[English] 日本語

Yorodumi

- EMDB-21690: Cryo-EM structure of apo-Photosystem II from Synechocystis sp. PC... -

+
Open data

-
Basic information

Entry

Database: EMDB / ID: EMD-21690

Title

Cryo-EM structure of apo-Photosystem II from Synechocystis sp. PCC 6803

Map data

apo-photosystem II

Sample

Complex: apo-Photosystem II
- Protein or peptide: x 13 types
Ligand: x 15 types

Keywords

Photosystem / oxidoreductase / water-splitting / photoactivation / PHOTOSYNTHESIS

Function / homology

Function and homology information

plasma membrane-derived thylakoid photosystem II / 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 / photosynthetic electron transport in photosystem II / chlorophyll binding ...
Similarity search - Function

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 ...
Similarity search - Domain/homology

Biological species

Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)

Method

single particle reconstruction / cryo EM / Resolution: 2.58 Å

Authors

Gisriel CJ

Funding support

United States, 1 items

Citation

Journal: Joule / Year: 2020
Title: Cryo-EM Structure of Monomeric Photosystem II from Synechocystis sp. PCC 6803 Lacking the Water-Oxidation Complex
Authors: Gisriel CJ / Zhou K / Huang H / Debus RJ / Xiong Y / Brudvig GW

History

Deposition	Apr 12, 2020	-
Header (metadata) release	Aug 26, 2020	-
Map release	Aug 26, 2020	-
Update	Mar 6, 2024	-
Current status	Mar 6, 2024	Processing site: RCSB / Status: Released

-
Structure visualization

Movie	Surface view with section colored by density value Surface level: 0.0394 Imaged by UCSF Chimera Download Surface view colored by height Surface level: 0.0394 Imaged by UCSF Chimera Download Surface view with fitted model Atomic models: PDB-6wj6 Surface level: 0.0394 Imaged by UCSF Chimera Download Movie viewer
Structure viewer	EM map: SurfViewMolmilJmol/JSmol
Supplemental images	emd_21690.png

-
Downloads & links

-
EMDB archive

Map data	emd_21690.map.gz	59.9 MB		EMDB map data format
Header (meta data)	emd-21690-v30.xml emd-21690.xml	28.8 KB 28.8 KB	Display Display	EMDB header
FSC (resolution estimation)	emd_21690_fsc.xml	9.1 KB	Display	FSC data file
Images	emd_21690.png	22.4 KB
Filedesc metadata	emd-21690.cif.gz	7.8 KB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-21690 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21690	HTTPS FTP

-
Validation report

Summary document	emd_21690_validation.pdf.gz	669 KB	Display	EMDB validaton report
Full document	emd_21690_full_validation.pdf.gz	668.6 KB	Display
Data in XML	emd_21690_validation.xml.gz	10.7 KB	Display
Data in CIF	emd_21690_validation.cif.gz	14.1 KB	Display
Arichive directory	https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21690 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21690	HTTPS FTP

-
Related structure data

Related structure data	6wj6MC M: atomic model generated by this map C: citing same article (ref.)
Similar structure data	3w2w-2 5o7x-2 5o7x-4 6nd1-d 7nho-d 5o7x-6 6hug-d 5o7x-5 2xja-d 6wj6-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

EMDB pages	EMDB (EBI/PDBe) / EMDataResource
Related items in Molecule of the Month	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (43) #59 - Nov 2004 Photosystem II similarity (43) #22 - Oct 2001 Photosystem I similarity (4)

-
Map

File

Download / File: emd_21690.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Annotation

apo-photosystem II

Projections & slices

Image control

Size
Brightness
Contrast
Others	InvertY flip

Axes	Z (Sec.)	Y (Row.)	X (Col.)
	1.18 Å/pix. x 256 pix. = 302.4 Å	1.18 Å/pix. x 256 pix. = 302.4 Å	1.18 Å/pix. x 256 pix. = 302.4 Å
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider.

