[English] 日本語
Yorodumi
- EMDB-60026: Cryo-EM structure of an intermediate-state PSII-PRF2' complex dur... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60026
TitleCryo-EM structure of an intermediate-state PSII-PRF2' complex during the process of photosystem II repair
Map dataThe cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle.
Sample
  • Complex: Cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle
    • Protein or peptide: x 16 types
  • Ligand: x 12 types
KeywordsPHOTOSYNTHESIS
Function / homology
Function and homology information


oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide / chlorophyll binding / photosynthetic electron transport in photosystem II ...oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide / chlorophyll binding / photosynthetic electron transport in photosystem II / : / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) ...Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / 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 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
Photosystem II CP47 reaction center protein / Uncharacterized protein / 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 reaction center protein L / Photosystem II reaction center protein T ...Photosystem II CP47 reaction center protein / Uncharacterized protein / 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 reaction center protein L / Photosystem II reaction center protein T / Cytochrome b559 subunit alpha / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II reaction center protein Z / Photosystem II reaction center protein M / Cytochrome b559 subunit beta
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLi A / Liu Z
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31925024 China
Chinese Academy of SciencesYSBR-015 China
Chinese Academy of SciencesXDB37020101 China
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii.
Authors: Anjie Li / Tingting You / Xiaojie Pang / Yidi Wang / Lijin Tian / Xiaobo Li / Zhenfeng Liu /
Abstract: Photosystem II (PSII) catalyzes water oxidation and plastoquinone reduction by utilizing light energy. It is highly susceptible to photodamage under high-light conditions and the damaged PSII needs ...Photosystem II (PSII) catalyzes water oxidation and plastoquinone reduction by utilizing light energy. It is highly susceptible to photodamage under high-light conditions and the damaged PSII needs to be restored through a process known as the PSII repair cycle. The detailed molecular mechanism underlying the PSII repair process remains mostly elusive. Here, we report biochemical and structural features of a PSII-repair intermediate complex, likely arrested at an early stage of the PSII repair process in the green alga Chlamydomonas reinhardtii. The complex contains three protein factors associated with a damaged PSII core, namely Thylakoid Enriched Factor 14 (TEF14), Photosystem II Repair Factor 1 (PRF1), and Photosystem II Repair Factor 2 (PRF2). TEF14, PRF1 and PRF2 may facilitate the release of the manganese-stabilizing protein PsbO, disassembly of peripheral light-harvesting complexes from PSII and blockage of the Q site, respectively. Moreover, an α-tocopherol quinone molecule is located adjacent to the heme group of cytochrome b, potentially fulfilling a photoprotective role by preventing the generation of reactive oxygen species.
History
DepositionMay 6, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60026.png

Downloads & links

-
Map

FileDownload / File: emd_60026.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 208 pix.
= 280.8 Å		1.35 Å/pix.
x 208 pix.
= 280.8 Å		1.35 Å/pix.
x 208 pix.
= 280.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.0036567594 - 0.21545635
Average (Standard dev.)-0.0001617863 (±0.0049706115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 280.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: The half cryo-EM map of the PSII-PRF2' complex...

Fileemd_60026_half_map_1.map
AnnotationThe half cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: The half cryo-EM map of the PSII-PRF2' complex...

Fileemd_60026_half_map_2.map
AnnotationThe half cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Cryo-EM map of the PSII-PRF2' complex functioning in the PSII-rep...

EntireName: Cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle
Components
  • Complex: Cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle
    • 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 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 protein Psb30
    • Protein or peptide: 4.1 kDa photosystem II subunit
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: Photosystem II CP43 reaction center protein
    • Protein or peptide: Photosystem II protein D1
    • Protein or peptide: Chains: 1
  • Ligand: CHLOROPHYLL A
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • 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: PHEOPHYTIN A
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: RRR-ALPHA-TOCOPHERYLQUINONE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: FE (II) ION

+
Supramolecule #1: Cryo-EM map of the PSII-PRF2' complex functioning in the PSII-rep...

SupramoleculeName: Cryo-EM map of the PSII-PRF2' complex functioning in the PSII-repair cycle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

