[English] 日本語
Yorodumi
- EMDB-6932: Structure of photosystem I supercomplex with light-harvesting com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6932
TitleStructure of photosystem I supercomplex with light-harvesting complexes I and II
Map data
Sample
  • Complex: Supercomplex of plant PSI-LHCI-LHCII from Zea Mays
    • Protein or peptide: x 20 types
  • Ligand: x 13 types
KeywordsPhotosystem / Antenna / Supercomplex / State transition / MEMBRANE PROTEIN
Function / homology
Function and homology information


thylakoid membrane / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II ...thylakoid membrane / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / protein domain specific binding / magnesium ion binding / metal ion binding / membrane
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 / 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 PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / 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 A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit IV A / Photosystem I reaction center subunit II, chloroplastic / 16kDa membrane protein / Photosystem I reaction center subunit III / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic ...Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit IV A / Photosystem I reaction center subunit II, chloroplastic / 16kDa membrane protein / Photosystem I reaction center subunit III / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit N, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Chlorophyll a-b binding protein 1, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX
Similarity search - Component
Biological speciesZea mays (maize) / Zea mays subsp. mays (maize)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPan XW / Ma J
Funding support China, 10 items
OrganizationGrant numberCountry
the National Key R&D Program of China2017YFA0503702 China
the National Key R&D Program of China2017YFA0504700 China
the National Key R&D Program of China2016YFA0502900 China
the Strategic Priority Research Program of CASXDB08020302 China
the Strategic Priority Research Program of CASXDB08030204 China
the Key Research Program of Frontier Sciences of CASQYZDB-SSW-SMC005 China
National Natural Science Foundation of China31770778 China
National Natural Science Foundation of China31700649 China
National Natural Science Foundation of China31600609 China
National Thousand (Young) Talents Program China
CitationJournal: Science / Year: 2018
Title: Structure of the maize photosystem I supercomplex with light-harvesting complexes I and II.
Authors: Xiaowei Pan / Jun Ma / Xiaodong Su / Peng Cao / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li /
Abstract: Plants regulate photosynthetic light harvesting to maintain balanced energy flux into photosystems I and II (PSI and PSII). Under light conditions favoring PSII excitation, the PSII antenna, light- ...Plants regulate photosynthetic light harvesting to maintain balanced energy flux into photosystems I and II (PSI and PSII). Under light conditions favoring PSII excitation, the PSII antenna, light-harvesting complex II (LHCII), is phosphorylated and forms a supercomplex with PSI core and the PSI antenna, light-harvesting complex I (LHCI). Both LHCI and LHCII then transfer excitation energy to the PSI core. We report the structure of maize PSI-LHCI-LHCII solved by cryo-electron microscopy, revealing the recognition site between LHCII and PSI. The PSI subunits PsaN and PsaO are observed at the PSI-LHCI interface and the PSI-LHCII interface, respectively. Each subunit relays excitation to PSI core through a pair of chlorophyll molecules, thus revealing previously unseen paths for energy transfer between the antennas and the PSI core.
History
DepositionMar 20, 2018-
Header (metadata) releaseJun 20, 2018-
Map releaseJun 20, 2018-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5zji
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6932.png

Downloads & links

-
Map

FileDownload / File: emd_6932.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 296.8 Å		1.06 Å/pix.
x 280 pix.
= 296.8 Å		1.06 Å/pix.
x 280 pix.
= 296.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.11124071 - 0.29227716
Average (Standard dev.)0.0006920389 (±0.011263453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-140-140-140
Dimensions280280280
Spacing280280280
CellA=B=C: 296.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z296.800296.800296.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-140-140-140
NC/NR/NS280280280
D min/max/mean-0.1110.2920.001

-
Supplemental data

-
Sample components

+
Entire : Supercomplex of plant PSI-LHCI-LHCII from Zea Mays

EntireName: Supercomplex of plant PSI-LHCI-LHCII from Zea Mays
Components
  • Complex: Supercomplex of plant PSI-LHCI-LHCII from Zea Mays
    • 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 subunit VII
    • Protein or peptide: Photosystem I reaction center subunit II
    • Protein or peptide: Photosystem I reaction center subunit IV A
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit V
    • 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
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: 16kDa membrane protein
    • Protein or peptide: Photosystem I reaction center subunit N
    • Protein or peptide: Chlorophyll a-b binding protein 1, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • 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