Voxel size

X=Y=Z: 1.18125 Å

Density

Histogram

Histogram (log scale)

Contour Level	By AUTHOR: 0.0394 / Movie #1: 0.0394
Minimum - Maximum	-0.11423279 - 0.24345654
Average (Standard dev.)	-0.00007884522 (±0.0075905714)

Symmetry

Space group: 1

Details

EMDB XML:

Map geometry

Axis order	X	Y	Z
Origin	0	0	0
Dimensions	256	256	256
Spacing	256	256	256

Cell

A=B=C: 302.4 Å
α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.18125	1.18125	1.18125
M x/y/z	256	256	256
origin x/y/z	0.000	0.000	0.000
length x/y/z	302.400	302.400	302.400
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	256	256	256
D min/max/mean	-0.114	0.243	-0.000

-
Supplemental data

-
Sample components

+
Entire : apo-Photosystem II

Entire	Name: apo-Photosystem II
Components	Complex: apo-Photosystem II Protein or peptide: Photosystem II protein D1 2 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 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 X protein Ligand: FE (II) ION Ligand: CHLOROPHYLL A Ligand: PHEOPHYTIN A Ligand: BETA-CAROTENE Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 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-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE Ligand: DODECYL-BETA-D-MALTOSIDE Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG) Ligand: CHLORIDE ION Ligand: BICARBONATE ION Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE Ligand: PROTOPORPHYRIN IX CONTAINING FE Ligand: N-FORMYLMETHIONINE Ligand: water

Entire

Name: apo-Photosystem II

Components

Complex: apo-Photosystem II
- Protein or peptide: Photosystem II protein D1 2
- 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 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 X protein
Ligand: FE (II) ION
Ligand: CHLOROPHYLL A
Ligand: PHEOPHYTIN A
Ligand: BETA-CAROTENE
Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
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-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
Ligand: DODECYL-BETA-D-MALTOSIDE
Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
Ligand: CHLORIDE ION
Ligand: BICARBONATE ION
Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
Ligand: PROTOPORPHYRIN IX CONTAINING FE
Ligand: N-FORMYLMETHIONINE
Ligand: water

+
Supramolecule #1: apo-Photosystem II

Supramolecule	Name: apo-Photosystem II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 267.067 KDa

+
Macromolecule #1: Photosystem II protein D1 2

Macromolecule	Name: Photosystem II protein D1 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 39.744117 KDa
Sequence	String: MTTTLQQRES ASLWEQFCQW VTSTNNRIYV GWFGTLMIPT LLTATTCFII AFIAAPPVDI DGIREPVAGS LLYGNNIISG AVVPSSNAI GLHFYPIWEA ASLDEWLYNG GPYQLVVFHF LIGIFCYMGR QWELSYRLGM RPWICVAYSA PVSAATAVFL I YPIGQGSF ...String: MTTTLQQRES ASLWEQFCQW VTSTNNRIYV GWFGTLMIPT LLTATTCFII AFIAAPPVDI DGIREPVAGS LLYGNNIISG AVVPSSNAI GLHFYPIWEA ASLDEWLYNG GPYQLVVFHF LIGIFCYMGR QWELSYRLGM RPWICVAYSA PVSAATAVFL I YPIGQGSF SDGMPLGISG TFNFMIVFQA EHNILMHPFH MLGVAGVFGG SLFSAMHGSL VTSSLVRETT EVESQNYGYK FG QEEETYN IVAAHGYFGR LIFQYASFNN SRSLHFFLGA WPVIGIWFTA MGVSTMAFNL NGFNFNQSIL DSQGRVIGTW ADV LNRANI GFEVMHERNA HNFPLDLASG EQAPVALTAP AVNG UniProtKB: Photosystem II protein D1 2

+
Macromolecule #2: Photosystem II CP47 reaction center protein

Macromolecule	Name: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 55.954355 KDa
Sequence	String: MGLPWYRVHT VVLNDPGRLI SVHLMHTALV AGWAGSMALY ELAIFDSSDA VLNPMWRQGM FVLPFMARLG VTSSWNGWSV TGETGLDPG FWSFEGVAAA HIVLSGLLFL AAVWHWVFWD LELFVDPRTG ESALDLPKMF GIHLFLSGLL CFGFGAFHLT G VWGPGMWV ...String: MGLPWYRVHT VVLNDPGRLI SVHLMHTALV AGWAGSMALY ELAIFDSSDA VLNPMWRQGM FVLPFMARLG VTSSWNGWSV TGETGLDPG FWSFEGVAAA HIVLSGLLFL AAVWHWVFWD LELFVDPRTG ESALDLPKMF GIHLFLSGLL CFGFGAFHLT G VWGPGMWV SDPYGLTGHV QPVAPEWGPA GFNPFNPGGV VAHHIAAGIV GIIAGLFHLT VRPPERLYKA LRMGNIETVL SS SIAAVFF AAFVVAGTMW YGNATTPIEL FGPTRYQWDK GYFQEEIQRR VDSQLAEGAS LSEAWSTIPE KLAFYDYVGN SPA KGGLFR TGAMNSGDGI AQEWIGHPIF KDKEGRELEV RRMPNFFETF PVIMTDADGV VRADIPFRRS ESKFSVEQTG VTVS FYGGA LDGQTFSNPS DVKKFARKAQ LGEGFDFDTE TFNSDGVFRT SPRGWFTFGH AVFALLFFFG HIWHGSRTLF RDVFA GVDP GLEEQVEFGV FAKVGDLSTR KEA UniProtKB: Photosystem II CP47 reaction center protein

