[English] 日本語
Yorodumi
- EMDB-24943: Structure of a monomeric photosystem II core complex from a cyano... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24943
TitleStructure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light
Map dataMonomeric photosystem II core complex from, sharpened
Sample
  • Complex: Monomeric photosystem II from cyanobacteria acclimated to far-red light
    • Protein or peptide: x 9 types
  • Ligand: x 15 types
KeywordsPhotosystem II / far-red light photoacclimation / chlorophyll f / chlorophyll d / bicarbonate / photoactivation / photosynthesis / cyanobacteria
Function / homology
Function and homology information


oxygen evolving activity / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity ...oxygen evolving activity / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II D2 protein ...Photosystem II CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosystem II protein D1 / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Cytochrome b559 subunit alpha / Photosystem q(B) protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein K
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7335 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsGisriel CJ / Bryant DA
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM140174 United States
National Science Foundation (NSF, United States)MCB-1613022 United States
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
CitationJournal: J Biol Chem / Year: 2022
Title: Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f.
Authors: Christopher J Gisriel / Gaozhong Shen / Ming-Yang Ho / Vasily Kurashov / David A Flesher / Jimin Wang / William H Armstrong / John H Golbeck / Marilyn R Gunner / David J Vinyard / Richard J ...Authors: Christopher J Gisriel / Gaozhong Shen / Ming-Yang Ho / Vasily Kurashov / David A Flesher / Jimin Wang / William H Armstrong / John H Golbeck / Marilyn R Gunner / David J Vinyard / Richard J Debus / Gary W Brudvig / Donald A Bryant /
Abstract: Far-red light (FRL) photoacclimation in cyanobacteria provides a selective growth advantage for some terrestrial cyanobacteria by expanding the range of photosynthetically active radiation to include ...Far-red light (FRL) photoacclimation in cyanobacteria provides a selective growth advantage for some terrestrial cyanobacteria by expanding the range of photosynthetically active radiation to include far-red/near-infrared light (700-800 nm). During this photoacclimation process, photosystem II (PSII), the water:plastoquinone photooxidoreductase involved in oxygenic photosynthesis, is modified. The resulting FRL-PSII is comprised of FRL-specific core subunits and binds chlorophyll (Chl) d and Chl f molecules in place of several of the Chl a molecules found when cells are grown in visible light. These new Chls effectively lower the energy canonically thought to define the "red limit" for light required to drive photochemical catalysis of water oxidation. Changes to the architecture of FRL-PSII were previously unknown, and the positions of Chl d and Chl f molecules had only been proposed from indirect evidence. Here, we describe the 2.25 Å resolution cryo-EM structure of a monomeric FRL-PSII core complex from Synechococcus sp. PCC 7335 cells that were acclimated to FRL. We identify one Chl d molecule in the Chl position of the electron transfer chain and four Chl f molecules in the core antenna. We also make observations that enhance our understanding of PSII biogenesis, especially on the acceptor side of the complex where a bicarbonate molecule is replaced by a glutamate side chain in the absence of the assembly factor Psb28. In conclusion, these results provide a structural basis for the lower energy limit required to drive water oxidation, which is the gateway for most solar energy utilization on earth.
History
DepositionSep 22, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7sa3
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24943.png

Downloads & links

-
Map

FileDownload / File: emd_24943.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMonomeric photosystem II core complex from, sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.058870178 - 0.12884623
Average (Standard dev.)0.00009027467 (±0.00198104)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8250.8250.825
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-140-140-140
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0590.1290.000

-
Supplemental data

-
Additional map: Monomeric photosystem II core complex from, unsharpened

Fileemd_24943_additional_1.map
AnnotationMonomeric photosystem II core complex from, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Monomeric photosystem II from cyanobacteria acclimated to far-red...

EntireName: Monomeric photosystem II from cyanobacteria acclimated to far-red light
Components
  • Complex: Monomeric photosystem II from cyanobacteria acclimated to far-red light
    • Protein or peptide: Photosystem q(B) protein
    • Protein or peptide: Photosystem II CP47 reaction center protein
    • Protein or peptide: Photosystem II CP43 reaction center protein
    • Protein or peptide: Photosystem II D2 protein
    • Protein or peptide: Cytochrome b559 subunit alpha
    • Protein or peptide: Cytochrome b559 subunit beta
    • Protein or peptide: Photosystem II reaction center protein I
    • Protein or peptide: Photosystem II reaction center protein K
    • Protein or peptide: Unknown
  • Ligand: CALCIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: CHLOROPHYLL A
  • Ligand: CHLOROPHYLL D
  • Ligand: PHEOPHYTIN A
  • Ligand: BETA-CAROTENE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: Chlorophyll F
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: FE (II) ION
  • Ligand: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: water

+
Supramolecule #1: Monomeric photosystem II from cyanobacteria acclimated to far-red...

