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- EMDB-9995: Structure of cyanobacterial photosystem I-IsiA supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-9995
TitleStructure of cyanobacterial photosystem I-IsiA supercomplex
Map dataThe overall map
Sample
  • Complex: Photosystem I-IsiA supercomplex
    • Protein or peptide: x 12 types
  • Ligand: x 9 types
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosynthetic electron transport chain / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosynthetic electron transport chain / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / 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 center subunit PsaK / Photosystem I reaction centre subunit PsaK / 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 PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / : / 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
Iron stress-induced chlorophyll-binding protein / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit PsaK / Photosystem I iron-sulfur center
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria) / Synechococcus elongatus (strain PCC 7942) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsCao P / Cao DF / Si L / Su XD / Chang WR / Liu ZF / Zhang XZ / Li M
CitationJournal: Nat Plants / Year: 2020
Title: Structural basis for energy and electron transfer of the photosystem I-IsiA-flavodoxin supercomplex.
Authors: Peng Cao / Duanfang Cao / Long Si / Xiaodong Su / Lijin Tian / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li /
Abstract: Under iron-deficiency stress, which occurs frequently in natural aquatic environments, cyanobacteria reduce the amount of iron-enriched proteins, including photosystem I (PSI) and ferredoxin (Fd), ...Under iron-deficiency stress, which occurs frequently in natural aquatic environments, cyanobacteria reduce the amount of iron-enriched proteins, including photosystem I (PSI) and ferredoxin (Fd), and upregulate the expression of iron-stress-induced proteins A and B (IsiA and flavodoxin (Fld)). Multiple IsiAs function as the peripheral antennae that encircle the PSI core, whereas Fld replaces Fd as the electron receptor of PSI. Here, we report the structures of the PSI-IsiA-Fld and PSI-IsiA supercomplexes from Synechococcus sp. PCC 7942, revealing features that are different from the previously reported PSI structures, and a sophisticated pigment network that involves previously unobserved pigment molecules. Spectroscopic results demonstrated that IsiAs are efficient light harvesters for PSI. Three Flds bind symmetrically to the trimeric PSI core-we reveal the detailed interaction and the electron transport path between PSI and Fld. Our results provide a structural basis for understanding the mechanisms of light harvesting, energy transfer and electron transport of cyanobacterial PSI under stressed conditions.
History
DepositionJul 18, 2019-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateMar 4, 2020-
Current statusMar 4, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kig
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9995.png

Downloads & links

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Map

FileDownload / File: emd_9995.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe overall map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 480 pix.
= 499.2 Å		1.04 Å/pix.
x 480 pix.
= 499.2 Å		1.04 Å/pix.
x 480 pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.0813502 - 0.17028174
Average (Standard dev.)0.00043071716 (±0.005058582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 499.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z499.200499.200499.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0810.1700.000

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Supplemental data

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Additional map: The local density of six IsiAs

Fileemd_9995_additional_1.map
AnnotationThe local density of six IsiAs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The local density of six IsiAs

Fileemd_9995_additional_2.map
AnnotationThe local density of six IsiAs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Photosystem I-IsiA supercomplex

EntireName: Photosystem I-IsiA supercomplex
Components
  • Complex: Photosystem I-IsiA supercomplex
    • 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 II
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I PsaI protein
    • 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: PsaM
    • Protein or peptide: Iron stress-induced chlorophyll-binding protein
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: water

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Supramolecule #1: Photosystem I-IsiA supercomplex

SupramoleculeName: Photosystem I-IsiA supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Synechococcus elongatus PCC 7942 (bacteria) / Strain: PCC 7942