+
Macromolecule #3: Photosystem II CP43 reaction center protein

Macromolecule	Name: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 50.330695 KDa
Sequence	String: MVTLSNTSMV GGRDLPSSGF AWWSGNARLI NLSGKLLGAH VAHAGLIVFW AGAMTLFEVA HFIPEKPMYE QGLILLPHIA TLGWGVGPA GEVTDIFPFF VVGVLHLISS AVLGLGGIYH ALRGPEVLEE YSSFFGYDWK DKNQMTNIIG YHLILLGCGA L LLVFKAMF ...String: MVTLSNTSMV GGRDLPSSGF AWWSGNARLI NLSGKLLGAH VAHAGLIVFW AGAMTLFEVA HFIPEKPMYE QGLILLPHIA TLGWGVGPA GEVTDIFPFF VVGVLHLISS AVLGLGGIYH ALRGPEVLEE YSSFFGYDWK DKNQMTNIIG YHLILLGCGA L LLVFKAMF FGGVYDTWAP GGGDVRVITN PTLNPAIIFG YLLKAPFGGE GWIISVNNME DIIGGHIWIG LICISGGIWH IL TKPFGWA RRALIWSGEA YLSYSLGALS LMGFIASVFV WFNNTAYPSE FYGPTGMEAS QSQAFTFLVR DQRLGANIAS AQG PTGLGK YLMRSPSGEI IFGGETMRFW DFRGPWLEPL RGPNGLDLDK LRNDIQPWQV RRAAEYMTHA PLGSLNSVGG VITD VNSFN YVSPRAWLAT SHFVLGFFFL VGHLWHAGRA RAAAAGFEKG IDRETEPTLF MPDLD UniProtKB: Photosystem II CP43 reaction center protein

+
Macromolecule #4: Photosystem II D2 protein

Macromolecule	Name: Photosystem II D2 protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 39.519238 KDa
Sequence	String: MTIAVGRAPV ERGWFDVLDD WLKRDRFVFI GWSGLLLFPC AFMALGGWLT GTTFVTSWYT HGLASSYLEG ANFLTVAVSS PADAFGHSL LFLWGPEAQG NLTRWFQIGG LWPFVALHGA FGLIGFMLRQ FEISRLVGIR PYNAIAFSGP IAVFVSVFLM Y PLGQSSWF ...String: MTIAVGRAPV ERGWFDVLDD WLKRDRFVFI GWSGLLLFPC AFMALGGWLT GTTFVTSWYT HGLASSYLEG ANFLTVAVSS PADAFGHSL LFLWGPEAQG NLTRWFQIGG LWPFVALHGA FGLIGFMLRQ FEISRLVGIR PYNAIAFSGP IAVFVSVFLM Y PLGQSSWF FAPSFGVAGI FRFILFLQGF HNWTLNPFHM MGVAGILGGA LLCAIHGATV ENTLFEDGED SNTFRAFEPT QA EETYSMV TANRFWSQIF GIAFSNKRWL HFFMLFVPVT GLWMSSVGIV GLALNLRAYD FVSQELRAAE DPEFETFYTK NIL LNEGMR AWMAPQDQPH ENFIFPEEVL PRGNAL UniProtKB: Photosystem II D2 protein

+
Macromolecule #5: Cytochrome b559 subunit alpha

Macromolecule	Name: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 9.454577 KDa
Sequence	String: MSGTTGERPF SDIVTSIRYW VIHSITIPML FIAGWLFVST GLAYDAFGTP RPDEYFTQTR QELPILQERY DINQEIQEFN Q UniProtKB: Cytochrome b559 subunit alpha