+
Supramolecule #1: Supercomplex of plant PSI-LHCI-LHCII from Zea Mays

SupramoleculeName: Supercomplex of plant PSI-LHCI-LHCII from Zea Mays / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Zea mays (maize)

+
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: Zea mays (maize)
Molecular weightTheoretical: 26.335127 KDa
SequenceString: MVMASSSGLR SCSAVGVPSL LAPSSRSGRL APFCANATTS GRVTMSAEWM PGQPRPAHLD GSSPGDFGFD PLGLATVPEN FERFKESEV YHCRWAMLAV PGILVPEALG LGNWVKAQEW AAVPGGQATY LGAPVPWGTL PTILVIEFVA IAFAEHQRTM E KDPEKKKY ...String:
MVMASSSGLR SCSAVGVPSL LAPSSRSGRL APFCANATTS GRVTMSAEWM PGQPRPAHLD GSSPGDFGFD PLGLATVPEN FERFKESEV YHCRWAMLAV PGILVPEALG LGNWVKAQEW AAVPGGQATY LGAPVPWGTL PTILVIEFVA IAFAEHQRTM E KDPEKKKY PGGAFDPLGF SKDPAKFEEY KLKEIKNGRL AMLAFVGFCV QQSAYPGTGP LENLASHLAD PWHNNIGDII IP RSISP

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: Zea mays (maize)
Molecular weightTheoretical: 29.237975 KDa
SequenceString: MALVSASSSS TTAVAALPRN GQQRASSSLF SSSSSSSFLV GKTLLRQAEA ARPSFAVRAA ADSDRPIWFP GSTPPPWLDG SLPGDFGFD PWGLGSDPES LRWNVQAELV HCRWAMLGAA GIFIPEFLTK IGVLNTPFWY TAGEQQYFTD TTTLFIIELI L IGWAEGRR ...String:
MALVSASSSS TTAVAALPRN GQQRASSSLF SSSSSSSFLV GKTLLRQAEA ARPSFAVRAA ADSDRPIWFP GSTPPPWLDG SLPGDFGFD PWGLGSDPES LRWNVQAELV HCRWAMLGAA GIFIPEFLTK IGVLNTPFWY TAGEQQYFTD TTTLFIIELI L IGWAEGRR WADIIKPGSV NTDPIFPSNK LTGTDVGYPG GLWFDPLGWG SGSPEKIKEL RTKEIKNGRL AMLAVMGAWF QA EYTGTGP IDNLFAHLAD PGHATIFQAF TPK

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: Zea mays (maize)
Molecular weightTheoretical: 29.011234 KDa
SequenceString: MAAQALLSGR QLLGRPVQSA VSRSSARKAP FVVRASSSPP AKQGADRQLW FASKQSLSYL DGTLPGDYGF DPLGLSDPEG TGGFIEPKW LAYGEVINGR YAMLGAVGAI APEIFGKMGI IPPETALPWF KTGVIPPAGT YNYWADSYTL FVFNMALMGF A EHRRLQDW ...String:
MAAQALLSGR QLLGRPVQSA VSRSSARKAP FVVRASSSPP AKQGADRQLW FASKQSLSYL DGTLPGDYGF DPLGLSDPEG TGGFIEPKW LAYGEVINGR YAMLGAVGAI APEIFGKMGI IPPETALPWF KTGVIPPAGT YNYWADSYTL FVFNMALMGF A EHRRLQDW YNPGSMGKQY FLGLEKFLAG SGDPSYPGGP LFNPLGFGKT EKEMNELKLK EIKNGRLAML AILGYFIQGL VT GVGPFQN LLDHLADPVN NNVLTSLKFH

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: Zea mays (maize)
Molecular weightTheoretical: 27.406082 KDa
SequenceString: MASVTARAPV AALRPSASLK SSSSSAAAFL GHSSRLGRTA TASPTRRSLK AEAKGEWLPG LPSPAYLDGS LPGDNGFDPL GLAEDPENL RWYVQAELVN GRWAMLGVAG MLIPEVLTKA GLINAPQWYD AGKSEYFASS STLFVIEFIL FHYVEIRRWQ D IKNPGSVN ...String:
MASVTARAPV AALRPSASLK SSSSSAAAFL GHSSRLGRTA TASPTRRSLK AEAKGEWLPG LPSPAYLDGS LPGDNGFDPL GLAEDPENL RWYVQAELVN GRWAMLGVAG MLIPEVLTKA GLINAPQWYD AGKSEYFASS STLFVIEFIL FHYVEIRRWQ D IKNPGSVN QDPIFKSYSL PPHECGYPGS VFNPLNFAPT LEAKEKELAN GRLAMLAFLA FLIQHNVTGK GPFDNLLQHL SD PWHNTII QTLSG

