[English] 日本語
Yorodumi
- EMDB-38596: Cryo-EM structure of cryptophyte photosystem II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38596
TitleCryo-EM structure of cryptophyte photosystem II
Map data
Sample
  • Complex: Photosystem II of cryptophyte
    • Protein or peptide: x 28 types
  • Ligand: x 17 types
KeywordsCryptophyte / Photosystem II / evolution / PHOTOSYNTHESIS
Function / homology
Function and homology information


thylakoid membrane / photosystem II stabilization / 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 / plastid / chlorophyll binding ...thylakoid membrane / photosystem II stabilization / 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 / plastid / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / chloroplast thylakoid membrane / photosynthetic electron transport in photosystem II / photosynthesis / respiratory electron transport chain / electron transfer activity / oxidoreductase activity / protein stabilization / iron ion binding / heme binding
Similarity search - Function
Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily ...Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / 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 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 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. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Photosystem II cytochrome c550 / Photosystem II D2 protein / Photosystem II protein D1 / Cytochrome b559 subunit beta / Photosystem II reaction center protein J / Photosystem II reaction center protein L / Photosystem II reaction center protein X / Photosystem II reaction center protein Psb30 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein I ...Photosystem II cytochrome c550 / Photosystem II D2 protein / Photosystem II protein D1 / Cytochrome b559 subunit beta / Photosystem II reaction center protein J / Photosystem II reaction center protein L / Photosystem II reaction center protein X / Photosystem II reaction center protein Psb30 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein I / Photosystem II reaction center protein Z / Photosystem II reaction center protein K / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H
Similarity search - Component
Biological speciesChroomonas placoidea (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsLi K / Zhao LS / Zhang YZ / Liu LN
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of cryptophyte photosystem II
Authors: Li K / Zhao LS / Zhang YZ / Liu LN
History
DepositionJan 6, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38596.png

Downloads & links

-
Map

FileDownload / File: emd_38596.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum0.000043330045 - 2.867777
Average (Standard dev.)0.08772699 (±0.1055664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Structure of cryptophyte photosystem II

Fileemd_38596_half_map_1.map
AnnotationStructure of cryptophyte photosystem II
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Structure of cryptophyte photosystem II

Fileemd_38596_half_map_2.map
AnnotationStructure of cryptophyte photosystem II
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Photosystem II of cryptophyte

EntireName: Photosystem II of cryptophyte
Components
  • Complex: Photosystem II of cryptophyte
    • Protein or peptide: ACPII-1
    • Protein or peptide: ACPII-2
    • Protein or peptide: ACPII-3
    • Protein or peptide: ACPII-4
    • Protein or peptide: ACPII-5
    • Protein or peptide: ACPII-6
    • Protein or peptide: Psb-gama_linker
    • Protein or peptide: Photosystem II protein D1
    • Protein or peptide: Photosystem II CP47 reaction center protein
    • Protein or peptide: PsbC_CP43
    • 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 J
    • Protein or peptide: Photosystem II reaction center protein K
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: PsbM
    • Protein or peptide: PsbO
    • Protein or peptide: PsbQ
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: PsbU
    • Protein or peptide: Photosystem II cytochrome c550
    • Protein or peptide: PsbW
    • Protein or peptide: Photosystem II reaction center protein Psb30
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: Photosystem II reaction center protein X
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: BICARBONATE IONBicarbonate
  • Ligand: CHLORIDE IONChloride
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN APheophytin
  • Ligand: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
  • 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: Chlorophyll c2
  • Ligand: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
  • Ligand: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: water

+
Supramolecule #1: Photosystem II of cryptophyte

SupramoleculeName: Photosystem II of cryptophyte / type: complex / ID: 1 / Parent: 0
Macromolecule list: #3-#5, #2, #6-#7, #19, #1, #8-#18, #20-#25, #27-#28, #26
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 1.1 MDa