SupramoleculeName: Monomeric photosystem II from cyanobacteria acclimated to far-red light
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)

+
Macromolecule #1: Photosystem q(B) protein

MacromoleculeName: Photosystem q(B) protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 40.111781 KDa
SequenceString: MTTISTRPTS RFPTWDRFCN WVTSTENRLY IGWFGVLMLP LLGVSITVFV TAFIAAPPVD IDGIREPLSG SLLYGNNIIT AAVVPTSNA IGLHFYPIWE AATLDEWLYN GGPYQMIAFH YIPALLCYLG REWELSYRLG MRPWICIAYS APVAATISVF L IYPIGQGS ...String:
MTTISTRPTS RFPTWDRFCN WVTSTENRLY IGWFGVLMLP LLGVSITVFV TAFIAAPPVD IDGIREPLSG SLLYGNNIIT AAVVPTSNA IGLHFYPIWE AATLDEWLYN GGPYQMIAFH YIPALLCYLG REWELSYRLG MRPWICIAYS APVAATISVF L IYPIGQGS FSDGLPMGIS GTFNFMFVFQ AEHNILMHPF HMLGVAGVLG GSLFCAMHGS LVTSSLVRET SDSQSQNEGY KF GQEEETY NILAAHGYFG RLIFQYASFN NSRQLHFFLA AWPVVCIWFV ALGISTMAFN LNGFNFNHSV LDSQGRVLPS WAD VVNRAS LGFEVMHERN AHNFPLDLAS GESVQVAMRA PHIGA

UniProtKB: Photosystem q(B) protein

+
Macromolecule #2: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 56.44098 KDa
SequenceString: MGLPWYRVHT SVLNDPGRLI AVHIMHNALC AGFAGSMLLF ELALFDPSDP VLNPMWRQGC FLMPFVSRLG VVNSWQGWSV TGETFTNPG FWTFETVAIA HIIFSGLSFL AACWHWVYWD VATFFDPKTD EPVIDLPKVF GIHLTLAGIL CFGFGAFHLT G LFGPGMWV ...String:
MGLPWYRVHT SVLNDPGRLI AVHIMHNALC AGFAGSMLLF ELALFDPSDP VLNPMWRQGC FLMPFVSRLG VVNSWQGWSV TGETFTNPG FWTFETVAIA HIIFSGLSFL AACWHWVYWD VATFFDPKTD EPVIDLPKVF GIHLTLAGIL CFGFGAFHLT G LFGPGMWV SDPLGLTGHI QGVAPEWGAA GFDPHNPGGV VAHHIALGIV AIIGGLFHIF VRPPEYLYKG LRMGNIEGTL AS GLAVFFS GAFIAAGTMW YGTATTPIEL WGPTRYQWDQ GFFQQAISRQ VKASISDGKS PSEAWSEIPT KLAFYDYIGN SPA KGGLFR VGRMVDGDGL PTGWLGHPVF KDGEGRELTV RRMPNFFENF PVVLFDQDGI VRADIPFRQA ESKYGIEQTG VTVS FYGGE LDGQTFSDPK DVKKYARRAQ LGEPFEFDRS VYDSDGLFRT SNRGFFAFFH VIFGLLWFFG HIWHGLRALF QDVFS GIDP SLSAEQVEWG YFKKVGDPTS QQTPA

UniProtKB: Photosystem II CP47 reaction center protein

+
Macromolecule #3: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 52.375664 KDa
SequenceString: METPLETIPD LSLSPTAEVG SILAPASPGY DEATSGYAWW AGNARLITPE LTGRFLGAHV AHAGLVALWA GGMLLFEVSH FNLSKPMYE QGCILMPHIA TLGIGVGQSG EITSMFPFFA IGVAHLIGSA VLGIGGMYHA IKGPEKLYGF FQFDWTDRAK V AQILGFHI ...String:
METPLETIPD LSLSPTAEVG SILAPASPGY DEATSGYAWW AGNARLITPE LTGRFLGAHV AHAGLVALWA GGMLLFEVSH FNLSKPMYE QGCILMPHIA TLGIGVGQSG EITSMFPFFA IGVAHLIGSA VLGIGGMYHA IKGPEKLYGF FQFDWTDRAK V AQILGFHI AILGIFALLF AAKAMYWGGL YDPWAPGGGD VRLVTNPTLD PRIIFGYLIK RPTGGEGWIV SVNNLEDIIG GH IWIGCIL IAGGIWHILV PPLRWTYNLF PWTGETYLSQ SLGNVAGQAF IAAAFIWFNN TAYPSVFYGP TVPESSQAQS FVF LMRDQG MGADVASAQG PTGLGKYLQR SPTGEIIFGG ETMRFWDARA PWLEPLRGKN GLDLDKLQHD VQPWQLRRAA EYMT HSPIG SLNSVAGLAT ESNAFNYVSP RTWLASAHFI FGFFFLVGHL WHAGRARAAA AGFETGLDRE DEPVLSMAPI DPSLR SD

