[English] 日本語
Yorodumi
- EMDB-18848: Cryo-EM Structure of native Photosystem II assembly intermediate ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18848
TitleCryo-EM Structure of native Photosystem II assembly intermediate fromChlamydomonas reinhardtii
Map data
Sample
  • Complex: Photosystem II assembly intermediate from Chlamydomonas reinhardtii
    • Protein or peptide: x 11 types
  • Ligand: x 13 types
KeywordsPhotosystem II / photosynthesis / biogenesis of PSII / assembly intermediate / CryoEM / assembly factor / Chlamydomonas reinhardtii
Function / homology
Function and homology information


photosystem II repair / chloroplast thylakoid lumen / photosystem II assembly / oxygen evolving activity / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II ...photosystem II repair / chloroplast thylakoid lumen / photosystem II assembly / oxygen evolving activity / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / chloroplast thylakoid membrane / : / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II Pbs27 / Photosystem II Pbs27 superfamily / Photosystem II Pbs27 / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component ...Photosystem II Pbs27 / Photosystem II Pbs27 superfamily / Photosystem II Pbs27 / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / 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 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 / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Uncharacterized protein / Photosystem II D2 protein / Photosystem II protein D1 / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein K / Photosystem II reaction center protein H / Photosystem II CP47 reaction center protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Cytochrome b559 subunit beta
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFadeeva M / Klaiman D / Kandiah E / Nelson N
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation199/21 Israel
CitationJournal: Front Plant Sci / Year: 2023
Title: Structure of native photosystem II assembly intermediate from .
Authors: Mariia Fadeeva / Daniel Klaiman / Eaazhisai Kandiah / Nathan Nelson /
Abstract: Photosystem II (PSII) is a dimer consisting of at least 13 nuclear-encoded and four chloroplast-encoded protein subunits that collectively function as a sunlight-driven oxidoreductase. In this ... Photosystem II (PSII) is a dimer consisting of at least 13 nuclear-encoded and four chloroplast-encoded protein subunits that collectively function as a sunlight-driven oxidoreductase. In this study, we present the inaugural structure of a green alga PSII assembly intermediate (pre-PSII-int). This intermediate was isolated from chloroplast membranes of the temperature-sensitive mutant TSP4, cultivated for 14 hours at a non-permissive temperature. The assembly state comprises a monomer containing subunits A, B, C, D, E, F, H, I, K, and two novel assembly factors, Psb1 and Psb2. Psb1 is identified as a novel transmembrane helix located adjacent to PsbE and PsbF (cytochrome b559). The absence of PsbJ, typically found in mature PSII close to this position, indicates that Psb1 functions as an assembly factor. Psb2 is an eukaryotic homolog of the cyanobacterial assembly factor Psb27. The presence of iron, coupled with the absence of Q, Q, and the manganese cluster, implies a protective mechanism against photodamage and provides insights into the intricate assembly process.
History
DepositionNov 6, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18848.png

Downloads & links

-
Map

FileDownload / File: emd_18848.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 340 pix.
= 285.6 Å		0.84 Å/pix.
x 340 pix.
= 285.6 Å		0.84 Å/pix.
x 340 pix.
= 285.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.016437694 - 0.042843655
Average (Standard dev.)0.00015245292 (±0.0015300463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 285.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_18848_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_18848_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Photosystem II assembly intermediate from Chlamydomonas reinhardtii

EntireName: Photosystem II assembly intermediate from Chlamydomonas reinhardtii
Components
  • Complex: Photosystem II assembly intermediate from Chlamydomonas reinhardtii
    • Protein or peptide: Photosystem II protein D1
    • 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 H
    • Protein or peptide: Photosystem II reaction center protein I
    • Protein or peptide: Photosystem II reaction center protein K
    • Protein or peptide: Photosystem II reaction center protein Ycf12
    • Protein or peptide: Chain U, Predicted protein
  • Ligand: FE (II) ION
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN A
  • Ligand: BETA-CAROTENE
  • Ligand: octyl beta-D-glucopyranoside
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: BICARBONATE 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: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: water

+
Supramolecule #1: Photosystem II assembly intermediate from Chlamydomonas reinhardtii

SupramoleculeName: Photosystem II assembly intermediate from Chlamydomonas reinhardtii
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9, #11, #10
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Location in cell: thylakoid membrane

