFLV ...String:
KGEWLPGLPS PTYLNGSLPG DNGFDPLGLA EDPENLRWFV QAELVNGRWA MLGVAGMLLP EVLTKIGLID APQWYDAGKA TYFASSSTL FVIEFILFHY VEIRRWQDIK NPGCVNQDPI FKSYSLPPHE CGYPGSVFNP LNFEPTLEAK EKELANGRLA M LAFLGFLV QHNVTQKGPF DNLLQHLSDP WHNTIIQTLS

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #5: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 82.463234 KDa
SequenceString: EPEVKIVVDR DPVKTSFEEW ARPGHFSRTI AKGPDTTTWI WNLHADAHDF DSHTGDLEEI SRKVFSAHFG QLSIIFLWLS GMYFHGARF SNYEAWLSDP THIGPSAQVV LPIVGQEILN GDVGGGFRGI QITSGFFQIW RASGITSELQ LYCTAIGALI F ASLMLFAG ...String:
EPEVKIVVDR DPVKTSFEEW ARPGHFSRTI AKGPDTTTWI WNLHADAHDF DSHTGDLEEI SRKVFSAHFG QLSIIFLWLS GMYFHGARF SNYEAWLSDP THIGPSAQVV LPIVGQEILN GDVGGGFRGI QITSGFFQIW RASGITSELQ LYCTAIGALI F ASLMLFAG WFHYHKAAPK LAWFQDVESM LNHHLAGLLG LGSLSWAGHQ IHVSLPINQF LDAGVDPKEI PLPHEFILNR DL LAQLYPS FAEGATPFFT LNWSKYAEFL SFRGGLDPIT GGLWLSDIAH HHLAIAILFL IAGHMYRTNW GIGHGLKDIL EAH KGPFTG QGHKGLYEIL TTSWHAQLSL NLAMLGSTTI VVAHHMYSMP PYPYLATDYG TQLSLFTHHM WIGGFLIVGA AAHA AIFMV RDYDPTTRYN DLLDRVLRHR DAIISHLNWV CIFLGFHSFG LYIHNDTMSA LGRPQDMFSD TAIQLQPIFA QWVQN LHAG APSVTAPGAT TSTSLTWGGG ELVAVGGKVA LLPIPLGTAD FLVHHIHAFT IHVTVLILLK GVLFARSSRL IPDKAN LGF RFPCDGPGRG GTCQVSAWDH VFLGLFWMYN SISVVIFHFS WKMQSDVWGT ISDQGVVTHI TGGNFAQSSI TINGWLR DF LWAQASQVIQ SYGSSLSAYG LFFLGAHFVW AFSLMFLFSG RGYWQELIES IVWAHNKLKV APATQPRALS IIQGRAVG V THYLLGGIAT TWAFFLARII AVG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

+
Macromolecule #6: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 82.638805 KDa
SequenceString: MELRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFESWIQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA AGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSTLS LIGGWLHLQP K WKPSLSWF ...String:
MELRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFESWIQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA AGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSTLS LIGGWLHLQP K WKPSLSWF KNAESRLNHH LSGLFGVSSL AWTGHLVHVA IPASRGEYVR WNNFLDVLPY PQGLGPLLTG QWNLYAQNPD SS NHLFGTT QGAGTAILTL LGGFHPQTQS LWLTDIAHHH LAIAFIFLIA GHMYRTNFGI GHSIKDLLEA HTPPGGRLGR GHK GLYDTI NNSIHFQLGL ALASLGVITS LVAQHMYSLP SYAFIAQDFT TQAALYTHHQ YIAGFIMTGA FAHGAIFFIR DYNP EQNED NVLARMLDHK EAIISHLSWA SLFLGFHTLG LYVHNDVMLA FGTPEKQILI EPIFAQWIQS AHGKTTYGFD ILLSS TSGP AFNAGRTLWL PGWLNAVNEN SNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLAVFWM LNTIGWVTFY WHWKHITLWQ GNVSQFNESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LSVWAWMFLF GHLVWATGFM FLISWRGYWQ ELIETLAWAH ERTPLANLIR WRDKPVALSI VQARLVGLAH FSVGYIFT Y AAFLIASTSG KFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

+
Macromolecule #7: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 8.909345 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPTDVLEMIP WDGCKAKQIA SAPRTEDCVG CKRCESACPT DFLSVRVYLG PETTRSMALS Y

UniProtKB: Photosystem I iron-sulfur center

+
Macromolecule #8: Photosystem I reaction center subunit II, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit II, chloroplastic
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 15.983311 KDa
SequenceString:
GFVPPQLDPN TPSPIFGGST GGLLRKAQVE EFYVITWTSP KEQVFEMPTG GAAIMREGPN LLKLARKEQC LALGTRLRSK YKINYQFYR VFPNGEVQYL HPKDGVYPEK VNAGRQGVGQ NFRSIGKNVS PIEVKFTGKN VFDI