+
Macromolecule #1: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 56.089703 KDa
SequenceString: MGLPWYRVHT VVINDPGRLI SVHLMHTALV SGWAGSMALF EISVFDPSDP VLNPMWRQGM FVLPFMTRLG ITQSWGGWTI SGETATNPG IWSYEGVAAA HIILSGALFL ASVWHWTYWD LELFRDPRTG KTALDLPKIF GIHLFLSGLL CFGFGAFHVT G VFGPGIWV ...String:
MGLPWYRVHT VVINDPGRLI SVHLMHTALV SGWAGSMALF EISVFDPSDP VLNPMWRQGM FVLPFMTRLG ITQSWGGWTI SGETATNPG IWSYEGVAAA HIILSGALFL ASVWHWTYWD LELFRDPRTG KTALDLPKIF GIHLFLSGLL CFGFGAFHVT G VFGPGIWV SDPYGLTGSV QPVAPSWGAD GFDPYNPGGI ASHHIAAGIL GVLAGLFHLC VRPSIRLYFG LSMGSIETVL SS SIAAVFW AAFVVAGTMW YGSAATPIEL FGPTRYQWDQ GFFQQEIQKR VQASLAEGAS LSDAWSRIPE KLAFYDYIGN NPA KGGLFR TGAMNSGDGI AVGWLGHASF KDQEGRELFV RRMPTFFETF PVLLLDKDGI VRADVPFRKA ESKYSIEQVG VSVT FYGGE LDGLTFTDPA TVKKYARKAQ LGEIFEFDRS TLQSDGVFRS SPRGWFTFGH VCFALLFFFG HIWHGARTIF RDVFA GIDD DINDQVEFGK YKKLGDTSSL REAF

UniProtKB: Photosystem II CP47 reaction center protein

+
Macromolecule #2: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 39.474031 KDa
SequenceString: MTIAIGTYQE KRTWFDDADD WLRQDRFVFV GWSGLLLFPC AYFALGGWLT GTTFVTSWYT HGLATSYLEG CNFLTAAVST PANSMAHSL LFVWGPEAQG DFTRWCQLGG LWAFVALHGA FGLIGFMLRQ FEIARSVNLR PYNAIAFSAP IAVFVSVFLI Y PLGQSGWF ...String:
MTIAIGTYQE KRTWFDDADD WLRQDRFVFV GWSGLLLFPC AYFALGGWLT GTTFVTSWYT HGLATSYLEG CNFLTAAVST PANSMAHSL LFVWGPEAQG DFTRWCQLGG LWAFVALHGA FGLIGFMLRQ FEIARSVNLR PYNAIAFSAP IAVFVSVFLI Y PLGQSGWF FAPSFGVAAI FRFILFFQGF HNWTLNPFHM MGVAGVLGAA LLCAIHGATV ENTLFEDGDG ANTFRAFNPT QA EETYSMV TANRFWSQIF GVAFSNKRWL HFFMLLVPVT GLWMSAIGVV GLALNLRAYD FVSQEIRAAE DPEFETFYTK NIL LNEGIR AWMAAQDQPH ERLVFPEEVL PRGNAL

UniProtKB: Photosystem II D2 protein

+
Macromolecule #3: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 9.312598 KDa
SequenceString:
MAGKPVERPF SDILTSIRYW VIHSITVPAL FIAGWLFVST GLAYDVFGTP RPNEYFTEDR QEAPLITDRF NALEQVKKLS GN

UniProtKB: Cytochrome b559 subunit alpha

+
Macromolecule #4: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.986013 KDa
SequenceString:
MTTKKSAEVL VYPIFTVRWL AIHGIAVPTI FFLGAITAMQ FIQR

UniProtKB: Cytochrome b559 subunit beta

+
Macromolecule #5: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 9.445063 KDa
SequenceString:
MATGTSKAKP SKVNSDFQEP GLVTPLGTLL RPLNSEAGKV LPGWGTTVLM AVFILLFAAF LLIILEIYNS SLILDDVSMS WETLAKVS

UniProtKB: Photosystem II reaction center protein H

+
Macromolecule #6: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.245035 KDa
SequenceString:
MLTLKIFVYT VVTFFVCLFI FGFLSNDPAR NPGKNLD

UniProtKB: Photosystem II reaction center protein I

+
Macromolecule #7: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 5.062142 KDa
SequenceString:
MTTLALVLAK LPEAYAPFAP IVDVLPVIPV FFILLAFVWQ AAVSFR

UniProtKB: Photosystem II reaction center protein K

+
Macromolecule #8: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.431229 KDa
SequenceString:
MARPNPNKQV VELNRTSLYW GLLLIFVLAV LFSSYIFN

UniProtKB: Photosystem II reaction center protein L

+
Macromolecule #9: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.762433 KDa
SequenceString:
MEVNIYGLTA TALFIIIPTS FLLILYVKTA STQD

UniProtKB: Photosystem II reaction center protein M

+
Macromolecule #10: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.639438 KDa
SequenceString:
MEALVYTFLL VGTLGIIFFS IFFRDPPRMI K

UniProtKB: Photosystem II reaction center protein T

+
Macromolecule #11: Photosystem II reaction center protein Psb30

MacromoleculeName: Photosystem II reaction center protein Psb30 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.333058 KDa
SequenceString:
MNIELALTLV SLVLVVSAGP LVVVLLSARG GNL

UniProtKB: Photosystem II reaction center protein Psb30

+
Macromolecule #12: 4.1 kDa photosystem II subunit

MacromoleculeName: 4.1 kDa photosystem II subunit / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 9.894716 KDa
SequenceString:
MAAVCVSSKA VAVRPATRVA SRPAARMVVR ASAKPAQISE KAIAAGVSAA AAASLALAPI AEAAVTPSLK NFLGSLIAGA TVLGGIALA ITAVSKFDKT IR