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 83.994336 KDa
SequenceString: MTISPPEREA KVKATVDKNP VPTSFEKWGK PGHFDRTLAK GPKTTTWIWN LHANAHDFDS HTSDLEDISR KIFSAHFGHL AVIFIWLSG AYFHGARFSN FSGWLADPTH VKPSAQVVWP IFGQEILNGD VGGGFHGIQI TSGLFQLWRA SGYTNEFQLY V TAIGALVM ...String:
MTISPPEREA KVKATVDKNP VPTSFEKWGK PGHFDRTLAK GPKTTTWIWN LHANAHDFDS HTSDLEDISR KIFSAHFGHL AVIFIWLSG AYFHGARFSN FSGWLADPTH VKPSAQVVWP IFGQEILNGD VGGGFHGIQI TSGLFQLWRA SGYTNEFQLY V TAIGALVM AGLMLFAGWF HYHKAAPKLE WFQNVESMLN HHLAGLLGLG SLSWAGHQIH VSLPVNKLLD AIDAGEPLVL NG KTIASAA DIPLPHEFLD VSLISQLFPG FEAGVKAFFT LNWSAYADFL TFKGGLNPVT GGLWLTDTAH HHLAIAVLFI VAG HMYRTN WGIGHSLKEI LEAHKGPFTG QGHKGLYEIL TTSWHAQLSI NLAILGSISI IVAHHMYAMP PYPYLATDYP TMLS LFTHH IWIGGFLIVG AGAHAAIFMV RDYDPAKNVD NLLDRVLRHR DAIISHLNWV CIWLGFHSFG LYIHNDTMRA LGRPQ DMFS DSAIQLQPIF AQWIQNIHAL APGNTAPNAL ASVSQVFGGD VVAVGGKVAA APIVLGTADF MVHHIHAFTI HVTALI LLK GVLYARSSRL VPDKANLGFR FPCDGPGRGG TCQVSGWDHV FLGLFWMYNS LSIVIFHYSW KMQSDVWGSV LPDGSVA HI ANGNFAQSAL TINGWLRDFL WAQASQVITS YGSSTSAYGL LFLGAHFVWA FSLMFLFSGR GYWQELIESI VWAHNKLK V APAIQPRALS IIQGRAVGVA HYLLGGIVTT WSFFLARIIA VG

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 81.554742 KDa
SequenceString: MATKFPKFSQ DLAQDPTTRR IWYGIATAHD FESHDGMTEE NLYQKIFASH FGHLAIIFLW VSGNLFHVAW QGNFEQWSQD PLHVRPIAH AIWDPHFGQG AIDAFTQAGA SSPVNVAYSG VYHWWYTIGM RTNGDLYQGS IFLLILSALF LFAGWLHLQP K FRPSLSWF ...String:
MATKFPKFSQ DLAQDPTTRR IWYGIATAHD FESHDGMTEE NLYQKIFASH FGHLAIIFLW VSGNLFHVAW QGNFEQWSQD PLHVRPIAH AIWDPHFGQG AIDAFTQAGA SSPVNVAYSG VYHWWYTIGM RTNGDLYQGS IFLLILSALF LFAGWLHLQP K FRPSLSWF KNAESRLNHH LAGLFGFSSL AWTGHLVHVA IPEARGQHVG WDNFLSTLPH PAGLAPFFTG NWSVYAENPD TA SHAFGTA EGAGTAILTF LGGFHPQTEA LWLTDIAHHH LAIAVIFIIA GHMYRTNFGI GHSIKEILEA HKPPAGGLGA GHK GLYETL NNSLHFQLAL ALASLGVVTS LVAQHMYSMP PYAFIAKDYT TMAALYTHHQ YIATFIMCGA FAHGAIFLIR DYDP EANKN NVLARVLEHK EAIISHLSWV SLFLGFHTLG LYVHNDVVVA FGTPEKQILI EPVFAQFVQA ASGKALYGFN VLLAN ADSA ATAASLGTYL PNWLDAINSG KTALFLPIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLAVFWA LNTVGWVTFY WHWKNLTVWQ GNVAQFNESS TYLMGWLRDY LWLNSSQLIN GYNPFGT NN LSVWSWMFLF GHLIWATGFM FLISWRGYWQ ELIETIVWAH QRTPLANIVG WKDKPVALSI VQARVVGLAH FTVGYFLT Y AAFLIASTAG KFG

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Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 8.807235 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPLDVLEMVP WDGCKAGQIA ASPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

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Macromolecule #4: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 15.536583 KDa
SequenceString:
AETLTGKTPV FGGSTGGLLK SAETEEKYAI TWTSTKEQVF ELPTGGAAVM HEGDNLLYFA RKEQALALGT QLRTKFKPKI ESYKIYRVF PGGDVEYLHP KDGVFPEKVN EGRSFAGKVD RRIGQNPNPA TIKFTGKQPY TA