+
Macromolecule #1: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 39.59091 KDa
SequenceString: MTATLERRES ASAWERFCSW ITSTDNRLYI GWFGVLMIPT LLTATTVYII AFVAAPPVDI DGIREPVAGS LLYGNNIITG AVIPSSASI GIHFYPIWEA ASLDEWLYNG GPYQLIVDHF LLGVCGWIGR EWEFSYRLGM RPWISVAFTA PVAAASAVFL V YPIGQGSF ...String:
MTATLERRES ASAWERFCSW ITSTDNRLYI GWFGVLMIPT LLTATTVYII AFVAAPPVDI DGIREPVAGS LLYGNNIITG AVIPSSASI GIHFYPIWEA ASLDEWLYNG GPYQLIVDHF LLGVCGWIGR EWEFSYRLGM RPWISVAFTA PVAAASAVFL V YPIGQGSF SDGMPLGISG TFNFMLVFQA EHNILMHPFH QLGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESANYGYK FG QEEETYN IVAAHGYFGR LIFQYASFNN SRALHFFLGL WPVVGIWFTA LGVMTMAFNL NGFNFNQSVV DSQGRVINTW ADI LNRANL GMEVMHERNA HNFPLDLAAG ESLPVALTAP AVNG

UniProtKB: Photosystem II protein D1

+
Macromolecule #2: ACPII-4

MacromoleculeName: ACPII-4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 23.658529 KDa
SequenceString: MLRTAILALC VAGASAFTAS PALYKSASRK AAVSGMKMQE ADRSYAMPFL SRPPALDGSM AGDVGFDPLG FSNYFDLKWL REAELKHGR VCMLGCLGFL VQEQANLPLP GFDNKLATEA FFSVPAGGLW QIFFSLGAIE IITNKGKLTP GSMFTGGRAP G DLDFDPLN ...String:
MLRTAILALC VAGASAFTAS PALYKSASRK AAVSGMKMQE ADRSYAMPFL SRPPALDGSM AGDVGFDPLG FSNYFDLKWL REAELKHGR VCMLGCLGFL VQEQANLPLP GFDNKLATEA FFSVPAGGLW QIFFSLGAIE IITNKGKLTP GSMFTGGRAP G DLDFDPLN LSVDETALRR FELAELKHAR LAMIGLGGML HQMLLTKQAP IEQLTNFKSL A

+
Macromolecule #3: ACPII-1

MacromoleculeName: ACPII-1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 23.755605 KDa
SequenceString: MFRAALLLAC LASASAFAPG SLMMPKSATR AAISRGPRMQ ANDDLAVPFL ERPPMLDGSY AGDIGFDPVG FSNYFDLRWL REAELKHGR VCMLGVVGFL VQEFVTLPMF SNGVTPVDDF FVVPATGLWQ IFFTIGFVEA FSNGFKLTPS DMFADDRAPG D LGFDPLGC ...String:
MFRAALLLAC LASASAFAPG SLMMPKSATR AAISRGPRMQ ANDDLAVPFL ERPPMLDGSY AGDIGFDPVG FSNYFDLRWL REAELKHGR VCMLGVVGFL VQEFVTLPMF SNGVTPVDDF FVVPATGLWQ IFFTIGFVEA FSNGFKLTPS DMFADDRAPG D LGFDPLGC GKDPAALARR QLVEVKNGRL AMIAFGGMLH QQLLTKQGVI EQLTNFKAIM

+
Macromolecule #4: ACPII-2

MacromoleculeName: ACPII-2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 22.144328 KDa
SequenceString: APRAVSKTAP RMAVFPGQFS DSVPFLKQPT NLDGSYVGDV GFDPLGFSDV FDIRVLREAE LKHGRIAMLA TLGMVVQDAY TFPFFDKVL PIPAHDVIVK SGGMSQILLW TSFAEIFGGI ALFQTIQGKR APGDYSFDPL NLSANDLEKR ERYALAEIKH S RLAMLAFS ...String:
APRAVSKTAP RMAVFPGQFS DSVPFLKQPT NLDGSYVGDV GFDPLGFSDV FDIRVLREAE LKHGRIAMLA TLGMVVQDAY TFPFFDKVL PIPAHDVIVK SGGMSQILLW TSFAEIFGGI ALFQTIQGKR APGDYSFDPL NLSANDLEKR ERYALAEIKH S RLAMLAFS GMVHQYFITN QGVIEQINNF RPINGFPDAT FS