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: Zea mays (maize)
Molecular weightTheoretical: 83.193156 KDa
SequenceString: MIIRSSEPEV KIAVDRDPIK TSFEEWARPG HFSRTIAKGP DTTTWIWNLH ADAHDFDSHT GDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQIWRASG ITSELQLYCT A IGALIFAS ...String:
MIIRSSEPEV KIAVDRDPIK TSFEEWARPG HFSRTIAKGP DTTTWIWNLH ADAHDFDSHT GDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQIWRASG ITSELQLYCT A IGALIFAS LMLFAGWFHY HKAAPKLAWF QDVESMLNHH LAGLLGLGSL SWAGHQIHVS LPINQFLDAG VDPKEIPLPH EF ILNRDLL AQLYPSFAEG ATPFFTLNWS KYAEFLSFRG GLDPITGGLW LSDIAHHHLA IAILFLIAGH MYRTNWGIGH GLK DILEAH KGPFTGQGHK GLYEILTTSW HAQLSLNLAM LGSTTIVVAH HMYSMPPYPY LATDYGTQLS LFTHHMWIGG FLIV GAAAH AAIFMVRDYD PTTRYNDLLD RVLRHRDAII SHLNWVCIFL GFHSFGLYIH NDTMSALGRP QDMFSDAAIQ LQPIF AQWI QNIHAGAPGV TAPGATTSTS LTWGGGELVA IGGKVALLPI PLGTADFLVH HIHAFTIHVT VLILLKGVLF ARSSRL IPD KANLGFRFPC DGPGRGGTCQ VSAWDHVFLG LFWMYNSISV VIFHFSWKMQ SDVWGTISDQ GIVTHITGGN FAQSSIT IN GWLRDFLWAQ ASQVIQSYGS SLSAYGLFFL GAHFVWAFSL MFLFSGRGYW QELIESIVWA HNKLKVAPAT QPRALSII Q GRAVGVTHYL LGGIATTWAF FLARIIAVG

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: Zea mays subsp. mays (maize)
Molecular weightTheoretical: 82.648797 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 IPGSRGEYVR WNNFLDVLPY PQGLGPLLTG QWNLYAQNPD SS NHLFGTT QGAGTAILTL LGGFHPQTQS LWLTDIAHHH LAIAFIFLIA GHMYRTNFGI GHSIKDLLEA HTPPGGRLGR GHK GLYDTI NNSIHFQLGL ALASLGVITS LVAQHMYSLP AYAFIAQDFT TQAALYTHHQ YIAGFIMTGA FAHGAIFFIR DYNP EQNED NVLARMLDHK EAIISHLSWA SLFLGFHTLG LYVHNDVMLA FGTPEKQILI EPIFAQWIQS AHGKTTYGFD ILLSS TNGP AFNAGRNIWL 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 subunit VII

MacromoleculeName: photosystem I subunit VII / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Zea mays subsp. mays (maize)
Molecular weightTheoretical: 8.909345 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPTDVLEMIP WDGCKAKQIA SAPRTEDCVG CKRCESACPT DFLSVRVYLG PETTRSMALS Y

+
Macromolecule #8: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 21.603672 KDa
SequenceString: MAMATQASAA TRHLLAAAWA PAAKPRQLSS QLALPSSSSR GPAPLRASTE EAVEAPKGFV APQLDPSTPS PIFGGSTGGL LRKAQVEEF YVITWTSPKE QVFEMPTGGA AIMREGPNLL KLARKEQCLA LGTRLRSKYK ITYQFYRVFP NGEVQYLHPK D GVYPEKVN ...String:
MAMATQASAA TRHLLAAAWA PAAKPRQLSS QLALPSSSSR GPAPLRASTE EAVEAPKGFV APQLDPSTPS PIFGGSTGGL LRKAQVEEF YVITWTSPKE QVFEMPTGGA AIMREGPNLL KLARKEQCLA LGTRLRSKYK ITYQFYRVFP NGEVQYLHPK D GVYPEKVN PGREGVGQNF RSIGKNVNPI DVKFTGKATF D

