[English] 日本語
Yorodumi
- EMDB-30902: PSII intermediate Psb28-RC47 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30902
TitlePSII intermediate Psb28-RC47
Map data
Sample
  • Complex: PSII intermediate Psb28-RC47 complex
    • Protein or peptide: x 14 types
  • Ligand: x 13 types
KeywordsPhotosystem II / Cryo-EM / assembly / repair / Psb28 / Tsl0063 / PLANT PROTEIN
Function / homology
Function and homology information


photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / plasma membrane-derived thylakoid membrane / chlorophyll binding ...photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthetic electron transport in photosystem II / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
: / Photosystem II Psb28, class 1 / Photosystem II Psb28, class 1 superfamily / Psb28 protein / Photosystem II PsbX, type 1 subfamily / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) ...: / Photosystem II Psb28, class 1 / Photosystem II Psb28, class 1 superfamily / Psb28 protein / Photosystem II PsbX, type 1 subfamily / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / 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 reaction centre protein H / Photosystem II protein D1 / 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 reaction centre protein H superfamily / 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 / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Photosystem II CP47 reaction center protein / Photosystem II reaction center protein X / Photosystem II D2 protein / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein L / Photosystem II reaction center protein M / Photosystem II reaction center protein T / Photosystem II reaction center protein H ...Photosystem II CP47 reaction center protein / Photosystem II reaction center protein X / Photosystem II D2 protein / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein L / Photosystem II reaction center protein M / Photosystem II reaction center protein T / Photosystem II reaction center protein H / Photosystem II protein D1 / Photosystem II assembly factor Psb28 protein / Photosystem II assembly protein Psb34
Similarity search - Component
Biological speciesThermosynechococcus vulcanus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsSui SF / Shen JR
CitationJournal: Nat Plants / Year: 2021
Title: Structural insights into cyanobacterial photosystem II intermediates associated with Psb28 and Tsl0063.
Authors: Yanan Xiao / Guoqiang Huang / Xin You / Qingjun Zhu / Wenda Wang / Tingyun Kuang / Guangye Han / Sen-Fang Sui / Jian-Ren Shen /
Abstract: Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyses light-induced water oxidation, leading to the conversion of light energy into chemical energy and the release of dioxygen. ...Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyses light-induced water oxidation, leading to the conversion of light energy into chemical energy and the release of dioxygen. We analysed the structures of two Psb28-bound PSII intermediates, Psb28-RC47 and Psb28-PSII, purified from a psbV-deletion strain of the thermophilic cyanobacterium Thermosynechococcus vulcanus, using cryo-electron microscopy. Both Psb28-RC47 and Psb28-PSII bind one Psb28, one Tsl0063 and an unknown subunit. Psb28 is located at the cytoplasmic surface of PSII and interacts with D1, D2 and CP47, whereas Tsl0063 is a transmembrane subunit and binds at the side of CP47/PsbH. Substantial structural perturbations are observed at the acceptor side, which result in conformational changes of the quinone (Q) and non-haem iron binding sites and thus may protect PSII from photodamage during assembly. These results provide a solid structural basis for understanding the assembly process of native PSII.
History
DepositionJan 18, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7dxa
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30902.png

Downloads & links

-
Map

FileDownload / File: emd_30902.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.30654 Å
Density
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.035
Minimum - Maximum-0.14868084 - 0.235512
Average (Standard dev.)0.0005316262 (±0.0064300783)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 261.308 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.306541.306541.30654
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z261.308261.308261.308
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ220220220
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1490.2360.001

-
Supplemental data

-
Sample components

+
Entire : PSII intermediate Psb28-RC47 complex

EntireName: PSII intermediate Psb28-RC47 complex
Components
  • Complex: PSII intermediate Psb28-RC47 complex
    • Protein or peptide: Photosystem II reaction center Psb28 protein
    • Protein or peptide: Tsl0063 protein
    • Protein or peptide: Photosystem II protein D1
    • Protein or peptide: Photosystem II CP47 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 H
    • Protein or peptide: Photosystem II reaction center protein I
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: Photosystem II reaction center protein M
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II reaction center protein X
    • Protein or peptide: unidentified transmembrane protein
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN A
  • Ligand: BETA-CAROTENE
  • Ligand: CHLORIDE ION
  • Ligand: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
  • Ligand: UNKNOWN LIGAND
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: FE (II) ION
  • Ligand: 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE
  • Ligand: heptyl 1-thio-beta-D-glucopyranoside
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

