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- PDB-5mdx: Cryo-EM structure of the PSII supercomplex from Arabidopsis thaliana -

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Entry
Database: PDB / ID: 5mdx
TitleCryo-EM structure of the PSII supercomplex from Arabidopsis thaliana
Components
  • (Chlorophyll a-b binding protein ...) x 3
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 13
  • Chlorophyll a-b binding protein, chloroplastic
  • Oxygen-evolving enhancer protein 1-1, chloroplastic
KeywordsPHOTOSYNTHESIS / photosystem II supercomplex / single particle analysis
Function / homology
Function and homology information


plastid thylakoid membrane / : / photoinhibition / photosystem II antenna complex / nonphotochemical quenching / sequestering of metal ion / PSII associated light-harvesting complex II / chloroplast stromal thylakoid / thylakoid lumen / thylakoid membrane ...plastid thylakoid membrane / : / photoinhibition / photosystem II antenna complex / nonphotochemical quenching / sequestering of metal ion / PSII associated light-harvesting complex II / chloroplast stromal thylakoid / thylakoid lumen / thylakoid membrane / plastoglobule / chloroplast thylakoid / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / apoplast / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / chloroplast envelope / thylakoid / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / photosynthetic electron transport chain / poly(U) RNA binding / response to herbicide / chloroplast stroma / plastid / photosystem II / photosynthesis, light reaction / chloroplast thylakoid membrane / phosphate ion binding / photosynthetic electron transport in photosystem II / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / chloroplast / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / heme binding / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / 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 PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / 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 CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / 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) / Chlorophyll A-B binding protein, plant and chromista / Photosystem II reaction centre protein H / 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. / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosystem II protein D1 / 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.
Similarity search - Domain/homology
CHLOROPHYLL B / CHLOROPHYLL A / : / PROTOPORPHYRIN IX CONTAINING FE / PHEOPHYTIN A / Chlorophyll a-b binding protein 1, chloroplastic / Oxygen-evolving enhancer protein 1-1, chloroplastic / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein ...CHLOROPHYLL B / CHLOROPHYLL A / : / PROTOPORPHYRIN IX CONTAINING FE / PHEOPHYTIN A / Chlorophyll a-b binding protein 1, chloroplastic / Oxygen-evolving enhancer protein 1-1, chloroplastic / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II reaction center protein Z / Photosystem II reaction center protein L / Photosystem II reaction center protein T / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Photosystem II protein D1 / Chlorophyll a-b binding protein CP29.1, chloroplastic / Photosystem II reaction center W protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Expressed protein / Chlorophyll a-b binding protein CP26, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.3 Å
Authorsvan Bezouwen, L.S. / Caffarri, S. / Kale, R.S. / Kouril, R. / Thunnissen, A.M.W.H. / Oostergetel, G.T. / Boekema, E.J.
CitationJournal: Nat Plants / Year: 2017
Title: Subunit and chlorophyll organization of the plant photosystem II supercomplex.
Authors: Laura S van Bezouwen / Stefano Caffarri / Ravindra S Kale / Roman Kouřil / Andy-Mark W H Thunnissen / Gert T Oostergetel / Egbert J Boekema /
Abstract: Photosystem II (PSII) is a light-driven protein, involved in the primary reactions of photosynthesis. In plant photosynthetic membranes PSII forms large multisubunit supercomplexes, containing a ...Photosystem II (PSII) is a light-driven protein, involved in the primary reactions of photosynthesis. In plant photosynthetic membranes PSII forms large multisubunit supercomplexes, containing a dimeric core and up to four light-harvesting complexes (LHCs), which act as antenna proteins. Here we solved a three-dimensional (3D) structure of the CSM supercomplex from Arabidopsis thaliana using cryo-transmission electron microscopy (cryo-EM) and single-particle analysis at an overall resolution of 5.3 Å. Using a combination of homology modelling and restrained refinement against the cryo-EM map, it was possible to model atomic structures for all antenna complexes and almost all core subunits. We located all 35 chlorophylls of the core region based on the cyanobacterial PSII structure, whose positioning is highly conserved, as well as all the chlorophylls of the LHCII S and M trimers. A total of 13 and 9 chlorophylls were identified in CP26 and CP24, respectively. Energy flow from LHC complexes to the PSII reaction centre is proposed to follow preferential pathways: CP26 and CP29 directly transfer to the core using several routes for efficient transfer; the S trimer is directly connected to CP43 and the M trimer can efficiently transfer energy to the core through CP29 and the S trimer.
History
DepositionNov 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Experimental preparation / Refinement description
Category: em_3d_fitting / em_sample_support / em_software
Item: _em_3d_fitting.target_criteria / _em_sample_support.grid_type ..._em_3d_fitting.target_criteria / _em_sample_support.grid_type / _em_software.details / _em_software.name
Revision 1.2Apr 24, 2019Group: Data collection / Derived calculations / Other
Category: em_admin / pdbx_database_proc ...em_admin / pdbx_database_proc / pdbx_database_status / pdbx_validate_chiral / struct_site / struct_site_gen
Item: _em_admin.last_update / _pdbx_database_status.process_site