UniProtKB: Photosystem I reaction center subunit II, chloroplastic

+
Macromolecule #9: Photosystem I reaction center subunit IV A

MacromoleculeName: Photosystem I reaction center subunit IV A / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 14.429237 KDa
SequenceString:
MASTNMASAT SRFMLAAGVP TGSSGGRVNF ASAPNRLGRR LVARADNEAA AAEAAEGEGA VATKPKAEKP PPIGPKRGAK VKILRRESY WYNGIGNVVT VDQDPNTRYP VVVRFNKVNY AGVSTNNYAL DEVSEVK

UniProtKB: Photosystem I reaction center subunit IV A

+
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: Zea mays (maize)
Molecular weightTheoretical: 23.833559 KDa
SequenceString: MAALAAASTA AFAAKPRARL SVACSAATGD SSSVSLASSV KTFSAALALS SVLLSSAATS PPPAAADIAG LTPCKESKAF AKREKNSIK KLTASLKKYA PDSAPALAIN ATIEKTKRRF ENYGKFGLLC GADGLPHLIV SGDQRHWGEF VTPGLLFLYI A GWIGWVGR ...String:
MAALAAASTA AFAAKPRARL SVACSAATGD SSSVSLASSV KTFSAALALS SVLLSSAATS PPPAAADIAG LTPCKESKAF AKREKNSIK KLTASLKKYA PDSAPALAIN ATIEKTKRRF ENYGKFGLLC GADGLPHLIV SGDQRHWGEF VTPGLLFLYI A GWIGWVGR SYLIAISGEK KPAMREIIID VELATRLLPR GFIWPVAAYR ELINGDLVVD DKDIGYY

UniProtKB: Photosystem I reaction center subunit III

+
Macromolecule #11: Photosystem I reaction center subunit V

MacromoleculeName: Photosystem I reaction center subunit V / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 15.329372 KDa
SequenceString:
MAATSTAAAV LSPPSVAGLR LAPSPGRARV SFRAAPAPAR RSVAARAELS SALVISLSTG VSLFLGRFVF FNFQRENVAK QVPAQNGKT HFDAGDERAK EFAALLKSND PVGFNLVDVL AWGSLGHIVA YYILATSSNG YDPNFF

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: Zea mays (maize)
Molecular weightTheoretical: 14.948259 KDa
SequenceString:
MASLAAVSVK PVAIKGLAGS SISGRKLAVA RPSARSIRRP RAAAVVAKYG DKSVYFDLDD IGNTTGQWDL YGSDAPSPYN PLQSKFFET FAAPFTKRGL LLKFLLLGGG SLLAYVSASA SPDLLPIKKG PQEPPQPGPR GKI

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: Zea mays (maize)
Molecular weightTheoretical: 4.029889 KDa
SequenceString:
MTDFNLPSIF VPLVGLVFPA IAMTSLFLYV QKNKIV

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: Zea mays (maize)
Molecular weightTheoretical: 4.74762 KDa
SequenceString:
MRDIKTYLSV APVLSTLWFG ALAGLLIEIN RLFPDALSFP FF

UniProtKB: Photosystem I reaction center subunit IX

+
Macromolecule #15: Photosystem I reaction center subunit psaK

MacromoleculeName: Photosystem I reaction center subunit psaK / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 13.668812 KDa
SequenceString:
MASQLSAAVP RFHGLRGYAA PRSAVAALPS VRVGRKRSSS QGIRCDYIGS ATNLIMVTTT TLMLFAGRFG LAPSANRKAT AGLKLEARD SGLQTGDPAG FTLADTLACG AVGHILGVGI VLGLKNTGAL DQIIG

UniProtKB: Photosystem I reaction center subunit psaK, chloroplastic

+
Macromolecule #16: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 22.347809 KDa
SequenceString: MATAYAPMAS QVMKSSLVVH SRPRGLSGAA ALTRRPGRFT VKAIQPEKAT YQVVQPINGD PFIGSLETPV TSSPLVAWYL SNLPAYRTA VSPLLRGVEV GLAHGYLLVG PFALTGPLRS TPVHGQAGAL GAAGLVAILS VCLTMYGVAS FNEGDPSTAP S LTLTGRKK ...String:
MATAYAPMAS QVMKSSLVVH SRPRGLSGAA ALTRRPGRFT VKAIQPEKAT YQVVQPINGD PFIGSLETPV TSSPLVAWYL SNLPAYRTA VSPLLRGVEV GLAHGYLLVG PFALTGPLRS TPVHGQAGAL GAAGLVAILS VCLTMYGVAS FNEGDPSTAP S LTLTGRKK EADKLQTSDG WAKFTGGFFF GGISGVLWAY FLLYVLDLPY FFK