+
Macromolecule #1: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane
Molecular weightTheoretical: 36.287348 KDa
SequenceString: SSLWARFCEW ITSTENRLYI GWFGVIMIPC LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVIPTSNAIG LHFYPIWEA ASLDEWLYNG GPYQLIVCHF LLGVYCYMGR EWELSFRLGM RPWIAVAYSA PVAAASAVFL VYPIGQGSFS D GMPLGISG ...String:
SSLWARFCEW ITSTENRLYI GWFGVIMIPC LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVIPTSNAIG LHFYPIWEA ASLDEWLYNG GPYQLIVCHF LLGVYCYMGR EWELSFRLGM RPWIAVAYSA PVAAASAVFL VYPIGQGSFS D GMPLGISG TFNFMIVFQA EHNILMHPFH MLGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESANEGYR FGQEEETYNI VA AHGYFGR LIFQYASFNN SRSLHFFLAA WPVIGIWFTA LGLSTMAFNL NGFNFNQSVV DSQGRVLNTW ADIINRANLG MEV MHERNA H

UniProtKB: Photosystem II protein D1

+
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: Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane
Molecular weightTheoretical: 53.739043 KDa
SequenceString: GLPWYRVHTV VINDPGRLIS VHLMHTALVS GWAGSMALFE ISVFDPSDPV LNPMWRQGMF VLPFMTRLGI TQSWGGWTIS GETATNPGI WSYEGVAAAH IILSGALFLA SVWHWTYWDL ELFRDPRTGK TALDLPKIFG IHLFLSGLLC FGFGAFHVTG V FGPGIWVS ...String:
GLPWYRVHTV VINDPGRLIS VHLMHTALVS GWAGSMALFE ISVFDPSDPV LNPMWRQGMF VLPFMTRLGI TQSWGGWTIS GETATNPGI WSYEGVAAAH IILSGALFLA SVWHWTYWDL ELFRDPRTGK TALDLPKIFG IHLFLSGLLC FGFGAFHVTG V FGPGIWVS DPYGLTGRVQ PVAPSWGADG FDPYNPGGIA SHHIAAGILG VLAGLFHLCV RPSIRLYFGL SMGSIETVLS SS IAAVFWA AFVVAGTMWY GSAATPIELF GPTRYQWDQG FFQQEIQKRV QASLAEGASL SDAWSRIPEK LAFYDYIGNN PAK GGLFRT GAMNSGDGIA VGWLGHASFK DQEGRELFVR RMPTFFETFP VLLLDKDGIV RADVPFRKAE SKYSIEQVGV SVTF YGGEL DGLTFTDPAT VKKYARKAQL GEIFEFDRST LQSDGVFRSS PRGWFTFGHV CFALLFFFGH IWHGARTIFR DVFAG IDDD IND

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: Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane
Molecular weightTheoretical: 46.468094 KDa
SequenceString: FAWWSGNARL INLSGKLLGA HVAHAGLIVF WAGAMNLFEV SHFVPEKPMY EQGLILLPHI ATLGYGVGPG GEIIDTFPYF VSGVLHLIS SAVLGFGGVY HSLIGPETLE ESYPFFGYVW KDKNKMTNIL GYHLIMLGLG AWLLVWKAMY FGGVYDTWAP G GGDVRVIT ...String:
FAWWSGNARL INLSGKLLGA HVAHAGLIVF WAGAMNLFEV SHFVPEKPMY EQGLILLPHI ATLGYGVGPG GEIIDTFPYF VSGVLHLIS SAVLGFGGVY HSLIGPETLE ESYPFFGYVW KDKNKMTNIL GYHLIMLGLG AWLLVWKAMY FGGVYDTWAP G GGDVRVIT NPTTNAAVIF GYLVKSPFGG DGWICSVDNM EDIIGGHIWI GTLEILGGIW HIYTTPWPWA RRAFVWSGEA YL SYSLGAI GVMGFIACCM SWFNNTAYPS EFYGPTGPEA SQSQAFTFLV RDQRLGANVA SAQGPTGLGK YLMRSPTGEI IFG GETMRF WDFRGPWLEP LRGPNGLDLN KLKNDIQPWQ ERRAAEYMTH APLGSLNSVG GVATEINAVN FVSPRSWLAC SHFC LGFFF FIGHLWHAGR ARAAAAGF

