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- PDB-4kt0: Crystal structure of a virus like photosystem I from the cyanobac... -

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Basic information

Entry
Database: PDB / ID: 4kt0
TitleCrystal structure of a virus like photosystem I from the cyanobacterium Synechocystis PCC 6803
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 4
  • (Photosystem I subunit ...) x 2
  • Photosystem I iron-sulfur center
KeywordsELECTRON TRANSPORT / photosynthetic reaction center / membrane complex / plastocyanin / cytochrome C6 / Ferredoxin
Function / homology
Function and homology information


plasma membrane-derived photosystem I / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding ...plasma membrane-derived photosystem I / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / magnesium ion binding / metal ion binding
Similarity search - Function
Alpha-t-alpha / Photosystem I PsaK, reaction centre / Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Single helix bin / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK ...Alpha-t-alpha / Photosystem I PsaK, reaction centre / Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Single helix bin / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / SH3 type barrels. - #50 / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 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 / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Alpha-Beta Plaits - #20 / 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 dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Helicase, Ruva Protein; domain 3 / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit XII / Photosystem I subunit II / Photosystem I reaction center subunit ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit XII / Photosystem I subunit II / Photosystem I reaction center subunit / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I subunit III / Photosystem I subunit X / Photosystem I reaction center subunit IV / Photosystem I subunit VII / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit PsaK 2 / Photosystem I reaction center subunit IX
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMazor, Y. / Nataf, D. / Toporik, H. / Nelson, N.
CitationJournal: Elife / Year: 2014
Title: Crystal structures of virus-like photosystem I complexes from the mesophilic cyanobacterium Synechocystis PCC 6803.
Authors: Mazor, Y. / Nataf, D. / Toporik, H. / Nelson, N.
History
DepositionMay 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 2.0Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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 subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I subunit III
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
M: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,998131
Polymers236,9789
Non-polymers98,020122
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.179, 173.308, 179.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHOR STATED THAT THERE IS NO QUATERNARY STRUCTURE FOR THIS ENTRY. PISA FAILED TO GENERATE ASSEMBLY. THEREFORE THE ASU IS INDICATED AS ASSEMBLY TEMPORARILY.

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / / PsaA


Mass: 83036.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 10HIS tag was added to the C terminus of PsaL. The mutated chain is lost during purification.
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: Synechocystis sp. PCC 6803 / Gene: BEST7613_2234, MYO_18690, psaA
References: UniProt: L8AHT3, UniProt: P29254*PLUS, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PsaB


Mass: 81369.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaB, BEST7613_2235, MYO_18700 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8AIC0, UniProt: P29255*PLUS, photosystem I

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Photosystem I subunit ... , 2 types, 2 molecules DF

#4: Protein Photosystem I subunit II /


Mass: 15663.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaD, BEST7613_1459, MYO_11100 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8AFM8, UniProt: P19569*PLUS, photosystem I
#6: Protein Photosystem I subunit III /


Mass: 18267.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaF, BEST7613_2928 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8AII8, UniProt: P29256*PLUS, photosystem I

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Photosystem I reaction center subunit ... , 4 types, 4 molecules EJKM

#5: Protein Photosystem I reaction center subunit IV /


Mass: 8154.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaE, BEST7613_5968, MYO_118260 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8ASH8, UniProt: P12975*PLUS, photosystem I
#7: Protein/peptide Photosystem I reaction center subunit IX /


Mass: 4535.415 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaJ, BEST7613_2927, MYO_115450 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8AGL9, UniProt: Q55329*PLUS, photosystem I
#8: Protein Photosystem I reaction center subunit PsaK / / Photosystem I subunit X


Mass: 13732.274 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaK, BEST7613_4536, MYO_129960 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8APJ0, UniProt: P74564*PLUS, photosystem I
#9: Protein/peptide Photosystem I reaction center subunit XII / / PSI-M


Mass: 3382.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psbM, psaM, BEST7613_1787, MYO_14340 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8ADF9, UniProt: P72986*PLUS, photosystem I

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Protein / Sugars , 2 types, 3 molecules C

#16: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8837.261 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaC, BEST7613_5694, MYO_120930 / Production host: Synechocystis sp. PCC 6803 (bacteria)
References: UniProt: L8AST2, UniProt: P32422*PLUS, photosystem I