UniProtKB: Photosystem II CP43 reaction center protein

+
Macromolecule #4: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 39.596496 KDa
SequenceString: MTITMGSLGS ARDWIKQLDD WLKRDRFVFI GWSGLLLFPC SFLAIGAWFT GTTFVTSWYT HGLVSSYLEG CNFLTVAVST PAESMGHSL LLLWGPEASG DFVRWCQIGG LWTFTALHGV FGLIGFMLRQ IEIARLVGIR PYNAIAFSAP IAVYCATFLI Y PLGQSSWF ...String:
MTITMGSLGS ARDWIKQLDD WLKRDRFVFI GWSGLLLFPC SFLAIGAWFT GTTFVTSWYT HGLVSSYLEG CNFLTVAVST PAESMGHSL LLLWGPEASG DFVRWCQIGG LWTFTALHGV FGLIGFMLRQ IEIARLVGIR PYNAIAFSAP IAVYCATFLI Y PLGQSSWF FGPGFGVSAI FRFLLFFQGF HNYTLNPFHM MGVTGVLGGA LLCAIHGATV QNTLFRDNQS KNTFKGFSTD QG EETYSMV TANRFWSQIF GIAFSNKRWL HFFMLFVPVT GLWMSAIGMA GLAFNLRAYD FVSQEIRAAE DPEFETFYTK NIL LNEGLR AWLSEMDQPA KKFVFPDEVL PRGFSE

UniProtKB: Photosystem II D2 protein

+
Macromolecule #5: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 9.136276 KDa
SequenceString:
MAGVTGERPF GDIVTSVRYW IIHSITIPAL FIAGWLFVST GLAYDAFGTP RPNEYYPSNQ MELPIVDDRY NPDRTLKYQD

UniProtKB: Cytochrome b559 subunit alpha

+
Macromolecule #6: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 5.02396 KDa
SequenceString:
MTNIGREQPI SYPIFTIRWL AIHALAIPSV FFLGSIAAMQ FIQR

UniProtKB: Cytochrome b559 subunit beta

+
Macromolecule #7: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 4.229917 KDa
SequenceString:
MVTLKIVVYL TVSFFVGLFI FGFLSGDPAR NPSGRDFD

UniProtKB: Photosystem II reaction center protein I

+
Macromolecule #8: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 5.069053 KDa
SequenceString:
MDVAFLVAEL PEAYRAFGPL IDVLPILPIF FLLLAFVWQA SVGFR

UniProtKB: Photosystem II reaction center protein K

+
Macromolecule #9: Unknown

MacromoleculeName: Unknown / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 1.975426 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

+
Macromolecule #10: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #11: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

+
Macromolecule #12: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 12 / Number of copies: 28 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #13: CHLOROPHYLL D

MacromoleculeName: CHLOROPHYLL D / type: ligand / ID: 13 / Number of copies: 1 / Formula: CL7
Molecular weightTheoretical: 895.462 Da
Chemical component information

ChemComp-CL7:
CHLOROPHYLL D

+
Macromolecule #14: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 14 / Number of copies: 2 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

+
Macromolecule #15: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 15 / Number of copies: 5 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #16: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 16 / Number of copies: 6 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

+
Macromolecule #17: Chlorophyll F

MacromoleculeName: Chlorophyll F / type: ligand / ID: 17 / Number of copies: 4 / Formula: F6C
Molecular weightTheoretical: 905.457 Da
Chemical component information


ChemComp, No image

ChemComp-F6C:
Chlorophyll F

+
Macromolecule #18: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 18 / Number of copies: 2 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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

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

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

+
Macromolecule #20: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 20 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #21: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...

MacromoleculeName: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
type: ligand / ID: 21 / Number of copies: 1 / Formula: PL9
Molecular weightTheoretical: 749.201 Da
Chemical component information

ChemComp-PL9:
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE

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

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

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

+
Macromolecule #23: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 23 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #24: water

MacromoleculeName: water / type: ligand / ID: 24 / Number of copies: 230 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 6.5
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.8 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

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

3wu2

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 315307
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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