+
Macromolecule #5: ACPII-3

MacromoleculeName: ACPII-3 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 24.136174 KDa
SequenceString: MLRAVVLAAC VASAAAFAPG ASVLPRAAAR ATSTKGPSMQ LLPLYGEGKL QGPGTQAIPG SEPPPALDGT WVGDVGFDPL GFSRVIDMR WLREAELKHG RVCMLAATGM IVQDIALFPG VTKTFGPAKI TALHDVAVKQ GSMQQLLVWL GFLEIFGFVA I VQMLQGSG ...String:
MLRAVVLAAC VASAAAFAPG ASVLPRAAAR ATSTKGPSMQ LLPLYGEGKL QGPGTQAIPG SEPPPALDGT WVGDVGFDPL GFSRVIDMR WLREAELKHG RVCMLAATGM IVQDIALFPG VTKTFGPAKI TALHDVAVKQ GSMQQLLVWL GFLEIFGFVA I VQMLQGSG RQPGDFGFDP LNCGANTDTL ARRQLVELKN GRLAMIATGG MIHHFFLTGK GPIEFITTLG A

+
Macromolecule #6: ACPII-5

MacromoleculeName: ACPII-5 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 23.400123 KDa
SequenceString: MLRVALIAAI LASASAFAPM GSLGLVKSAR SGAAISPRMQ SGDFSAAVPF LKRPSNLDGT LAGDVGFDPL GFSDVFDLRV LREAELKHG RFAMLAVLGF LVQEVYTFPF FPKMAPVDAH DYFVTQGGGS QIIFWISFVE IFGVVALFEL IQGKRDAGDF A FDPLGLGK ...String:
MLRVALIAAI LASASAFAPM GSLGLVKSAR SGAAISPRMQ SGDFSAAVPF LKRPSNLDGT LAGDVGFDPL GFSDVFDLRV LREAELKHG RFAMLAVLGF LVQEVYTFPF FPKMAPVDAH DYFVTQGGGS QIIFWISFVE IFGVVALFEL IQGKRDAGDF A FDPLGLGK DEATLARYKV AEIKHARLAM IAIGGFIHQF WVTKQTVLEQ LGNFQSLA

+
Macromolecule #7: ACPII-6

MacromoleculeName: ACPII-6 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 25.022043 KDa
SequenceString: MLRLSILAAC LAAAQAFTSP AALLRPSTRA AVSRGPSMQL YKDGIIQGLG VEAIPGAGRP ANLDGTLVGD VGFDPLGFSN WLDLRWARE AEIKHGRVAM LAATGMIVQD AYKFPGFEGE FGGAAMMKLH NLAVEQGAMQ QLLLWLGLLE IISGVPAIIQ T LNGSERQP ...String:
MLRLSILAAC LAAAQAFTSP AALLRPSTRA AVSRGPSMQL YKDGIIQGLG VEAIPGAGRP ANLDGTLVGD VGFDPLGFSN WLDLRWARE AEIKHGRVAM LAATGMIVQD AYKFPGFEGE FGGAAMMKLH NLAVEQGAMQ QLLLWLGLLE IISGVPAIIQ T LNGSERQP GDFGFDPLNC GANPDTLARR QLTELKNGRL AMIAVGGMVH HYLLVGRGPI EFITNIPNFK NPLPPF

+
Macromolecule #8: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 56.354172 KDa
SequenceString: MGLPWYRVHT VVLNDPGRLI AVHLMHTALV AGWAGSMALY ELAVFDPSDP VLNPMWRQGM FVMPFMARIG VTDSWGGWSV TGESVANPG FWSFEGVALA HIGLSGLLFL AAVWHWVYWD LELFRDPRTG NPALDLPKIF GIHLLLSGVL CFGFGAFHVT G AWGPGIWV ...String:
MGLPWYRVHT VVLNDPGRLI AVHLMHTALV AGWAGSMALY ELAVFDPSDP VLNPMWRQGM FVMPFMARIG VTDSWGGWSV TGESVANPG FWSFEGVALA HIGLSGLLFL AAVWHWVYWD LELFRDPRTG NPALDLPKIF GIHLLLSGVL CFGFGAFHVT G AWGPGIWV SDAYGITGKV QPVAPAWGAE GFNPFNPSGV ASHHIAAGIL GFLAGIFHIA VRPPQRLYRA LRMGNIETVL SS SIAAVFW SAFITTGTMW YGSATTPIEL FGPTRYQWDS GYFQQEIERR VENSLNEGLN LSEAWSRIPD KLAFYDYIGN NPA KGGLFR AGPMNKGDGI AEAWLGHPIF QDKEGKELTV RRMPAFFETF PVILVDKDGI IRADIPFRRA ESKYSIEQVG VTVS FYGGK LNGQVFKDAP TVKKYARKAQ LGEVLEFDRT TLESDGVFRS SPRGWYTFGH ANFALLFFLG HLWHGSRTLF RDVFS GIGA EVTEQVEFGA FQKLGDRSTK KQGAV

