[English] 日本語
Yorodumi
- EMDB-10461: Photosystem I tetramer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10461
TitlePhotosystem I tetramer
Map data
Sample
  • Complex: Photosystem I
    • Protein or peptide: x 18 types
  • Ligand: x 10 types
Keywordsphotosynthesis / tetramer / anabaena / PSI
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / 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 PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / 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 iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A2 1 / Photosystem I 4.8 kDa protein / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XI ...Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A2 1 / Photosystem I 4.8 kDa protein / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChen M / Perez-Boerema A
Funding support Sweden, China, 5 items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
European Research Council (ERC)ERC-2018-StG-805230 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
National Natural Science Foundation of China (NSFC)21506113 China
National Natural Science Foundation of China (NSFC)31470229 China
CitationJournal: Nat Plants / Year: 2020
Title: Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly.
Authors: Ming Chen / Annemarie Perez-Boerema / Laixing Zhang / Yanxue Li / Maojun Yang / Shizhong Li / Alexey Amunts /
Abstract: Photosystem I (PSI) is able to form different oligomeric states across various species. To reveal the structural basis for PSI dimerization and tetramerization, we structurally investigated PSI from ...Photosystem I (PSI) is able to form different oligomeric states across various species. To reveal the structural basis for PSI dimerization and tetramerization, we structurally investigated PSI from the cyanobacterium Anabaena. This revealed a disrupted trimerization domain due to lack of the terminal residues of PsaL in the lumen, which resulted in PSI dimers with loose connections between monomers and weaker energy-coupled chlorophylls than in the trimer. At the dimer surface, specific phospholipids, cofactors and interactions in combination facilitated recruitment of another dimer to form a tetramer. Taken together, the relaxed luminal connections and lipid specificity at the dimer interface account for membrane curvature. PSI tetramer assembly appears to increase the surface area of the thylakoid membrane, which would contribute to PSI crowding.
History
DepositionNov 6, 2019-
Header (metadata) releaseFeb 19, 2020-
Map releaseFeb 19, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.434
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.434
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6tcl
  • Surface level: 0.434
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10461.png

Downloads & links

-
Map

FileDownload / File: emd_10461.map.gz / Format: CCP4 / Size: 193.2 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 370 pix.
= 392.2 Å		1.06 Å/pix.
x 370 pix.
= 392.2 Å		1.06 Å/pix.
x 370 pix.
= 392.2 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: 0.434 / Movie #1: 0.434
Minimum - Maximum-1.1677458 - 4.3900123
Average (Standard dev.)0.014446365 (±0.10832126)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions370370370
Spacing370370370
CellA=B=C: 392.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z370370370
origin x/y/z0.0000.0000.000
length x/y/z392.200392.200392.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS370370370
D min/max/mean-1.1684.3900.014

-
Supplemental data

-
Mask #1

Fileemd_10461_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_10461_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_10461_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Photosystem I

EntireName: Photosystem I
Components
  • Complex: Photosystem I
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2 1
    • 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 reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit PsaK 1
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Photosystem I 4.8 kDa protein
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit PsaK 1
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit XI
  • Ligand: CHLOROPHYLL A
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: PHYLLOQUINONE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENE
  • Ligand: Digitonin
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: beta,beta-caroten-4-one
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Supramolecule #1: Photosystem I

SupramoleculeName: Photosystem I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)

+
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: 4 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 81.932125 KDa
SequenceString: KARVIVDKDP VPTSFEKWAQ PGHFDRTLAR GPKTTTWIWN LHALAHDFDT HTSDLEDISR KIFAAHFGHL AVVTIWLSGM IFHGAKFSN YEAWLSDPLN VRPSAQVVWP IVGQDILNGD VGGGFHGIQI TSGLFQVWRG WGITNSFQLY CTAIGGLVLA G LFLFAGWF ...String:
KARVIVDKDP VPTSFEKWAQ PGHFDRTLAR GPKTTTWIWN LHALAHDFDT HTSDLEDISR KIFAAHFGHL AVVTIWLSGM IFHGAKFSN YEAWLSDPLN VRPSAQVVWP IVGQDILNGD VGGGFHGIQI TSGLFQVWRG WGITNSFQLY CTAIGGLVLA G LFLFAGWF HYHKRAPKLE WFQNVESMLN HHLQVLLGCG SLGWAGHLIH VSAPINKLMD AGVAVKDIPL PHEFILNKSL LI DLFPGFA AGLTPFFTLN WGQYADFLTF KGGLNPVTGG LWMTDIAHHH LAIAVVFIIA GHQYRTNWGI GHSIKEILEN HKG PFTGEG HKGLYENLTT SWHAQLATNL AFLGSLTIII AHHMYAMPPY PYLATDYATQ LCIFTHHIWI GGFLIVGGAA HAAI FMVRD YDPVVNQNNV LDRVIRHRDA IISHLNWVCI FLGFHSFGLY IHNDTMRALG RPQDMFSDTA IQLQPVFAQW VQNLH TLAP GGTAPNALEP VSYAFGGGVL AVGGKVAMMP IALGTADFLI HHIHAFTIHV TVLILLKGVL FARSSRLIPD KANLGF RFP CDGPGRGGTC QVSGWDHVFL GLFWMYNSLS IVIFHFSWKM QSDVWGTVDA AGNVSHITGG NFAQSAITIN GWLRDFL WA QASQVINSYG SALSAYGLMF LGAHFVWAFS LMFLFSGRGY WQELIESIVW AHNKLKVAPA IQPRALSITQ GRAVGVAH Y LLGGIATTWA FFHAHILSV

