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- PDB-8j6z: Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-L... -

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Entry
Database: PDB / ID: 8j6z
TitleCryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2)
Components
  • (Chlorophyll a-b binding protein ...Light-harvesting complexes of green plants) x 4
  • (Photosystem I ...) x 15
KeywordsPHOTOSYNTHESIS / photosystem I / PSI / CELL CYCLE
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem II / response to desiccation / cellular response to abscisic acid stimulus / response to red light / PSII associated light-harvesting complex II / photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus ...photosynthesis, light harvesting in photosystem II / response to desiccation / cellular response to abscisic acid stimulus / response to red light / PSII associated light-harvesting complex II / photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / plastoglobule / chloroplast membrane / regulation of stomatal closure / response to high light intensity / response to far red light / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / apoplast / response to fructose / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / thylakoid / photosynthetic electron transport chain / photosystem I / photosystem II / positive regulation of reactive oxygen species biosynthetic process / plastid / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / protein stabilization / protein domain specific binding / mRNA binding / magnesium ion binding / mitochondrion / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Photosystem I PsaO / 4Fe-4S dicluster domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. ...Photosystem I PsaO / 4Fe-4S dicluster domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / PHYLLOQUINONE ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / Chlorophyll a-b binding protein 2, chloroplastic / Chlorophyll a-b binding protein 4, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein 6, chloroplastic / Photosystem I subunit O / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit IV A, chloroplastic / Photosystem I reaction center subunit II-2, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Chlorophyll a-b binding protein 2.1, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit VI-2, chloroplastic / Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic / Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsChen, S.J.B. / Wu, J.H. / Sui, S.F. / Zhang, L.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2)
Authors: Chen, S.J.B. / Wu, J.H.
History
DepositionApr 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Chlorophyll a-b binding protein 6, chloroplastic
2: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
3: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
4: Chlorophyll a-b binding protein 4, chloroplastic
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II-2, chloroplastic
E: Photosystem I reaction center subunit IV A, chloroplastic
F: Photosystem I reaction center subunit III, chloroplastic
G: Photosystem I reaction center subunit V, chloroplastic
H: Photosystem I reaction center subunit VI-2, chloroplastic
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit psaK, chloroplastic
L: Photosystem I reaction center subunit XI, chloroplastic
O: Photosystem I subunit O
x: Chlorophyll a-b binding protein 2, chloroplastic
y: Chlorophyll a-b binding protein 2, chloroplastic
z: Chlorophyll a-b binding protein 2.1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)740,834283
Polymers525,46220
Non-polymers215,371263
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Chlorophyll a-b binding protein ... , 4 types, 5 molecules 14xyz

#1: Protein Chlorophyll a-b binding protein 6, chloroplastic / LHCI-730 / LHCII type III CAB-6 / Light-harvesting complex protein Lhca1


Mass: 26021.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHCA1, CAB6, At3g54890, F28P10.130 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q01667
#4: Protein Chlorophyll a-b binding protein 4, chloroplastic / LHCI type III CAB-4


Mass: 27760.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHCA4, CAB4, At3g47470, F1P2.20 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: P27521
#18: Protein Chlorophyll a-b binding protein 2, chloroplastic / Chlorophyll a-b protein 165 / CAB-165 / LHCII type I CAB-2


Mass: 28250.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHCB1.1, AB165, CAB2, LHCP-B, At1g29920, F1N18.4 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: P0CJ48
#19: Protein Chlorophyll a-b binding protein 2.1, chloroplastic / Photosystem II light harvesting complex gene 2.1 / Protein LIGHT-HARVESTING CHLOROPHYLL B-BINDING 2.1


Mass: 28753.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHCB2.1, LHCB2.3, At2g05100, F15L11.2 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SHR7

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Photosystem I ... , 15 types, 15 molecules 23ABCDEFGHIJKLO

#2: Protein Photosystem I chlorophyll a/b-binding protein 2, chloroplastic / / Lhca2 / LHCI type III LHCA2


Mass: 27782.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHCA2, At3g61470, F2A19.70 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SYW8
#3: Protein Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic / / Lhca3*1 / LHCI type III LHCA3


Mass: 29206.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHCA3, At1g61520, T25B24.12 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SY97
#5: Protein Photosystem I P700 chlorophyll a apoprotein A1 / / PSI-A / PsaA


Mass: 83315.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: psaA, AtCg00350 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: P56766, photosystem I
#6: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 82555.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: psaB, AtCg00340 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: P56767, photosystem I
#7: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 9049.509 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: psaC, frxA, AtCg01060 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: P62090, photosystem I
#8: Protein Photosystem I reaction center subunit II-2, chloroplastic / / Photosystem I 20 kDa subunit 2 / PSI-D2


Mass: 22336.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAD2, At1g03130, F10O3_4 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SA56
#9: Protein Photosystem I reaction center subunit IV A, chloroplastic / / PSI-E A


Mass: 14984.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAE1, At4g28750, F16A16.140 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9S831
#10: Protein Photosystem I reaction center subunit III, chloroplastic / / Light-harvesting complex I 17 kDa protein / PSI-F


Mass: 24203.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAF, At1g31330, T19E23.12 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SHE8
#11: Protein Photosystem I reaction center subunit V, chloroplastic / / PSI-G


Mass: 17103.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAG, At1g55670, F20N2.21, F20N2.33, F20N2_3 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9S7N7
#12: Protein Photosystem I reaction center subunit VI-2, chloroplastic / / PSI-H1


Mass: 15291.522 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAH2, At1g52230, F9I5.11 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI6
#13: Protein/peptide Photosystem I reaction center subunit VIII / / PSI-I


Mass: 4137.024 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: psaI, AtCg00510 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: P56768
#14: Protein/peptide Photosystem I reaction center subunit IX / / PSI-J


Mass: 5011.897 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: psaJ, AtCg00630 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: P56769
#15: Protein Photosystem I reaction center subunit psaK, chloroplastic / / PSI-K / Photosystem I subunit X


Mass: 13219.431 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAK, At1g30380, T4K22.2 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI5
#16: Protein Photosystem I reaction center subunit XI, chloroplastic / / PSI-L / PSI subunit V


Mass: 23070.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAL, At4g12800, T20K18.150 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI4
#17: Protein Photosystem I subunit O / / PSI-O


Mass: 15156.470 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAO, At1g08380, T27G7 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q949Q5

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Sugars , 1 types, 1 molecules

#30: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 11 types, 262 molecules

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


Mass: 907.472 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 168 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#22: 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.: 6 / Source method: obtained synthetically / Formula: C40H56O4
#23: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#24: 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.: 11 / Source method: obtained synthetically / Formula: C40H56O2
#25: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C40H56
#26: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H86O10
#27: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#29: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#31: 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.: 3 / Source method: obtained synthetically / Formula: C40H56O4

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Details

Has ligand of interestY

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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: photosystem I / Type: COMPLEX / Entity ID: #1-#19 / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.4
SpecimenEmbedding 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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188490 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00546672
ELECTRON MICROSCOPYf_angle_d1.98166656
ELECTRON MICROSCOPYf_dihedral_angle_d17.2258482
ELECTRON MICROSCOPYf_chiral_restr0.055545
ELECTRON MICROSCOPYf_plane_restr0.0046772

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