UniProtKB: Uncharacterized protein

+
Macromolecule #13: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 6.565863 KDa
SequenceString:
MTSILQVALL ALIFVSFALV VGVPVVFATP NGWTDNKGAV FSGLSLWLLL VFVVGILNSF VV

UniProtKB: Photosystem II reaction center protein Z

+
Macromolecule #14: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 50.680738 KDa
SequenceString: METLFNGTLT VGGRDQETTG FAWWSGNARL INLSGKLLGA HVAHAGLIVF WAGAMNLFEV SHFVPEKPMY EQGLILLPHI ATLGYGVGP GGEIIDTFPY FVSGVLHLIS SAVLGFGGVY HSLIGPETLE ESYPFFGYVW KDKNKMTNIL GYHLIMLGLG A WLLVWKAM ...String:
METLFNGTLT VGGRDQETTG FAWWSGNARL INLSGKLLGA HVAHAGLIVF WAGAMNLFEV SHFVPEKPMY EQGLILLPHI ATLGYGVGP GGEIIDTFPY FVSGVLHLIS SAVLGFGGVY HSLIGPETLE ESYPFFGYVW KDKNKMTNIL GYHLIMLGLG A WLLVWKAM YFGGVYDTWA PGGGDVRVIT NPTTNAAVIF GYLVKSPFGG DGWICSVDNM EDIIGGHIWI GTLEILGGIW HI YTTPWPW ARRAFVWSGE AYLSYSLGAI GVMGFIACCM SWFNNTAYPS EFYGPTGPEA SQSQAFTFLV RDQRLGANVA SAQ GPTGLG KYLMRSPTGE IIFGGETMRF WDFRGPWLEP LRGPNGLDLN KLKNDIQPWQ ERRAAEYMTH APLGSLNSVG GVAT EINAV NFVSPRSWLA CSHFCLGFFF FIGHLWHAGR ARAAAAGFEK GIDRFDEPVL SMRPLD

UniProtKB: Photosystem II CP43 reaction center protein

+
Macromolecule #15: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 36.515551 KDa
SequenceString: NSSLWARFCE WITSTENRLY IGWFGVIMIP CLLTATSVFI IAFIAAPPVD IDGIREPVSG SLLYGNNIIT GAVIPTSNAI GLHFYPIWE AASLDEWLYN GGPYQLIVCH FLLGVYCYMG REWELSFRLG MRPWIAVAYS APVAAASAVF LVYPIGQGSF S DGMPLGIS ...String:
NSSLWARFCE WITSTENRLY IGWFGVIMIP CLLTATSVFI IAFIAAPPVD IDGIREPVSG SLLYGNNIIT GAVIPTSNAI GLHFYPIWE AASLDEWLYN GGPYQLIVCH FLLGVYCYMG REWELSFRLG MRPWIAVAYS APVAAASAVF LVYPIGQGSF S DGMPLGIS GTFNFMIVFQ AEHNILMHPF HMLGVAGVFG GSLFSAMHGS LVTSSLIRET TENESANEGY RFGQEEETYN IV AAHGYFG RLIFQYASFN NSRSLHFFLA AWPVIGIWFT ALGLSTMAFN LNGFNFNQSV VDSQGRVLNT WADIINRANL GME VMHERN AHN

UniProtKB: Photosystem II protein D1

+
Macromolecule #16: Chains: 1

MacromoleculeName: Chains: 1 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 10.153907 KDa
SequenceString:
MALTTLASRK AAAFSSVSSR KVALAPTPAK RMVSTRAVGD VNAPIEYAVG AAILVSLVAT AIIPIVLNPG QQAADKIFNA KQKAPLDKP TTPGKNSGKK

UniProtKB: Uncharacterized protein

+
Macromolecule #17: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 17 / Number of copies: 35 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #18: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 18 / Number of copies: 10 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 19 / Number of copies: 6 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #20: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 20 / Number of copies: 8 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
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

+
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: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 23 / Number of copies: 2 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

+
Macromolecule #24: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 24 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #25: RRR-ALPHA-TOCOPHERYLQUINONE

MacromoleculeName: RRR-ALPHA-TOCOPHERYLQUINONE / type: ligand / ID: 25 / Number of copies: 1 / Formula: VTQ
Molecular weightTheoretical: 446.706 Da
Chemical component information

ChemComp-VTQ:
RRR-ALPHA-TOCOPHERYLQUINONE

+
Macromolecule #26: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 26 / Number of copies: 3 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #27: 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: 27 / Number of copies: 1 / 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 #28: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 28 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

-
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 K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

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

8kde

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 159928
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

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

New format data for meta-information of EMDB entries

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

Related info.:EMDB header

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

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more