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

+
Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2 1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 83.254734 KDa
SequenceString: TKFPKFSQDL AQDPTTRRIW YAMAMGNDFE SHDGMTEENL YQKIFATHFG HLAIIFLWAS SLLFHVAWQG NFEQWIKDPL HVRPIAHAI WDPHFGKPAI EAFTQAGANG PVNIAYSGVY HWWYTIGMRT NTELYTGSVF LLLFASLFLF AGWLHLQPKF R PSLAWFKS ...String:
TKFPKFSQDL AQDPTTRRIW YAMAMGNDFE SHDGMTEENL YQKIFATHFG HLAIIFLWAS SLLFHVAWQG NFEQWIKDPL HVRPIAHAI WDPHFGKPAI EAFTQAGANG PVNIAYSGVY HWWYTIGMRT NTELYTGSVF LLLFASLFLF AGWLHLQPKF R PSLAWFKS AESRLNHHLA GLFGVSSLAW AGHLIHVAIP ESRGQHVGWD NFLSTAPHPA GLQPFFTGNW GVYAQNPDTA GH IFSTSQG AGTAILTFLG GFHPQTESLW LTDMAHHHLA IAVLFIVAGH MYRTNFGIGH SIKEMMNAKT FFGKPVEGPF NMP HQGIYD TYNNSLHFQL GWHLACLGVV TSWVAQHMYS LPSYAFIAKD YTTQAALYTH HQYIAIFLMV GAFAHGAIFL VRDY DPEQN KGNVLERVLQ HKEAIISHLS WVSLFLGFHT LGLYVHNDVV VAFGTPEKQI LIEPVFAQFI QAAHGKVLYG LDTLL SNPD SVAYTAYPNY ANVWLPGWLD AINSGTNSLF LTIGPGDFLV HHAIALGLHT TTLILVKGAL DARGSKLMPD KKDFGY AFP CDGPGRGGTC DISAWDSFYL SLFWALNTVG WVTFYWHWKH LGIWQGNVAQ FNENSTYLMG WFRDYLWANS AQLINGY NP YGVNNLSVWA WMFLFGHLVW ATGFMFLISW RGYWQELIET LVWAHERTPI ANLVRWKDKP VALSIVQARV VGLAHFTV G YVLTYAAFLI ASTAGKFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2 1

+
Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 8.69401 KDa
SequenceString:
SHTVKIYDTC IGCTQCVRAC PTDVLEMVPW DGCKAAQVAS SPRTEDCVGC KRCETACPTD FLSIRVYLGA ETTRSMGLAY

UniProtKB: Photosystem I iron-sulfur center

+
Macromolecule #4: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 14.67267 KDa
SequenceString:
LSGKTPLFAG STGGLLTKAV EEEKYAITWT SPKAQVFELP TGGAATMHEG ENLLYIARKE YGIALGGQLR KFKITNYKIY RILPSGETT FIHPADGVFP EKVNAGREKV RFNARSIGEN PNPSQVKFSG KATYD

UniProtKB: Photosystem I reaction center subunit II

+
Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 6.809673 KDa
SequenceString:
VQRGSKVRIL RPESYWFQDV GTVASVDQSG IKYPVIVRFD KVNYAGINTN NFAVDELIEV

UniProtKB: Photosystem I reaction center subunit IV

+
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: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 15.030004 KDa
SequenceString:
GADLTPCAEN PAFQALAKNA RNTTADPQSG QKRFERYSQA LCGPEGYPHL IVDGRLDRAG DFLIPSILFL YIAGWIGWVG RAYLQAIKK DSDTEQKEIQ LDLGIALPII ATGFAWPAAA VKELLSGELT AKDSEITVSP

UniProtKB: Photosystem I reaction center subunit III

+
Macromolecule #7: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 3.550169 KDa
SequenceString:
ASFLSSIFVP VIGWVVPIAT FSFLFLYIER E

UniProtKB: Photosystem I reaction center subunit VIII

+
Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 5.368227 KDa
SequenceString:
ADKADQSSYL IKFISTAPVA ATIWLTITAG ILIEFNRFFP DLLFHPLP