+
Macromolecule #6: Cytochrome b559 subunit beta

Macromolecule	Name: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 4.935784 KDa
Sequence	String: MATQNPNQPV TYPIFTVRWL AVHTLAVPSV FFVGAIAAMQ FIQR UniProtKB: Cytochrome b559 subunit beta

+
Macromolecule #7: Photosystem II reaction center protein H

Macromolecule	Name: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 7.120404 KDa
Sequence	String: MAQRTRLGDI LRPLNSEYGK VVPGWGTTPV MGVFMALFLV FLLIILQIYN SSLILEGFSV DWAG UniProtKB: Photosystem II reaction center protein H

+
Macromolecule #8: Photosystem II reaction center protein I

Macromolecule	Name: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 4.310109 KDa
Sequence	String: MLTLKIAVYI VVGLFISLFI FGFLSSDPTR NPGRKDFE UniProtKB: Photosystem II reaction center protein I

+
Macromolecule #9: Photosystem II reaction center protein K

Macromolecule	Name: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 5.114127 KDa
Sequence	String: METIYLLAKL PEAYQIFDPL VDVLPVIPLF FLALAFVWQA AVGFK UniProtKB: Photosystem II reaction center protein K

+
Macromolecule #10: Photosystem II reaction center protein L

Macromolecule	Name: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 4.476145 KDa
Sequence	String: MDRNSNPNRQ PVELNRTSLY LGLLLVAVLG ILFSSYFFN UniProtKB: Photosystem II reaction center protein L

+
Macromolecule #11: Photosystem II reaction center protein M

Macromolecule	Name: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 3.88263 KDa
Sequence	String: MQVNNLGFIA SILFVLVPTV FLLILFIQTG KQSES UniProtKB: Photosystem II reaction center protein M

+
Macromolecule #12: Photosystem II reaction center protein T

Macromolecule	Name: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 3.543308 KDa
Sequence	String: MESVAYILVL TMALAVLFFA IAFREPPRIE K UniProtKB: Photosystem II reaction center protein T

+
Macromolecule #13: Photosystem II reaction center X protein

Macromolecule	Name: Photosystem II reaction center X protein / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)	Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa
Molecular weight	Theoretical: 4.189036 KDa
Sequence	String: MTPSLANFLW SLVLGAAIVL IPATVGLIFI SQKDKITRS UniProtKB: Photosystem II reaction center protein X

+
Macromolecule #14: FE (II) ION

Macromolecule	Name: FE (II) ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: FE2
Molecular weight	Theoretical: 55.845 Da

+
Macromolecule #15: CHLOROPHYLL A

Macromolecule	Name: CHLOROPHYLL A / type: ligand / ID: 15 / Number of copies: 35 / Formula: CLA
Molecular weight	Theoretical: 893.489 Da
Chemical component information	ChemComp-CLA: CHLOROPHYLL A

+
Macromolecule #16: PHEOPHYTIN A

Macromolecule	Name: PHEOPHYTIN A / type: ligand / ID: 16 / Number of copies: 2 / Formula: PHO
Molecular weight	Theoretical: 871.2 Da
Chemical component information	ChemComp-PHO: PHEOPHYTIN A

+
Macromolecule #17: BETA-CAROTENE

Macromolecule	Name: BETA-CAROTENE / type: ligand / ID: 17 / Number of copies: 9 / Formula: BCR
Molecular weight	Theoretical: 536.873 Da
Chemical component information	ChemComp-BCR: BETA-CAROTENE

+
Macromolecule #18: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

Macromolecule	Name: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL type: ligand / ID: 18 / Number of copies: 7 / Formula: SQD
Molecular weight	Theoretical: 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 #19: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...