UniProtKB: Photosystem II CP47 reaction center protein

+
Macromolecule #9: PsbC_CP43

MacromoleculeName: PsbC_CP43 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 52.077359 KDa
SequenceString: MKTLYSLRRF YHVETPFNSS LSVAGRDIES TGFAWWSGNS RLINVSGKLL GAHVAHAGLM VFWCGAMTLF EVAHYIPEKP LYEQGLILL PHLAVLGWGV GPGGEIIDIY PYFVVGVLHL ISSAVLGFGG VYHSLIGPDT LEESFPAFGY DWRDKNKITT I LGIHLIVL ...String:
MKTLYSLRRF YHVETPFNSS LSVAGRDIES TGFAWWSGNS RLINVSGKLL GAHVAHAGLM VFWCGAMTLF EVAHYIPEKP LYEQGLILL PHLAVLGWGV GPGGEIIDIY PYFVVGVLHL ISSAVLGFGG VYHSLIGPDT LEESFPAFGY DWRDKNKITT I LGIHLIVL GIGAFLLVIK AMYVGGIYDT WAPGGGDVRI IDSPTLNPGV IFGYVLKSPW GGDGWIVSVN NMEDLVGGHI WI GIICIVG GFWHIFTKPF AWARRAYVWS GEAYLSYSLV AVSLMGFIAS QYSWYNNTAY PSEFYGPTGP EASQSQAFTF LVR DQRLGA NVSSAQGPTG LGKYLMRSPS GEIILGGETQ RFWDLRAPWI EPLRGPNGLD LNKIKNDIQP WQERRAAEYM THAP LGSLN SVGGVATEIN SVNYVSPRSW LTCAHFFLGF AFYIGHLWHA GRARAAAAGF EKGINRENEP TLSLRPID

+
Macromolecule #10: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 39.216812 KDa
SequenceString: MTIAIGQEEG RGWFDLIDDW LKRDRFVFVG WSGLLLFPTS YLSIGGWFTG TTFVTSWYTH GLASSYLEGC NFFTAAVSTP ANSMGHSLL LLWGPEAQGD FTRWCQIGGL WAFCALHGSF ALIGFCLRQF EIARLVGIRP YNAIAFSGPI AIFVSVFLMY P LGQASWFF ...String:
MTIAIGQEEG RGWFDLIDDW LKRDRFVFVG WSGLLLFPTS YLSIGGWFTG TTFVTSWYTH GLASSYLEGC NFFTAAVSTP ANSMGHSLL LLWGPEAQGD FTRWCQIGGL WAFCALHGSF ALIGFCLRQF EIARLVGIRP YNAIAFSGPI AIFVSVFLMY P LGQASWFF APSLGVAAIF RFLLFIQGFH NFTLNPFHMM GVAGILGAAL LCAIHGATVQ NTIFEDGDAA NTFRAFTPTQ AE ETYSMVT ANRFWSQIFG VAFSNKRWLH FFMLFVPLAG LWTSAIGIVG LALNLRAYDF VSQELRAAED PEFETFYTKN ILL NEGIRS WMAAQDQPHE NFIFPEEVLP RGNAL

UniProtKB: Photosystem II D2 protein

+
Macromolecule #11: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 9.505693 KDa
SequenceString:
MSGGSTGERP FSDIITSIRY WIIHSITIPA LYVAGWLFVS TGLAYDIFGT PRPNEYFTQD RQQVPLVNDR FSAKQELEDL TKGL

UniProtKB: Cytochrome b559 subunit alpha

+
Macromolecule #12: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 4.845769 KDa
SequenceString:
MSKIQQPVSY PIFTFRWLAI HGLAVPTVFF LGAITSMQFI QR

UniProtKB: Cytochrome b559 subunit beta

+
Macromolecule #13: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 7.519887 KDa
SequenceString:
MALRTRLGEL LRPLNSEYGK VAPGWGTTPI MGFVMLLFFL FLLIILQIYN SSLIIENVDV DWASLGS

UniProtKB: Photosystem II reaction center protein H

+
Macromolecule #14: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 4.424081 KDa
SequenceString:
MFTLKIVVYT TVTFFVSLFT FGFLSNDASR NPNRKDLE