+
Supramolecule #1: PSII intermediate Psb28-RC47 complex

SupramoleculeName: PSII intermediate Psb28-RC47 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)

+
Macromolecule #1: Photosystem II reaction center Psb28 protein

MacromoleculeName: Photosystem II reaction center Psb28 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 13.188769 KDa
SequenceString:
MGAMAEIQFI RGINEEVVPD VRLTRARDGS SGQAMFYFDN PKIVQEGNLE VTGMYMVDEE GEIVTRDVNA KFINGQPVAI EATYTMRSP QEWDRFIRFM DRYAASHGLG FQKSENS

UniProtKB: Photosystem II assembly factor Psb28 protein

+
Macromolecule #2: Tsl0063 protein

MacromoleculeName: Tsl0063 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 5.943893 KDa
SequenceString:
MRYTTDEGGR LNNFAIEPKV YQAQPWTPQQ KVRAALLVGG GLLLVAGLVA IAVGVS

UniProtKB: Photosystem II assembly protein Psb34

+
Macromolecule #3: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 39.792367 KDa
SequenceString: MTTTLQRRES ANLWERFCNW VTSTDNRLYV GWFGVIMIPT LLAATICFVI AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVVPSSNAI GLHFYPIWEA ASLDEWLYNG GPYQLIIFHF LLGASCYMGR QWELSYRLGM RPWICVAYSA PLASAFAVFL I YPIGQGSF ...String:
MTTTLQRRES ANLWERFCNW VTSTDNRLYV GWFGVIMIPT LLAATICFVI AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVVPSSNAI GLHFYPIWEA ASLDEWLYNG GPYQLIIFHF LLGASCYMGR QWELSYRLGM RPWICVAYSA PLASAFAVFL I YPIGQGSF SDGMPLGISG TFNFMIVFQA EHNILMHPFH QLGVAGVFGG ALFCAMHGSL VTSSLIRETT ETESANYGYK FG QEEETYN IVAAHGYFGR LIFQYASFNN SRSLHFFLAA WRVVGVWFAA LGISTMAFNL NGFNFNHSVI DAKGNVINTW ADI INRANL GMEVMHERNA HNFPLDLASA ESAPVAMIAP SING

UniProtKB: Photosystem II protein D1

+
Macromolecule #4: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 56.068742 KDa
SequenceString: GLPWYRVHTV LINDPGRLIA AHLMHTALVA GWAGSMALYE LATFDPSDPV LNPMWRQGMF VLPFMARLGV TGSWSGWSIT GETGIDPGF WSFEGVALAH IVLSGLLFLA ACWHWVYWDL ELFRDPRTGE PALDLPKMFG IHLFLAGLLC FGFGAFHLTG L FGPGMWVS ...String:
GLPWYRVHTV LINDPGRLIA AHLMHTALVA GWAGSMALYE LATFDPSDPV LNPMWRQGMF VLPFMARLGV TGSWSGWSIT GETGIDPGF WSFEGVALAH IVLSGLLFLA ACWHWVYWDL ELFRDPRTGE PALDLPKMFG IHLFLAGLLC FGFGAFHLTG L FGPGMWVS DPYGLTGSVQ PVAPEWGPDG FNPYNPGGVV AHHIAAGIVG IIAGLFHILV RPPQRLYKAL RMGNIETVLS SS IAAVFFA AFVVAGTMWY GSATTPIELF GPTRYQWDSS YFQQEINRRV QASLASGATL EEAWSAIPEK LAFYDYIGNN PAK GGLFRT GPMNKGDGIA QAWKGHAVFR NKEGEELFVR RMPAFFESFP VILTDKNGVV KADIPFRRAE SKYSFEQQGV TVSF YGGEL NGQTFTDPPT VKSYARKAIF GEIFEFDTET LNSDGIFRTS PRGWFTFAHA VFALLFFFGH IWHGARTLFR DVFSG IDPE LSPEQVEWGF YQKVGDVTTR K