UniProtKB: Photosystem I reaction center subunit II, chloroplastic

+
Macromolecule #9: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 7.692722 KDa
SequenceString:
KPPPIGPKRG TKVKILRRES YWYNGTGSVV TVDQDPNTRY PVVVRFAKVN YAGVSTNNYA LDEIQEVK

UniProtKB: Photosystem I reaction center subunit IV

+
Macromolecule #10: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 17.514418 KDa
SequenceString:
DIAGLTPCKE SKAFAKREKQ SIKKLQSSLK KYAPDSAPAL AINATIEKTK RRFENYGKFG LLCGADGLPH LIVSGDQRHW GEFITPGLL FLYIAGWIGW VGRSYLIAIS GEKKPAMREI IIDVELAVKL LPRGFIWPVA AYRELITGNL VVDDADIGY

UniProtKB: Photosystem I reaction center subunit III

+
Macromolecule #11: Photosystem I reaction center subunit V, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit V, chloroplastic
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 10.711042 KDa
SequenceString:
LSPSLVISLS TGVSLFLGRF VFFNFQRENV AKQVPEQNGK THFDAGDERA KEFAGLLRSN DPVGFNLVDV LAWGSLGHIV AYYILATCS NGYNPNFF

UniProtKB: Photosystem I reaction center subunit V, chloroplastic

+
Macromolecule #12: Photosystem I reaction center subunit VI, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit VI, chloroplastic
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 10.002326 KDa
SequenceString:
YGEKSVYFDL EDIGNTTGQW DLYGSDAPSP YNPLQSKFFE TFAGPFTKRG LLLKFLLLGG GSLVAYVSAS ASPDLLPIKK GPQLPPTPG PRGK

UniProtKB: Photosystem I reaction center subunit VI, chloroplastic

+
Macromolecule #13: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 3.293013 KDa
SequenceString:
NLPSIFVPLV GLVFPAIAMA SLFLYVQKNK

UniProtKB: Photosystem I reaction center subunit VIII

+
Macromolecule #14: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 4.981871 KDa
SequenceString:
MRDIKTYLSV APVLSTLWFG ALAGLLIEIN RLFPDALSFP FFSF

UniProtKB: Photosystem I reaction center subunit IX

+
Macromolecule #15: Photosystem I reaction center subunit psaK, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit psaK, chloroplastic
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 8.884315 KDa
SequenceString:
YIGSATNVIM VTTTTLMLFA GRFGLAPSAN RKSTAGLKLE ARDSGLQTGD PAGFTLADTL ACGAVGHIMG VGVVLGLKNI GVLDQIIG

UniProtKB: Photosystem I reaction center subunit psaK, chloroplastic

+
Macromolecule #16: Photosystem I reaction center subunit XI, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit XI, chloroplastic
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 17.252824 KDa
SequenceString:
PTYQVVQPIN GDPFIGSLET PVTSSPLVAW YLSNLPAYRT AVSPLLRGIE VGLAHGYLLV GPFALTGPLR NTPVHGQAGA LGAAGLVAI LSVCLTMYGV ASFGEGEPST APTLTLTGRK KEADKLQTAD GWAKFTGGFF FGGISGVLWA YFLLYVLDLP Y FFK

UniProtKB: Photosystem I reaction center subunit XI, chloroplastic

+
Macromolecule #17: Photosystem I reaction center subunit N, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit N, chloroplastic
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 9.746997 KDa
SequenceString:
VFDEYLEKSK ANKELNDKKR LATSGANFAR AYTVEFGSCQ FPYNFTGCQD LAKQKKVPFI SDDLEIECEG KEKYKCGSNV FWKW

UniProtKB: Photosystem I reaction center subunit N, chloroplastic

+
Macromolecule #18: Os04g0414700 protein

MacromoleculeName: Os04g0414700 protein / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 10.276702 KDa
SequenceString:
TFPQDWLRRD LNVIGFGLIG WIAPSSVPAI NGNSLTGLFF SSIGQELSHF PSPPALDSPF WLWLVTWHLG LFLALTFGQI GFKGRTEGY FDK

UniProtKB: Os04g0414700 protein

+
Macromolecule #19: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 19 / Number of copies: 12 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

+
Macromolecule #20: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 20 / Number of copies: 152 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #21: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 21 / Number of copies: 5 / 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

+
Macromolecule #22: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 22 / Number of copies: 4 / 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

+
Macromolecule #23: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 23 / Number of copies: 31 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 24 / Number of copies: 18 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #25: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL...

MacromoleculeName: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
type: ligand / ID: 25 / Number of copies: 12 / Formula: MGE
Molecular weightTheoretical: 688.972 Da
Chemical component information

ChemComp-MGE:
(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE

+
Macromolecule #26: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 26 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

+
Macromolecule #27: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 27 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

+
Macromolecule #28: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 28 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

+
Macromolecule #29: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 29 / Number of copies: 4 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.375 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: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

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

6yez

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 182666
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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