UniProtKB: Photosystem II reaction center protein I

+
Macromolecule #15: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 3.964609 KDa
SequenceString:
MASTGRIPLW LIATVGGTLA LTVVGIFFYG SYSGVGSSL

UniProtKB: Photosystem II reaction center protein J

+
Macromolecule #16: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 5.005114 KDa
SequenceString:
MEAILLIAKL PEAYAVFKPI IDVAPVIPVF FLLLAFVWQA AVGFR

UniProtKB: Photosystem II reaction center protein K

+
Macromolecule #17: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 4.363087 KDa
SequenceString:
MSGPNPNKQP VELNRTSLFW GLLLIFVLAV LFSSYFFN

UniProtKB: Photosystem II reaction center protein L

+
Macromolecule #18: PsbM

MacromoleculeName: PsbM / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 3.933613 KDa
SequenceString:
MNVSVAAYLA VLLGTFVPVV FLVTLYIQSE SRKAGSS

+
Macromolecule #19: Psb-gama_linker

MacromoleculeName: Psb-gama_linker / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 31.745117 KDa
SequenceString: TRLVSDWSSD VCSSDLSRMM KSLALAAVGL AVGAEAFAPT PMVGGAKLAL RTSSTRSVAT VGPKMAMDVN AIVEGAQYLT AAVPNVPFV DEITGEPQGL TAPIVHFGSV ISLWLLFALP VWSAAYKAAG ADTAEWVGVS QVTEDAPGIG LYGKYAPEYD G PTFREGLE ...String:
TRLVSDWSSD VCSSDLSRMM KSLALAAVGL AVGAEAFAPT PMVGGAKLAL RTSSTRSVAT VGPKMAMDVN AIVEGAQYLT AAVPNVPFV DEITGEPQGL TAPIVHFGSV ISLWLLFALP VWSAAYKAAG ADTAEWVGVS QVTEDAPGIG LYGKYAPEYD G PTFREGLE YVLSFAWKPP ILIAWKPRAD LDRAMMDPAR DTVVSSLYKS LGGALDKTAV YDEEDQLLIL SDMETFPETE LG RRRVAQA EAAGWFTGNP SFGKSLIEYS EETKKGMREP GTVSISAKEL AALRAEAAKK

+
Macromolecule #20: PsbO

MacromoleculeName: PsbO / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 32.104006 KDa
SequenceString: NRAAACSVTM QDNSLAKKAA GIAAIPLSFL LGVNAANAIT TEDIRGLTYS QVKGTGLANR CPEVSEQNAG GTIKFADDKK YKVTELCLE PKSFQIEEEV TKRRGETKKE FVDTKLMTRA TYSLTGIEGP IVFKDGGLTF LEKGGIDYAA TTVQLPGGER V PFLFTIKE ...String:
NRAAACSVTM QDNSLAKKAA GIAAIPLSFL LGVNAANAIT TEDIRGLTYS QVKGTGLANR CPEVSEQNAG GTIKFADDKK YKVTELCLE PKSFQIEEEV TKRRGETKKE FVDTKLMTRA TYSLTGIEGP IVFKDGGLTF LEKGGIDYAA TTVQLPGGER V PFLFTIKE LEGKFSSSQV SAGTELGGNF KTPSYRTGLF LDPKGRGGTT GYDMAVALPG LEADGGEGQD ELFAETNKVF QV TDGSIEM AFNRVDGTNG EFSGVFVSEQ LSDTDMGSKA PKKVLLKGIV FGKIEEQTGD EDY

+
Macromolecule #21: PsbQ

MacromoleculeName: PsbQ / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 15.74891 KDa
SequenceString:
AASGDFPKQS YFGAAPISAP FGDTYGTAGA PIWEKLGETE KGIFTRIAQT TKDQLEQASE LISLGSWEAS RQRLRMTMYE TRKSMVRLT DVDGSKDAKD LFATFKKKLE ALDRALVAKD KALSIKLIGD VRASYNKWAA TVGGV

+
Macromolecule #22: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 3.664447 KDa
SequenceString:
METLVYVFLL AGTLGVIFFA VFFRDPPRIA KK