UniProtKB: Photosystem I reaction center subunit IX

+
Macromolecule #9: Photosystem I reaction center subunit PsaK 1

MacromoleculeName: Photosystem I reaction center subunit PsaK 1 / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 7.580861 KDa
SequenceString:
AATTPLEWSP TVGIIMVIAN VIAITFGRQT IKYPSAEPAL PSAKFFGGFG APALLATTAF GHILGVGLVL GLHN

UniProtKB: Photosystem I reaction center subunit PsaK 1

+
Macromolecule #10: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 17.545008 KDa
SequenceString:
AQAVDASKNL PSDPRNREVV FPAGRDPQWG NLETPVNASP LVKWFINNLP AYRPGLTPFR RGLEVGMAHG YFLFGPFAKL GPLRDAANA NLAGLLGAIG LVVLFTLALS LYANSNPPTA LASVTVPNPP DAFQSKEGWN NFASAFLIGG IGGAVVAYFL T SNLALI

UniProtKB: Photosystem I reaction center subunit XI

+
Macromolecule #11: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 11 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 3.407008 KDa
SequenceString:
SSISDTQVYI ALVVALIPGL LAWRLATELY K

UniProtKB: Photosystem I reaction center subunit XII

+
Macromolecule #12: Photosystem I 4.8 kDa protein

MacromoleculeName: Photosystem I 4.8 kDa protein / type: protein_or_peptide / ID: 12 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 4.342132 KDa
SequenceString:
KISPVANTGA KPPYTFRTGW ALLLLAVNFL VAAYYFHII

UniProtKB: Photosystem I 4.8 kDa protein

+
Macromolecule #13: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 14.84581 KDa
SequenceString:
GADLTPCAEN PAFQALAKNA RNTTADPQSG QKRFERYSQA LCGPEGYPHL IVDGRLDRAG DFLIPSILFL YIAGWIGWVG RAYLQAIKK DSDTEQKEIQ LDLGIALPII ATGFAWPAAA VKELLSGELT AKDSEITV

UniProtKB: Photosystem I reaction center subunit III

+
Macromolecule #14: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 3.764388 KDa
SequenceString:
ASFLSSIFVP VIGWVVPIAT FSFLFLYIER EDV

UniProtKB: Photosystem I reaction center subunit VIII

+
Macromolecule #15: Photosystem I reaction center subunit PsaK 1

MacromoleculeName: Photosystem I reaction center subunit PsaK 1 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 7.509784 KDa
SequenceString:
ATTPLEWSPT VGIIMVIANV IAITFGRQTI KYPSAEPALP SAKFFGGFGA PALLATTAFG HILGVGLVLG LHN

UniProtKB: Photosystem I reaction center subunit PsaK 1

+
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: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 17.673137 KDa
SequenceString:
AQAVDASKNL PSDPRNREVV FPAGRDPQWG NLETPVNASP LVKWFINNLP AYRPGLTPFR RGLEVGMAHG YFLFGPFAKL GPLRDAANA NLAGLLGAIG LVVLFTLALS LYANSNPPTA LASVTVPNPP DAFQSKEGWN NFASAFLIGG IGGAVVAYFL T SNLALIQ

UniProtKB: Photosystem I reaction center subunit XI

+
Macromolecule #17: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 7.106979 KDa
SequenceString:
VQRGSKVRIL RPESYWFQDV GTVASVDQSG IKYPVIVRFD KVNYAGINTN NFAVDELIEV EAP

UniProtKB: Photosystem I reaction center subunit IV

+
Macromolecule #18: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 16.290655 KDa
SequenceString:
NREVVFPAGR DPQWGNLETP VNASPLVKWF INNLPAYRPG LTPFRRGLEV GMAHGYFLFG PFAKLGPLRD AANANLAGLL GAIGLVVLF TLALSLYANS NPPTALASVT VPNPPDAFQS KEGWNNFASA FLIGGIGGAV VAYFLTSNLA LIQGL

UniProtKB: Photosystem I reaction center subunit XI

+
Macromolecule #19: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 19 / Number of copies: 378 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #20: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 20 / Number of copies: 4 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

+
Macromolecule #21: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 21 / Number of copies: 8 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

+
Macromolecule #22: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 22 / Number of copies: 24 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #23: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 23 / Number of copies: 94 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #24: Digitonin

MacromoleculeName: Digitonin / type: ligand / ID: 24 / Number of copies: 22 / Formula: AJP
Molecular weightTheoretical: 1.229312 KDa
Chemical component information

ChemComp-AJP:
Digitonin / detergent*YM

+
Macromolecule #25: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 25 / Number of copies: 30 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #26: beta,beta-caroten-4-one

MacromoleculeName: beta,beta-caroten-4-one / type: ligand / ID: 26 / Number of copies: 4 / Formula: ECH
Molecular weightTheoretical: 550.856 Da
Chemical component information

ChemComp-ECH:
beta,beta-caroten-4-one

+
Macromolecule #27: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 27 / Number of copies: 12 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

+
Macromolecule #28: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 28 / Number of copies: 2 / 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: 6.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 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

Particle selectionNumber selected: 428587
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69247
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
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