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: Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane
Molecular weightTheoretical: 39.241734 KDa
SequenceString: IAIGTYQEKR TWFDDADDWL RQDRFVFVGW SGLLLFPCAY FALGGWLTGT TFVTSWYTHG LATSYLEGCN FLTAAVSTPA NSMAHSLLF VWGPEAQGDF TRWCQLGGLW AFVALHGAFG LIGFMLRQFE IARSVNLRPY NAIAFSAPIA VFVSVFLIYP L GQSGWFFA ...String:
IAIGTYQEKR TWFDDADDWL RQDRFVFVGW SGLLLFPCAY FALGGWLTGT TFVTSWYTHG LATSYLEGCN FLTAAVSTPA NSMAHSLLF VWGPEAQGDF TRWCQLGGLW AFVALHGAFG LIGFMLRQFE IARSVNLRPY NAIAFSAPIA VFVSVFLIYP L GQSGWFFA PSFGVAAIFR FILFFQGFHN WTLNPFHMMG VAGVLGAALL CAIHGATVEN TLFEDGDGAN TFRAFNPTQA EE TYSMVTA NRFWSQIFGV AFSNKRWLHF FMLLVPVTGL WMSAIGVVGL ALNLRAYDFV SQEIRAAEDP EFETFYTKNI LLN EGIRAW MAAQDQPHER LVFPEEVLPR GNAL

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: Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane
Molecular weightTheoretical: 8.727849 KDa
SequenceString:
ERPFSDILTS IRYWVIHSIT VPALFIAGWL FVSTGLAYDV FGTPRPNEYF TEDRQEAPLI TDRFNALEQV KKLSGN

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: Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane
Molecular weightTheoretical: 3.795562 KDa
SequenceString:
YPIFTVRWLA IHGIAVPTIF FLGAITAMQF IQR

UniProtKB: Cytochrome b559 subunit beta

+
Macromolecule #7: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane
Molecular weightTheoretical: 7.063317 KDa
SequenceString:
EPGLVTPLGT LLRPLNSEAG KVLPGWGTTV LMAVFILLFA AFLLIILEIY NSSLILDDVS MSWET

UniProtKB: Photosystem II reaction center protein H

+
Macromolecule #8: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane
Molecular weightTheoretical: 3.276967 KDa
SequenceString:
MLTLKIFVYT VVTFFVCLFI FGFLSNDP

UniProtKB: Photosystem II reaction center protein I

+
Macromolecule #9: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane
Molecular weightTheoretical: 4.147979 KDa
SequenceString:
KLPEAYAPFA PIVDVLPVIP VFFILLAFVW QAAVSFR

UniProtKB: Photosystem II reaction center protein K

+
Macromolecule #10: Chain U, Predicted protein

MacromoleculeName: Chain U, Predicted protein / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane
Molecular weightTheoretical: 11.213722 KDa
SequenceString:
FDTYTAETSA ILDKVKVTLA LDKDDPAKED SVKGLRKDIN NWVAKYRREP KVSGKPSFGN TYSALNALAG HFNSFGATAP IPKKRLERL QKELDDATLL LT

UniProtKB: Uncharacterized protein

+
Macromolecule #11: Photosystem II reaction center protein Ycf12

MacromoleculeName: Photosystem II reaction center protein Ycf12 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organ: thylakoid membrane
Molecular weightTheoretical: 3.2199 KDa
SequenceString:
MNIELALTLV SLVLVVSAGP LVVVLLSARG GN

UniProtKB: Photosystem II reaction center protein Psb30

+
Macromolecule #12: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #13: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 13 / Number of copies: 35 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
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: 8 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #16: octyl beta-D-glucopyranoside

MacromoleculeName: octyl beta-D-glucopyranoside / type: ligand / ID: 16 / Number of copies: 3 / Formula: BOG
Molecular weightTheoretical: 292.369 Da
Chemical component information

ChemComp-BOG:
octyl beta-D-glucopyranoside / detergent*YM

+
Macromolecule #17: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 17 / Number of copies: 2 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #18: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 18 / Number of copies: 2 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #19: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 19 / Number of copies: 1 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #20: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 20 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #21: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 21 / Number of copies: 1 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

+
Macromolecule #22: 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: 22 / 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 #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: 5 / 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

Concentration0.5 mg/mL
BufferpH: 6
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 25758 / Average exposure time: 1.8 sec. / Average electron dose: 1.07 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 6408350
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kac

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 327737
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 6 / Avg.num./class: 56272 / Software - Name: RELION (ver. 4.0.0)
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