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Non-polymers , 9 types, 149 molecules

#10: 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
#11: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#12: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C40H56
#15: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 90 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#17: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10
#18: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#19: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.75 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 4.5% PEG3350, 30mM Tricine-NaOH pH8, 55mM NaCl, 50mM Glycine, 0.005% Nonyl- beta -D-Maltoside., pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 92450 / Num. obs: 91895 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 61.4 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 2.382 / Mean I/σ(I) obs: 1.1

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Processing

Software
NameClassification
XDSdata scaling
MOLREPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JB0 with truncated side chains and chlorophyll tails
Resolution: 2.8→29.977 Å / SU ML: 0.4 / Isotropic thermal model: single parameter per residue. / σ(F): 1.35 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 4558 5 %
Rwork0.1977 --
obs0.2 91218 98.61 %
all-92518 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.61 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15758 0 6264 29 22051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423288
X-RAY DIFFRACTIONf_angle_d1.73433063
X-RAY DIFFRACTIONf_dihedral_angle_d28.2499045
X-RAY DIFFRACTIONf_chiral_restr0.0462902
X-RAY DIFFRACTIONf_plane_restr0.0123907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83180.38171400.35042428X-RAY DIFFRACTION85
2.8318-2.86510.35951490.32962743X-RAY DIFFRACTION95
2.8651-2.90.35061560.31332826X-RAY DIFFRACTION98
2.9-2.93670.34541460.30722912X-RAY DIFFRACTION99
2.9367-2.97530.38311430.29312842X-RAY DIFFRACTION99
2.9753-3.0160.3661560.28942894X-RAY DIFFRACTION99
3.016-3.05910.35521450.27412881X-RAY DIFFRACTION100
3.0591-3.10470.34281530.26992888X-RAY DIFFRACTION100
3.1047-3.15310.36171560.27062896X-RAY DIFFRACTION100
3.1531-3.20480.32021560.2572895X-RAY DIFFRACTION100
3.2048-3.260.30711610.23852888X-RAY DIFFRACTION100
3.26-3.31920.27591440.2382907X-RAY DIFFRACTION100
3.3192-3.38290.29411530.23412871X-RAY DIFFRACTION100
3.3829-3.45190.30451450.22922862X-RAY DIFFRACTION98
3.4519-3.52680.28431600.21352877X-RAY DIFFRACTION99
3.5268-3.60870.27211670.19942883X-RAY DIFFRACTION100
3.6087-3.69880.24161760.19112851X-RAY DIFFRACTION100
3.6988-3.79860.27971460.18312933X-RAY DIFFRACTION100
3.7986-3.91020.20651620.17942901X-RAY DIFFRACTION100
3.9102-4.03610.20411390.16562918X-RAY DIFFRACTION99
4.0361-4.180.19131450.16012906X-RAY DIFFRACTION100
4.18-4.34690.2041570.16252941X-RAY DIFFRACTION100
4.3469-4.54410.20981530.16112898X-RAY DIFFRACTION99
4.5441-4.78270.20451610.15672914X-RAY DIFFRACTION99
4.7827-5.0810.20421300.15932969X-RAY DIFFRACTION100
5.081-5.47120.23131370.16532961X-RAY DIFFRACTION100
5.4712-6.01770.22941590.18182985X-RAY DIFFRACTION100
6.0177-6.87930.21571350.18312929X-RAY DIFFRACTION98
6.8793-8.63280.22161840.17582977X-RAY DIFFRACTION99
8.6328-29.97880.21911440.22213084X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -9.005 Å / Origin y: -7.8261 Å / Origin z: 21.7491 Å
111213212223313233
T0.6394 Å20.1236 Å2-0.1111 Å2-0.5398 Å2-0.0396 Å2--0.6407 Å2
L1.0077 °20.0284 °20.0181 °2-0.6814 °20.1622 °2--1.5999 °2
S0.0244 Å °-0.0161 Å °-0.0826 Å °0.1128 Å °0.0938 Å °-0.1135 Å °0.2188 Å °0.2096 Å °0.0099 Å °
Refinement TLS groupSelection details: chain A or chain B or chain C or chain D or chain E or chain F or chain J or chain K or chain M

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