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- PDB-5xnm: Structure of unstacked C2S2M2-type PSII-LHCII supercomplex from P... -

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Entry
Database: PDB / ID: 5xnm
TitleStructure of unstacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Components
  • (Chlorophyll a-b binding ...) x 2
  • (Cytochrome b559 subunit ...) x 2
  • (Light harvesting chlorophyll a/b-binding protein ...) x 3
  • (Photosystem II ...) x 15
  • Oxygen-evolving enhancer protein 1, chloroplastic
KeywordsMEMBRANE PROTEIN / Photosystem II / PSII-LHCII / C2S2M2 / Supercomplex
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I ...photosynthesis, light harvesting / photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II 5kDa protein, chloroplastic / Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbZ, reaction centre / Photosystem II reaction center protein H / photosystem ii from thermosynechococcus elongatus / Photosystem II cytochrome b559, alpha subunit / Photosystem II CP47 reaction center protein ...Photosystem II 5kDa protein, chloroplastic / Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbZ, reaction centre / Photosystem II reaction center protein H / photosystem ii from thermosynechococcus elongatus / Photosystem II cytochrome b559, alpha subunit / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / 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 / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Arc Repressor Mutant, subunit A / Roll / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Chem-XAT / Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSII 6.1 kDa protein / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center protein K / Photosystem II reaction center protein I / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein J / Oxygen-evolving enhancer protein 1, chloroplastic / Chlorophyll a-b binding protein 8, chloroplastic / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Photosystem II reaction center protein M / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center protein Z / Photosystem II reaction center protein T / Ultraviolet-B-repressible protein / Photosystem II reaction center protein H / Photosystem II CP47 reaction center protein
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSu, X.D. / Ma, J. / Wei, X.P. / Cao, P. / Zhu, D.J. / Chang, W.R. / Liu, Z.F. / Zhang, X.Z. / Li, M.
Funding support China, 4items
OrganizationGrant numberCountry
The Strategic Priority Research Program of CASXDB08020302 China
The Key Research Program of Frontier Sciences of CASQYZDB-SSW-SMC005 China
National 973 project grant2011CBA00900 China
National Natural Science Foundation of China31570724 and 31270793 China
CitationJournal: Science / Year: 2017
Title: Structure and assembly mechanism of plant CSM-type PSII-LHCII supercomplex.
Authors: Xiaodong Su / Jun Ma / Xuepeng Wei / Peng Cao / Dongjie Zhu / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li /
Abstract: In plants, the photosynthetic machinery photosystem II (PSII) consists of a core complex associated with variable numbers of light-harvesting complexes II (LHCIIs). The supercomplex, comprising a ...In plants, the photosynthetic machinery photosystem II (PSII) consists of a core complex associated with variable numbers of light-harvesting complexes II (LHCIIs). The supercomplex, comprising a dimeric core and two strongly bound and two moderately bound LHCIIs (CSM), is the dominant form in plants acclimated to limited light. Here we report cryo-electron microscopy structures of two forms of CSM (termed stacked and unstacked) from at 2.7- and 3.2-angstrom resolution, respectively. In each CSM, the moderately bound LHCII assembles specifically with a peripheral antenna complex CP24-CP29 heterodimer and the strongly bound LHCII, to establish a pigment network that facilitates light harvesting at the periphery and energy transfer into the core. The high mobility of peripheral antennae, including the moderately bound LHCII and CP24, provides insights into functional regulation of plant PSII.
History
DepositionMay 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Advisory / Data collection / Other
Category: cell / database_PDB_caveat ...cell / database_PDB_caveat / em_software / pdbx_validate_chiral
Item: _cell.Z_PDB / _cell.length_a ..._cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _em_software.name

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Structure visualization

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Assembly

Deposited unit
1: Chlorophyll a-b binding protein 8, chloroplastic
2: Chlorophyll a-b binding protein 8, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
4: Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24
A: Photosystem II protein D1
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta, PsbF
G: Chlorophyll a-b binding protein 8, chloroplastic
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I, PsbI
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
N: Chlorophyll a-b binding protein 8, chloroplastic
O: Oxygen-evolving enhancer protein 1, chloroplastic
R: Light harvesting chlorophyll a/b-binding protein Lhcb4, CP29
S: Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26
T: Photosystem II reaction center protein T
U: Photosystem II luminal extrinsic protein Tn, PsbTn
W: Photosystem II reaction center protein W, PSBW
X: Photosystem II reaction center protein X
Y: Chlorophyll a-b binding protein 8, chloroplastic
Z: Photosystem II reaction center protein Z
5: Chlorophyll a-b binding protein 8, chloroplastic
6: Chlorophyll a-b binding protein 8, chloroplastic
7: Chlorophyll a-b binding protein, chloroplastic
8: Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta, PsbF
g: Chlorophyll a-b binding protein 8, chloroplastic
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I, PsbI
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
n: Chlorophyll a-b binding protein 8, chloroplastic
o: Oxygen-evolving enhancer protein 1, chloroplastic
r: Light harvesting chlorophyll a/b-binding protein Lhcb4, CP29
s: Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26
t: Photosystem II reaction center protein T
u: Photosystem II luminal extrinsic protein Tn, PsbTn
w: Photosystem II reaction center protein W, PSBW
x: Photosystem II reaction center protein X
y: Chlorophyll a-b binding protein 8, chloroplastic
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,436,522540
Polymers1,042,75154
Non-polymers393,772486
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Chlorophyll a-b binding ... , 2 types, 12 molecules 12GNY56gny37