Macromolecule	Name: 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: 19 / Number of copies: 2 / Formula: PL9
Molecular weight	Theoretical: 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 #20: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

Macromolecule	Name: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 20 / Number of copies: 3 / Formula: LMG
Molecular weight	Theoretical: 787.158 Da
Chemical component information	ChemComp-LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

+
Macromolecule #21: DODECYL-BETA-D-MALTOSIDE

Macromolecule	Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 21 / Number of copies: 2 / Formula: LMT
Molecular weight	Theoretical: 510.615 Da
Chemical component information	ChemComp-LMT: DODECYL-BETA-D-MALTOSIDE / detergent*YM

+
Macromolecule #22: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

Macromolecule	Name: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 22 / Number of copies: 2 / Formula: DGD
Molecular weight	Theoretical: 949.299 Da
Chemical component information	ChemComp-DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #23: CHLORIDE ION

Macromolecule	Name: CHLORIDE ION / type: ligand / ID: 23 / Number of copies: 1 / Formula: CL
Molecular weight	Theoretical: 35.453 Da

+
Macromolecule #24: BICARBONATE ION

Macromolecule	Name: BICARBONATE ION / type: ligand / ID: 24 / Number of copies: 1 / Formula: BCT
Molecular weight	Theoretical: 61.017 Da
Chemical component information	ChemComp-BCT: BICARBONATE ION / pH buffer*YM

+
Macromolecule #25: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

Macromolecule	Name: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 25 / Number of copies: 4 / Formula: LHG
Molecular weight	Theoretical: 722.97 Da
Chemical component information	ChemComp-LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

+
Macromolecule #26: PROTOPORPHYRIN IX CONTAINING FE

Macromolecule	Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 26 / Number of copies: 1 / Formula: HEM
Molecular weight	Theoretical: 616.487 Da
Chemical component information	ChemComp-HEM: PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #27: N-FORMYLMETHIONINE

Macromolecule	Name: N-FORMYLMETHIONINE / type: ligand / ID: 27 / Number of copies: 3 / Formula: FME
Molecular weight	Theoretical: 177.221 Da
Chemical component information	ChemComp-FME: N-FORMYLMETHIONINE

+
Macromolecule #28: water

Macromolecule	Name: water / type: ligand / ID: 28 / Number of copies: 198 / Formula: HOH
Molecular weight	Theoretical: 18.015 Da
Chemical component information	ChemComp-HOH: WATER

-
Experimental details

-
Structure determination

Method	cryo EM
Processing	single particle reconstruction
Aggregation state	particle

-
Sample preparation

Concentration	0.025 mg/mL
Buffer	pH: 7 Details: 10 mM HEPES pH 7.0 100 mM NaCl 0.03% beta-dodecylmaltoside
Grid	Model: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
Vitrification	Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Details	Monodisperse single particles

-
Electron microscopy

Microscope	FEI TITAN KRIOS
Image recording	Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.07 e/Å²
Electron beam	Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics	Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup model	Type of model: OTHER / Details: Homology
Final reconstruction	Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 212640
Initial angle assignment	Type: MAXIMUM LIKELIHOOD
Final angle assignment	Type: 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

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-EMDB archive

-Validation report

-Related structure data

-Links

-Map

Image controlX

-Supplemental data

-Sample components

+Entire : apo-Photosystem II

+Supramolecule #1: apo-Photosystem II

+Macromolecule #1: Photosystem II protein D1 2

+Macromolecule #2: Photosystem II CP47 reaction center protein

+Macromolecule #3: Photosystem II CP43 reaction center protein

+Macromolecule #4: Photosystem II D2 protein

+Macromolecule #5: Cytochrome b559 subunit alpha

+Macromolecule #6: Cytochrome b559 subunit beta

+Macromolecule #7: Photosystem II reaction center protein H

+Macromolecule #8: Photosystem II reaction center protein I

+Macromolecule #9: Photosystem II reaction center protein K

+Macromolecule #10: Photosystem II reaction center protein L

+Macromolecule #11: Photosystem II reaction center protein M

+Macromolecule #12: Photosystem II reaction center protein T

+Macromolecule #13: Photosystem II reaction center X protein

+Macromolecule #14: FE (II) ION

+Macromolecule #15: CHLOROPHYLL A

+Macromolecule #16: PHEOPHYTIN A

+Macromolecule #17: BETA-CAROTENE

+Macromolecule #18: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

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

+Macromolecule #20: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

+Macromolecule #21: DODECYL-BETA-D-MALTOSIDE

+Macromolecule #22: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+Macromolecule #23: CHLORIDE ION

+Macromolecule #24: BICARBONATE ION

+Macromolecule #25: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

+Macromolecule #26: PROTOPORPHYRIN IX CONTAINING FE

+Macromolecule #27: N-FORMYLMETHIONINE

+Macromolecule #28: water

-Experimental details

-Structure determination

-Sample preparation

-Electron microscopy

+Image processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options