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Structure visualization

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Assembly

Deposited unit
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)
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Oxygen-evolving enhancer protein 1-1, chloroplastic
T: Photosystem II reaction center protein T
W: Photosystem II reaction center W protein, chloroplastic
X: Photosystem II reaction center protein X
Z: Photosystem II reaction center protein Z
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta (PsbF)
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Oxygen-evolving enhancer protein 1-1, chloroplastic
x: Photosystem II reaction center protein X
z: Photosystem II reaction center protein Z
w: Photosystem II reaction center W protein, chloroplastic
t: Photosystem II reaction center protein T
c: Photosystem II CP43 reaction center protein
R: Chlorophyll a-b binding protein CP29.1, chloroplastic
S: Chlorophyll a-b binding protein CP26, chloroplastic
G: Chlorophyll a-b binding protein 1, chloroplastic
N: Chlorophyll a-b binding protein 1, chloroplastic
Y: Chlorophyll a-b binding protein 1, chloroplastic
r: Chlorophyll a-b binding protein CP29.1, chloroplastic
s: Chlorophyll a-b binding protein CP26, chloroplastic
g: Chlorophyll a-b binding protein 1, chloroplastic
n: Chlorophyll a-b binding protein 1, chloroplastic
y: Chlorophyll a-b binding protein 1, chloroplastic
1: Chlorophyll a-b binding protein 1, chloroplastic
2: Chlorophyll a-b binding protein 1, chloroplastic
3: Chlorophyll a-b binding protein 1, chloroplastic
4: Chlorophyll a-b binding protein, chloroplastic
5: Chlorophyll a-b binding protein 1, chloroplastic
6: Chlorophyll a-b binding protein 1, chloroplastic
7: Chlorophyll a-b binding protein 1, chloroplastic
8: Chlorophyll a-b binding protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,272,947366
Polymers991,58050
Non-polymers281,366316
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem II ... , 13 types, 26 molecules AaBbCcDdHhIiKkLlMmTtWwXxZz

#1: Protein Photosystem II protein D1 / PSII D1 protein / Photosystem II Q(B) protein


Mass: 38003.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P83755, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 55960.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56777
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 50086.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56778
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39444.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56761, photosystem II
#7: Protein Photosystem II reaction center protein H / PSII-H / Photosystem II 10 kDa phosphoprotein


Mass: 7575.691 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56780
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 4170.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62100
#9: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4239.112 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56782
#10: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4471.075 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P60129
#11: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3783.538 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62109
#13: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3825.642 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P61839
#14: Protein Photosystem II reaction center W protein, chloroplastic / PSII 6.1 kDa protein