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Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 8.147134 KDa
SequenceString:
MAIARGDKVR ILRPESYWFN EVGTVASVDQ SGIKYPVVVR FEKVNYNGFS GSDGGVNTNN FAEAELQVVA AAAKK

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Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 17.125742 KDa
SequenceString:
MRRLFAVVLA ACLWLGFAPQ ASADVAGLTP CSESPRFIQR AEAAATPQAK ARFENYSQAL CGADGLPHLI VDGRLDHAGD FIIPSLLFL YIAGWIGWVG RSYLQAIKSD KDAAGKEIVI DVPLAVKFSL TGFAWPLAAF QEFSSGKLLA KADEITVSPR

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Macromolecule #7: Photosystem I PsaI protein

MacromoleculeName: Photosystem I PsaI protein / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 4.002733 KDa
SequenceString:
MSGDFAAAFL PTIFVPLVGL GLPAVLMSLL FTYIESEA

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Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 4.713585 KDa
SequenceString:
MDGLKRYLSS APILATIWFA ITAGILIEFN RFFPDLLFHP L

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Macromolecule #9: Photosystem I reaction center subunit PsaK

MacromoleculeName: Photosystem I reaction center subunit PsaK / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 8.39712 KDa
SequenceString:
MLPVLAAIPQ TVAWSPKVAL VMILSNIVAI AIGKATIKIQ NAGPALPSPQ LFGGFGLPAV LATASFGHIL GIGVILGLAN IGNL

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Macromolecule #10: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 17.302688 KDa
SequenceString:
MAQDVIANGG TPEIGNLATP INSSPFTRTF INALPIYRRG LSSNRRGLEI GMAHGFLLYG PFSILGPLRN TETAGSAGLL ATVGLVVIL TVCLSLYGNA GSGPSAAEST VTTPNPPQEL FTKEGWSEFT SGFILGGLGG AFFAFYLAST PYVQPLVKIA A GVWSVH

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Macromolecule #11: PsaM

MacromoleculeName: PsaM / type: protein_or_peptide / ID: 11 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 3.239867 KDa
SequenceString:
MTDTQVFVAL LLALVPAVLA YRLGTELYR

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Macromolecule #12: Iron stress-induced chlorophyll-binding protein

MacromoleculeName: Iron stress-induced chlorophyll-binding protein / type: protein_or_peptide / ID: 12 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 37.004453 KDa
SequenceString: MQTYNNPEVT YDWWAGNARF ANLSGLFIAA HVAQAALIMF WAGAFTLYEI SWLTADQSMG EQGLILLPHL ATLGLGVGDG GQVTDTYPL FVVGAVHLIA SAVLGAGALF HTFRAPSDLA AASGAAKRFH FDWNDPKQLG LILGHHLLFL GVGALLLVAK A TTWGGLYD ...String:
MQTYNNPEVT YDWWAGNARF ANLSGLFIAA HVAQAALIMF WAGAFTLYEI SWLTADQSMG EQGLILLPHL ATLGLGVGDG GQVTDTYPL FVVGAVHLIA SAVLGAGALF HTFRAPSDLA AASGAAKRFH FDWNDPKQLG LILGHHLLFL GVGALLLVAK A TTWGGLYD AASQTVRLVT EPTLNPAVIY GYQTHFASID NLEDLVGGHV YVGVMLIAGG IWHILVPPFQ WTKKVLIYSG EA ILSYSLG GIALAGFVAA YFCAVNTLAY PVEFYGAPLE IKLGVTPYFA DTVQLPFGAH TPRAWLSNAH FFLAFFCLQG HLW HALRAM GFDFRRVEKA LSSVEA

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Macromolecule #13: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 13 / Number of copies: 594 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #14: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 14 / Number of copies: 6 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #15: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 15 / Number of copies: 9 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #16: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 16 / Number of copies: 144 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #17: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 17 / Number of copies: 45 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #18: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 18 / Number of copies: 18 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #19: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 19 / Number of copies: 6 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #20: 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: 20 / Number of copies: 24 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

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

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Macromolecule #21: water

MacromoleculeName: water / type: ligand / ID: 21 / Number of copies: 54 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5oy0

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63332
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6kig:
Structure of cyanobacterial photosystem I-IsiA supercomplex

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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

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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

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