UniProtKB: Photosystem II reaction center protein T

+
Macromolecule #23: PsbU

MacromoleculeName: PsbU / type: protein_or_peptide / ID: 23 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 13.211063 KDa
SequenceString:
MQAESVDRRG FLGALGAAVV AAPLAASANV EYPNVPYLGG SDIIDVNNAN VRVYTRLPGM YPAIAKKIIK RAPYKDINEM LEKGDFTAA EKDILDKYLP NLTALEPAPE YVIDNINNGL YR

+
Macromolecule #24: Photosystem II cytochrome c550

MacromoleculeName: Photosystem II cytochrome c550 / type: protein_or_peptide / ID: 24 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 17.708234 KDa
SequenceString:
MLKRFSSLNI ILGMLLVSFV ASPVHATDLD ENTRTVPLDS SGTTVILTPE QVKRGKRLFN SSCGNCHVGG ITKTNPNLGL EPDALSLAT PARDNIDALV DYMKNPTTYD GLESIAELHP SVKSADIFPK MRSLSDEDLF AIGGHILLQP KLSSEKWGGG K IYY

UniProtKB: Photosystem II cytochrome c550

+
Macromolecule #25: PsbW

MacromoleculeName: PsbW / type: protein_or_peptide / ID: 25 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 13.751879 KDa
SequenceString:
TRSLCDWSSD VCSSDLSKVL FLALCLVAGA SAFNAPAPMA LRASKTAMTM KAEGPMPKLA KALAPAIAAA NIAIASPVFA EGTGEALGI DDTRLIVPVI LIPVITFILY AGFASEQDNE DFFDTYDQRR K

+
Macromolecule #26: Photosystem II reaction center protein X

MacromoleculeName: Photosystem II reaction center protein X / type: protein_or_peptide / ID: 26 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 4.149939 KDa
SequenceString:
MTPSLSAFIN SLLLGLFVVV IPIGAALFLV SQSDRVTRT

UniProtKB: Photosystem II reaction center protein X

+
Macromolecule #27: Photosystem II reaction center protein Psb30

MacromoleculeName: Photosystem II reaction center protein Psb30 / type: protein_or_peptide / ID: 27 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 3.763581 KDa
SequenceString:
MFNPTTLFQL IALFLVITSG PAIIVLIAFR RGNL

UniProtKB: Photosystem II reaction center protein Psb30

+
Macromolecule #28: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 28 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Molecular weightTheoretical: 6.57399 KDa
SequenceString:
MVGLLQILVS ILILLSFALV VGVPVILVSP GEWEKSKGLV YSAAGLWFGL VIVIAAFNSF VI

UniProtKB: Photosystem II reaction center protein Z

+
Macromolecule #29: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 29 / Number of copies: 2 / Formula: OEX
Molecular weightTheoretical: 339.827 Da
Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

+
Macromolecule #30: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 30 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #31: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 31 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM / Bicarbonate

+
Macromolecule #32: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 32 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

+
Macromolecule #33: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 33 / Number of copies: 210 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

+
Macromolecule #34: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 34 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A / Pheophytin

+
Macromolecule #35: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta...

MacromoleculeName: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
type: ligand / ID: 35 / Number of copies: 24 / Formula: 8CT
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-8CT:
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene

+
Macromolecule #36: 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: 36 / Number of copies: 4 / 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 / Plastoquinone

+
Macromolecule #37: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 37 / Number of copies: 24 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #38: Chlorophyll c2

MacromoleculeName: Chlorophyll c2 / type: ligand / ID: 38 / Number of copies: 14 / Formula: KC2
Molecular weightTheoretical: 608.926 Da
Chemical component information

ChemComp-KC2:
Chlorophyll c2 / Chlorophyll c

+
Macromolecule #39: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...

MacromoleculeName: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17- ...Name: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
type: ligand / ID: 39 / Number of copies: 48 / Formula: II0
Molecular weightTheoretical: 564.84 Da
Chemical component information

ChemComp-II0:
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol

+
Macromolecule #40: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...

MacromoleculeName: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
type: ligand / ID: 40 / Number of copies: 8 / Formula: IHT
Molecular weightTheoretical: 550.856 Da
Chemical component information

ChemComp-IHT:
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol

+
Macromolecule #41: 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: 41 / Number of copies: 8 / 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 #42: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 42 / Number of copies: 16 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #43: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 43 / Number of copies: 8 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #44: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 44 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

+
Macromolecule #45: water

MacromoleculeName: water / type: ligand / ID: 45 / Number of copies: 84 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168683
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