Mass: 6036.749 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q39194
#15: Protein Photosystem II reaction center protein X / PSBX / Photosystem II subunit X / Putative PSII-X protein / Putative uncharacterized protein ...PSBX / Photosystem II subunit X / Putative PSII-X protein / Putative uncharacterized protein At2g06520 / T12H3.7


Mass: 11826.013 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SKI3
#16: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6569.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56790

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

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


Mass: 9393.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56779
#6: Protein/peptide Cytochrome b559 subunit beta (PsbF)


Mass: 4428.228 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62095

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Protein , 2 types, 4 molecules Oo48

#12: Protein Oxygen-evolving enhancer protein 1-1, 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 / Manganese-stabilizing protein 1 / MSP-1 / OEC 33 kDa subunit


Mass: 26594.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P23321
#20: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23014.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LMQ2

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Chlorophyll a-b binding protein ... , 3 types, 16 molecules RrSsGNYgny123567

#17: Protein Chlorophyll a-b binding protein CP29.1, chloroplastic / LHCB4.1 / LHCII protein 4.1


Mass: 27302.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q07473
#18: Protein Chlorophyll a-b binding protein CP26, chloroplastic / LHCB5 / LHCIIc / Light-harvesting complex II protein 5


Mass: 25232.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9XF89
#19: Protein
Chlorophyll a-b binding protein 1, chloroplastic / Chlorophyll a-b protein 140 / CAB-140 / LHCII type I CAB-1


Mass: 23971.910 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P04778

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Non-polymers , 5 types, 316 molecules

#21: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#22: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 212 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#23: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#24: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#25: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 96 / Source method: obtained synthetically / Formula: C55H70MgN4O6

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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 supercomplex of Photosystem II / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.5
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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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 FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 38 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 5198
EM imaging opticsSpherical aberration corrector: Microscope had a Cs corrector
Image scansMovie frames/image: 7 / Used frames/image: 1-7

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Processing

SoftwareName: PHENIX / Version: dev_2474: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4RELION1.3CTF correction
7Coot0.8.6model fitting
9RELION1.3initial Euler assignment
10RELION1.3final Euler assignment
11RELION1.3classification
12RELION1.33D reconstruction
19PHENIXdev_2474model refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23434 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: Initial fitting of the subunits in the cryo-EM map was performed by rigid body real space refinement, using as templates the high resolution crystal structures of Thermosynechococcus ...Details: Initial fitting of the subunits in the cryo-EM map was performed by rigid body real space refinement, using as templates the high resolution crystal structures of Thermosynechococcus vulcanus PSII (PDB code 3WU2), pea LHC-II (PDB code 2BHW for the S- and M-trimers, and spinach CP29 (PDB code 3PL9) for CP29, CP26 and CP24. Local fitting and adjustment of the subunits in the cryo-EM maps was performed using manual rebuilding and restrained real space refinement as explained in the primary reference. Due to large differences in local resolution of the cryo-EM map, refinement of the PSII core, the S-trimer with CP26/CP29 and the M-trimer with CP24 was performed separately in excised parts of the cryo-EM map. The core was refined at 4.5 angstrom, the S-trimer+CP26+CP29 at 5.5 angstrom and the M-trimer+CP24 at 6.5 angstrom. Core: chains A,B,C,D,E,F,H,I,J,K,L,M,O,T,W,X,Z and a,b,c,d,e,f,h,i,j,k,l,m,o,t,w,x,z. S-trimer+CP26+CP29: chains G,N,Y,S,R and g,n,y,s,r. M-trimer+CP24: chains 1,2,3,4 and 5,6,7,8.
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0069546
ELECTRON MICROSCOPYf_angle_d1.94113919
ELECTRON MICROSCOPYf_dihedral_angle_d11.3284386
ELECTRON MICROSCOPYf_chiral_restr0.0551098
ELECTRON MICROSCOPYf_plane_restr0.0171587

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