UniProtKB: Photosystem II CP47 reaction center protein

+
Macromolecule #5: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 38.404949 KDa
SequenceString: ERGWFDILDD WLKRDRFVFV GWSGILLFPC AYLALGGWLT GTTFVTSWYT HGLASSYLEG CNFLTVAVST PANSMGHSLL LLWGPEAQG DFTRWCQLGG LWTFIALHGA FGLIGFMLRQ FEIARLVGVR PYNAIAFSAP IAVFVSVFLI YPLGQSSWFF A PSFGVAAI ...String:
ERGWFDILDD WLKRDRFVFV GWSGILLFPC AYLALGGWLT GTTFVTSWYT HGLASSYLEG CNFLTVAVST PANSMGHSLL LLWGPEAQG DFTRWCQLGG LWTFIALHGA FGLIGFMLRQ FEIARLVGVR PYNAIAFSAP IAVFVSVFLI YPLGQSSWFF A PSFGVAAI FRFLLFFQGF HNWTLNPFHM MGVAGVLGGA LLCAIHGATV ENTLFQDGEG ASTFRAFNPT QAEETYSMVT AN RFWSQIF GIAFSNKRWL HFFMLFVPVT GLWMSAIGVV GLALNLRSYD FISQEIRAAE DPEFETFYTK NLLLNEGIRA WMA PQDQPH ENFVFPEEVL PRGNAL

UniProtKB: Photosystem II D2 protein

+
Macromolecule #6: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 9.58084 KDa
SequenceString:
MAGTTGERPF SDIITSVRYW VIHSITIPAL FIAGWLFVST GLAYDVFGTP RPDSYYAQEQ RSIPLVTDRF EAKQQVETFL EQLK

UniProtKB: Cytochrome b559 subunit alpha

+
Macromolecule #7: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 5.0679 KDa
SequenceString:
MTSNTPNQEP VSYPIFTVRW VAVHTLAVPT IFFLGAIAAM QFIQR

UniProtKB: Cytochrome b559 subunit beta

+
Macromolecule #8: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 7.227559 KDa
SequenceString:
ARRTWLGDIL RPLNSEYGKV APGWGTTPLM AVFMGLFLVF LLIILEIYNS TLILDGVNVS WKALG

UniProtKB: Photosystem II reaction center protein H

+
Macromolecule #9: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.410245 KDa
SequenceString:
METLKITVYI VVTFFVLLFV FGFLSGDPAR NPKRKDLE

UniProtKB: Photosystem II reaction center protein I

+
Macromolecule #10: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.299044 KDa
SequenceString:
MEPNPNRQPV ELNRTSLYLG LLLILVLALL FSSYFFN

UniProtKB: Photosystem II reaction center protein L

+
Macromolecule #11: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.015688 KDa
SequenceString:
MEVNQLGFIA TALFVLVPSV FLIILYVQTE SQQKSS

UniProtKB: Photosystem II reaction center protein M

+
Macromolecule #12: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.878728 KDa
SequenceString:
METITYVFIF ACIIALFFFA IFFREPPRIT KK

UniProtKB: Photosystem II reaction center protein T

+
Macromolecule #13: Photosystem II reaction center protein X

MacromoleculeName: Photosystem II reaction center protein X / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.19103 KDa
SequenceString:
TITPSLKGFF IGLLSGAVVL GLTFAVLIAI SQIDKVQRSL

UniProtKB: Photosystem II reaction center protein X

+
Macromolecule #14: unidentified transmembrane protein

MacromoleculeName: unidentified transmembrane protein / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 1.652805 KDa
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAA

+
Macromolecule #15: 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: 15 / Number of copies: 2 / 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

+
Macromolecule #16: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 16 / Number of copies: 22 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #17: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 17 / Number of copies: 2 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

+
Macromolecule #18: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 18 / Number of copies: 6 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #19: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

+
Macromolecule #20: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL...

MacromoleculeName: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
type: ligand / ID: 20 / Number of copies: 7 / Formula: MGE
Molecular weightTheoretical: 688.972 Da
Chemical component information

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

+
Macromolecule #21: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 21 / Number of copies: 2 / Formula: UNL
Molecular weightTheoretical: 35.453 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

+
Macromolecule #22: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 22 / Number of copies: 3 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #23: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 23 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #24: 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA...

MacromoleculeName: 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE
type: ligand / ID: 24 / Number of copies: 1 / Formula: PQ9
Molecular weightTheoretical: 612.967 Da
Chemical component information

ChemComp-PQ9:
5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE

+
Macromolecule #25: heptyl 1-thio-beta-D-glucopyranoside

MacromoleculeName: heptyl 1-thio-beta-D-glucopyranoside / type: ligand / ID: 25 / Number of copies: 1 / Formula: HTG
Molecular weightTheoretical: 294.408 Da
Chemical component information

ChemComp-HTG:
heptyl 1-thio-beta-D-glucopyranoside / detergent*YM

+
Macromolecule #26: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 26 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #27: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 27 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 241790
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.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