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- PDB-1nwx: COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURA... -

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Basic information

Entry
Database: PDB / ID: 1nwx
TitleCOMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773
Components
  • (ribosomal protein ...) x 28
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • general stress protein Ctc
KeywordsRIBOSOME / ABT-773 / MACROLIDE / KETOLIDE / 50S / RIBOSOMAL SUBUNIT
Function / homology
Function and homology information


ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding ...ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4
Similarity search - Domain/homology
CETHROMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 ...CETHROMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.5 Å
AuthorsSchluenzen, F. / Harms, J. / Franceschi, F. / Hansen, H.A.S. / Bartels, H. / Zarivach, R. / Yonath, A.
CitationJournal: Structure / Year: 2003
Title: Structural basis for the antibiotic activity of ketolides and azalides.
Authors: Schlunzen, F. / Harms, J.M. / Franceschi, F. / Hansen, H.A. / Bartels, H. / Zarivach, R. / Yonath, A.
History
DepositionFeb 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 23S RIBOSOMAL RNA
9: 5S RIBOSOMAL RNA
A: ribosomal protein L2
B: ribosomal protein L3
C: ribosomal protein L4
D: ribosomal protein L5
E: ribosomal protein L6
F: ribosomal protein L9
G: ribosomal protein L11
H: ribosomal protein L13
I: ribosomal protein L14
J: ribosomal protein L15
K: ribosomal protein L16
L: ribosomal protein L17
M: ribosomal protein L18
N: ribosomal protein L19
O: ribosomal protein L20
P: ribosomal protein L21
Q: ribosomal protein L22
R: ribosomal protein L23
S: ribosomal protein L24
T: general stress protein Ctc
U: ribosomal protein L27
W: ribosomal protein L29
X: ribosomal protein L30
Y: ribosomal protein L31
Z: ribosomal protein L32
1: ribosomal protein L33
2: ribosomal protein L34
3: ribosomal protein L35
4: ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,380,42832
Polymers1,379,66231
Non-polymers7661
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.000, 409.500, 695.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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RNA chain , 2 types, 2 molecules 09

#1: RNA chain 23S RIBOSOMAL RNA /


Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: GenBank: 15805042
#2: RNA chain 5S RIBOSOMAL RNA /


Mass: 39911.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: GenBank: 15805042

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Ribosomal protein ... , 28 types, 28 molecules ABCDEFGHIJKLMNOPQRSUWXYZ1234

#3: Protein ribosomal protein L2 / / Coordinate model: Cα atoms only


Mass: 29976.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ9
#4: Protein ribosomal protein L3 / / Coordinate model: Cα atoms only


Mass: 22477.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXK2
#5: Protein ribosomal protein L4 / 60S ribosomal protein L4 / Coordinate model: Cα atoms only


Mass: 22176.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXK1
#6: Protein ribosomal protein L5 / 60S ribosomal protein L5 / Coordinate model: Cα atoms only


Mass: 20379.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ0
#7: Protein ribosomal protein L6 / / Coordinate model: Cα atoms only


Mass: 19613.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSL3
#8: Protein ribosomal protein L9 / / Coordinate model: Cα atoms only


Mass: 16089.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RY49
#9: Protein ribosomal protein L11 / / Coordinate model: Cα atoms only


Mass: 14889.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSS7
#10: Protein ribosomal protein L13 / 60S ribosomal protein L13 / Coordinate model: Cα atoms only


Mass: 19223.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXY1
#11: Protein ribosomal protein L14 / / Coordinate model: Cα atoms only


Mass: 14256.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ2
#12: Protein ribosomal protein L15 / / Coordinate model: Cα atoms only


Mass: 16894.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSK9
#13: Protein ribosomal protein L16 / / Coordinate model: Cα atoms only


Mass: 16125.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ5
#14: Protein ribosomal protein L17 / / Coordinate model: Cα atoms only


Mass: 12926.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSJ5
#15: Protein ribosomal protein L18 / / Coordinate model: Cα atoms only


Mass: 12032.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSL2
#16: Protein ribosomal protein L19 / / Coordinate model: Cα atoms only


Mass: 18347.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RWB4
#17: Protein ribosomal protein L20 / / Coordinate model: Cα atoms only


Mass: 13991.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSW7
#18: Protein ribosomal protein L21 / / Coordinate model: Cα atoms only


Mass: 11165.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RY64
#19: Protein ribosomal protein L22 / 60S ribosomal protein L22 / Coordinate model: Cα atoms only


Mass: 15190.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ7
#20: Protein ribosomal protein L23 / / Coordinate model: Cα atoms only


Mass: 10408.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXK0
#21: Protein ribosomal protein L24 / / Coordinate model: Cα atoms only


Mass: 12384.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ1
#23: Protein ribosomal protein L27 / / Coordinate model: Cα atoms only


Mass: 9609.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RY65
#24: Protein ribosomal protein L29 / / Coordinate model: Cα atoms only


Mass: 7774.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ4
#25: Protein ribosomal protein L30 / / Coordinate model: Cα atoms only


Mass: 6079.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSL0
#26: Protein ribosomal protein L31 / / Coordinate model: Cα atoms only


Mass: 8597.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RW44
#27: Protein ribosomal protein L32 / / Coordinate model: Cα atoms only


Mass: 6678.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: P49228
#28: Protein ribosomal protein L33 / / Coordinate model: Cα atoms only


Mass: 6374.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSS4
#29: Protein/peptide ribosomal protein L34 / / Coordinate model: Cα atoms only


Mass: 5626.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSH2
#30: Protein ribosomal protein L35 / / Coordinate model: Cα atoms only


Mass: 7316.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSW6
#31: Protein/peptide ribosomal protein L36 / / Coordinate model: Cα atoms only


Mass: 4322.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSK0

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Protein / Non-polymers , 2 types, 2 molecules T

#22: Protein general stress protein Ctc / Coordinate model: Cα atoms only


Mass: 25415.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RX88
#32: Chemical ChemComp-773 / CETHROMYCIN / ABT-773 / Cethromycin


Mass: 765.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H59N3O10 / Comment: antibiotic*YM

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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: 4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.8 / Method: vapor diffusion
Details: Harms, J.M., (2001) Cell (Cambridge,Mass.), 107, 679.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mM1reservoirMgCl2
260 mM1reservoirNH4Cl
35 mM1reservoirKCl
410 mMHEPES1reservoirpH7.8

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 / Wavelength: 1.0332 Å
DetectorType: SBC / Detector: CCD / Date: Nov 14, 2001
RadiationMonochromator: SI111 OR SI311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. all: 269598 / Num. obs: 269598 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.13 / Net I/σ(I): 9
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.36 / % possible all: 88.9
Reflection
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.131
Reflection shell
*PLUS
% possible obs: 88.9 % / Rmerge(I) obs: 0.358

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1LNR

1lnr
PDB Unreleased entry


Resolution: 3.5→15 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: THE STRUCTURE CONTAINS CA COORDINATES ONLY FOR THE PROTEIN CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.313 13371 5 %RANDOM
Rwork0.285 ---
all0.285 264153 --
obs0.285 264153 --
Refinement stepCycle: LAST / Resolution: 3.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 61878 55 0 65355
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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