UniProtKB: Photosystem I reaction center subunit XI, chloroplastic

+
Macromolecule #17: 16kDa membrane protein

MacromoleculeName: 16kDa membrane protein / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 14.381669 KDa
SequenceString:
MHLLASCCFT RGSRVSARNP LMSRNLERNG RITCMTFPRD WLRRDLSVIG FGLIGWMGPS SVPAINGNSL TGLFFSSIGQ ELAHFPTPP PVTSQFWLWL VTWHLGLFIV LTFGQIGFKG RTEDYFEK

UniProtKB: 16kDa membrane protein

+
Macromolecule #18: Photosystem I reaction center subunit N

MacromoleculeName: Photosystem I reaction center subunit N / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 15.663827 KDa
SequenceString:
MNSSFIGLKP AAAAAQATAA ASSPMKQQQV QVAPQSRRAA LLGLAAVFAV TATTAGSAKA GVFDEYLEKS KANKELNDKK RMATSAANF ARAYTVEFGS CQFPYNFTGC QDLAKQKKVP FLSDDLEIEC EGKEKFKCGS NVFWKW

UniProtKB: Photosystem I reaction center subunit N, chloroplastic

+
Macromolecule #19: Chlorophyll a-b binding protein 1, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 1, chloroplastic / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 24.879148 KDa
SequenceString: RKTVGKPKVA ASGSPWYGPD RVKYLGPFSG EPPSYLTGEF PGDYGWDTAG LSADPETFAK NRELEVIHSR WAMLGALGCV FPELLSRNG VKFGEAVWFK AGSQIFSEGG LDYLGNPSLI HAQSILAIWA CQVVLMGAVE GYRIAGGPLG EVVDPLYPGG S FDPLGLAD ...String:
RKTVGKPKVA ASGSPWYGPD RVKYLGPFSG EPPSYLTGEF PGDYGWDTAG LSADPETFAK NRELEVIHSR WAMLGALGCV FPELLSRNG VKFGEAVWFK AGSQIFSEGG LDYLGNPSLI HAQSILAIWA CQVVLMGAVE GYRIAGGPLG EVVDPLYPGG S FDPLGLAD DPEAFAELKV KELKNGRLAM FSMFGFFVQA IVTGKGPLEN LADHIADPVN NNAWAYATNF VPGN

UniProtKB: Chlorophyll a-b binding protein 1, chloroplastic

+
Macromolecule #20: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 24.7809 KDa
SequenceString: RR(TPO)VKSVPQS IWYGPDRPKY LGPFSEQTPS YLTGEFPGDY GWDTAGLSAD PETFARNREL EVIHSRWAML GALGCV FPE ILAKNGVKFG EAVWFKAGAQ IFSEGGLDYL GNPNLVHAQS ILAIWACQVV LMGFVEGYRV GGGPLGEGLD KVYPGGA FD PLGLADDPDT ...String:
RR(TPO)VKSVPQS IWYGPDRPKY LGPFSEQTPS YLTGEFPGDY GWDTAGLSAD PETFARNREL EVIHSRWAML GALGCV FPE ILAKNGVKFG EAVWFKAGAQ IFSEGGLDYL GNPNLVHAQS ILAIWACQVV LMGFVEGYRV GGGPLGEGLD KVYPGGA FD PLGLADDPDT AAELKVKELK NGRLAMFSMF GFFVQAIVTG KGPIENLFDH VADPVANNAW AYATNFVPGN

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #21: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 21 / Number of copies: 30 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

+
Macromolecule #22: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 22 / Number of copies: 171 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #23: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 23 / Number of copies: 11 / 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 #24: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 24 / Number of copies: 7 / 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 #25: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 25 / Number of copies: 26 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #26: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 26 / Number of copies: 8 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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

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

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

+
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: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 29 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

+
Macromolecule #30: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 30 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

+
Macromolecule #31: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 31 / Number of copies: 2 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #32: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 32 / Number of copies: 2 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #33: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

MacromoleculeName: (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: 33 / Number of copies: 3 / Formula: NEX
Molecular weightTheoretical: 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 635845
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

+
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