#1: Protein
Chlorophyll a-b binding protein 8, chloroplastic / LHCII type I CAB-8


Mass: 24952.113 Da / Num. of mol.: 10 / Fragment: UNP residues 23-265 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P27490
#2: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 26545.240 Da / Num. of mol.: 2 / Fragment: UNP residues 23-265 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q04918

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Light harvesting chlorophyll a/b-binding protein ... , 3 types, 6 molecules 48RrSs

#3: Protein Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24


Mass: 22858.957 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A2D0TCJ3*PLUS
#17: Protein Light harvesting chlorophyll a/b-binding protein Lhcb4, CP29


Mass: 27138.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A2D0TCJ0*PLUS
#18: Protein Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26


Mass: 26541.545 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A2D0TCJ1*PLUS

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Photosystem II ... , 15 types, 30 molecules AaBbCcDdHhIiJjKkLlMmTtUuWwXxZz

#4: Protein Photosystem II protein D1 / / PSII D1 protein / 32 kDa thylakoid membrane protein / Photosystem II Q(B) protein


Mass: 38147.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P06585, photosystem II
#5: Protein Photosystem II CP47 reaction center protein / / PSII 47 kDa protein / Protein CP-47


Mass: 56117.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9XQR6
#6: Protein Photosystem II CP43 reaction center protein / / PSII 43 kDa protein / Photosystem II 44 kDa chlorophyll apoprotein / Protein CP-43


Mass: 52035.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P06004
#7: Protein Photosystem II D2 protein / / PSII D2 protein / Photosystem Q(A) protein


Mass: 39557.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P06006, photosystem II
#10: Protein Photosystem II reaction center protein H / / PSII-H / Photosystem II 10 kDa phosphoprotein / Photosystem II 9 kDa phosphoprotein


Mass: 7863.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9XQR3
#11: Protein/peptide Photosystem II reaction center protein I, PsbI /


Mass: 4184.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: D5MAJ9*PLUS
#12: Protein/peptide Photosystem II reaction center protein J / / PSII-J


Mass: 4116.847 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P13555
#13: Protein Photosystem II reaction center protein K / / PSII-K


Mass: 6912.290 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: D5MAJ8
#14: Protein/peptide Photosystem II reaction center protein L / / PSII-L


Mass: 4498.100 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P60147
#15: Protein/peptide Photosystem II reaction center protein M / / PSII-M


Mass: 3756.513 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P69529
#19: Protein/peptide Photosystem II reaction center protein T / / PSII-T


Mass: 4036.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q8HS25
#20: Protein Photosystem II luminal extrinsic protein Tn, PsbTn /


Mass: 10676.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0K9RHP1*PLUS
#21: Protein Photosystem II reaction center protein W, PSBW /


Mass: 5914.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A2D0TCJ2*PLUS
#22: Protein Photosystem II reaction center protein X /


Mass: 8692.072 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q8VYY1
#23: Protein Photosystem II reaction center protein Z / / PSII-Z


Mass: 6555.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q32902

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#8: Protein Cytochrome b559 subunit alpha / / PSII reaction center subunit V


Mass: 9421.555 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P13554
#9: Protein/peptide Cytochrome b559 subunit beta, PsbF /


Mass: 4488.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P62096*PLUS

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Protein / Sugars , 2 types, 12 molecules Oo

#16: Protein Oxygen-evolving enhancer protein 1, chloroplastic / OEE1 / 33 kDa subunit of oxygen evolving system of photosystem II / 33 kDa thylakoid membrane ...OEE1 / 33 kDa subunit of oxygen evolving system of photosystem II / 33 kDa thylakoid membrane protein / OEC 33 kDa subunit


Mass: 26554.646 Da / Num. of mol.: 2 / Fragment: UNP residues 82-329 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P14226
#37: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 15 types, 476 molecules

#24: Chemical...
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 98 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#25: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 216 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#26: Chemical...
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL, LUTEIN / Lutein


Mass: 568.871 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C40H56O2
#27: Chemical
ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN / Violaxanthin


Mass: 600.870 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C40H56O4
#28: Chemical
ChemComp-NEX / (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL, 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C40H56O4
#29: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#30: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H56
#31: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#32: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#33: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#34: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C41H78O12S
#35: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C45H86O10
#36: Chemical
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 9 / Plastoquinone


Mass: 749.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#38: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#39: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
Type: COMPLEX / Entity ID: #1-#23 / Source: NATURAL
Source (natural)Organism: Pisum sativum (garden pea)
Buffer solutionpH: 7.5
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2747: / Classification: refinement
EM software
IDNameCategory
7Chimeramodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50237 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01297837
ELECTRON MICROSCOPYf_angle_d2.543137666
ELECTRON MICROSCOPYf_dihedral_angle_d15.80349080
ELECTRON MICROSCOPYf_chiral_restr0.09612248
ELECTRON MICROSCOPYf_plane_restr0.00917286

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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

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