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- PDB-2waq: The complete structure of the archaeal 13-subunit DNA-directed RN... -

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Entry
Database: PDB / ID: 2waq
TitleThe complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase
Components(DNA-DIRECTED RNA POLYMERASE ...) x 13
KeywordsTRANSCRIPTION / MULTI-SUBUNIT / RNA POLYMERASE
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : ...3 iron, 4 sulfur cluster binding / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / protein dimerization activity / nucleotide binding / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
DNA Excision Repair, Uvrb; Chain A - #10 / DNA Excision Repair, Uvrb; Chain A / Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G ...DNA Excision Repair, Uvrb; Chain A - #10 / DNA Excision Repair, Uvrb; Chain A / Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / DNA polymerase; domain 1 - #390 / DNA-directed RNA polymerase subunit Rpo4 / Dihydrolipoamide Transferase / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / HRDC domain / RNA polymerase ii / N-terminal domain of TfIIb / RNA polymerase Rpb7-like, N-terminal domain / HRDC domain superfamily / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / Alpha-Beta Plaits - #20 / Barwin-like endoglucanases - #20 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / Other non-globular / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Rubrerythrin, domain 2 / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Gyrase A; domain 2 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Homeodomain-like / HRDC-like superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / : / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Single Sheet / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Helix non-globular / Beta Complex / DNA-directed RNA polymerase, subunit beta-prime / Special / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4
Similarity search - Domain/homology
FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo10
Similarity search - Component
Biological speciesSULFOLOBUS SHIBATAE (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsKorkhin, Y. / Unligil, U.M. / Littlefield, O. / Nelson, P.J. / Stuart, D.I. / Sigler, P.B. / Bell, S.D. / Abrescia, N.G.A.
CitationJournal: Plos Biol. / Year: 2009
Title: Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure.
Authors: Korkhin, Y. / Unligil, U.M. / Littlefield, O. / Nelson, P.J. / Stuart, D.I. / Sigler, P.B. / Bell, S.D. / Abrescia, N.G.
History
DepositionFeb 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / citation_author / exptl_crystal_grow
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method
Revision 1.4Aug 28, 2019Group: Data collection / Database references / Category: citation / reflns / Item: _citation.journal_abbrev / _reflns.pdbx_Rmerge_I_obs
Revision 1.5Apr 28, 2021Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / reflns / struct_conn / struct_site
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _reflns.pdbx_redundancy / _struct_conn.pdbx_dist_value / _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 1.6Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BJ" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE RPO1N SUBUNIT
B: DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT
C: DNA-DIRECTED RNA POLYMERASE RPO1C SUBUNIT
D: DNA-DIRECTED RNA POLYMERASE RPO3 SUBUNIT
E: DNA-DIRECTED RNA POLYMERASE RPO7 SUBUNIT
F: DNA-DIRECTED RNA POLYMERASE RPO4 SUBUNIT
G: DNA-DIRECTED RNA POLYMERASE RPO8 SUBUNIT
H: DNA-DIRECTED RNA POLYMERASE RPO5 SUBUNIT
K: DNA-DIRECTED RNA POLYMERASE RPO6 SUBUNIT
L: DNA-DIRECTED RNA POLYMERASE RPO11 SUBUNIT
N: DNA-DIRECTED RNA POLYMERASE RPO10 SUBUNIT
P: DNA-DIRECTED RNA POLYMERASE RPO12 SUBUNIT
Q: DNA-DIRECTED RNA POLYMERASE RPO13 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,59524
Polymers405,68713
Non-polymers90911
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area71970 Å2
ΔGint-446.1 kcal/mol
Surface area172810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)193.501, 212.620, 128.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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DNA-DIRECTED RNA POLYMERASE ... , 13 types, 13 molecules ABCDEFGHKLNPQ

#1: Protein DNA-DIRECTED RNA POLYMERASE RPO1N SUBUNIT


Mass: 99766.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB53*PLUS
#2: Protein DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT


Mass: 127582.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB55*PLUS
#3: Protein DNA-DIRECTED RNA POLYMERASE RPO1C SUBUNIT


Mass: 43779.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea)
#4: Protein DNA-DIRECTED RNA POLYMERASE RPO3 SUBUNIT


Mass: 30179.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB56*PLUS
#5: Protein DNA-DIRECTED RNA POLYMERASE RPO7 SUBUNIT


Mass: 20324.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea)
#6: Protein DNA-DIRECTED RNA POLYMERASE RPO4 SUBUNIT


Mass: 12822.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB58*PLUS
#7: Protein DNA-DIRECTED RNA POLYMERASE RPO8 SUBUNIT


Mass: 15139.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB59*PLUS
#8: Protein DNA-DIRECTED RNA POLYMERASE RPO5 SUBUNIT


Mass: 9688.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB60*PLUS
#9: Protein DNA-DIRECTED RNA POLYMERASE RPO6 SUBUNIT


Mass: 10799.589 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea)
#10: Protein DNA-DIRECTED RNA POLYMERASE RPO11 SUBUNIT


Mass: 10211.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB62*PLUS
#11: Protein DNA-DIRECTED RNA POLYMERASE RPO10 SUBUNIT


Mass: 7617.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB63*PLUS
#12: Protein/peptide DNA-DIRECTED RNA POLYMERASE RPO12 SUBUNIT


Mass: 5606.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea)
#13: Protein DNA-DIRECTED RNA POLYMERASE RPO13 SUBUNIT


Mass: 12168.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea)

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Non-polymers , 3 types, 11 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4

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Details

Has protein modificationY

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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: 3.6 Å3/Da / Density % sol: 66 %
Description: THE STATISTICS FOR THIS DATA ARE DERIVED FROM MERGED IOBS AND SIGMAIOBS PRESENT IN THE ONLY MTZ AVAILABLE. RAW IMAGES COLLECTED IN 2001-2002 AND PROCESSING LOG-FILES HAVE BEEN LOST.
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 7MG/ML ENZYME, 150MM KCL, 100MM SRCL2, 1MM ZNCL2, 100MM CACODYLATE PH 6.5, 12% PEG MME 5K, 5% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.35→42.8 Å / Num. obs: 59401 / % possible obs: 77 % / Observed criterion σ(I): -3 / Net I/σ(I): 8.5
Reflection shellHighest resolution: 3.35 Å / Mean I/σ(I) obs: 1.7 / % possible all: 44.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALEPACKdata scaling
GLRFphasing
MOLREPphasing
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EN0

1en0
PDB Unreleased entry


Resolution: 3.35→42.78 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.769 / SU B: 87.522 / SU ML: 0.652 / Cross valid method: THROUGHOUT / ESU R Free: 0.869 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE REFINEMENT HAS ALSO BEEN CARRIED OUT USING NORMAL-MODE TO ANISOTROPICALLY REFINE THE OVERALL THERMAL MOTIONS. PLEASE SEE ARTICLE FOR MORE DETAILS.
RfactorNum. reflection% reflectionSelection details
Rfree0.341 3012 5.1 %RANDOM
Rwork0.271 ---
obs0.274 56389 77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 88.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2---0.9 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 3.35→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26454 0 17 0 26471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02226946
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0271.98236436
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.88153313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2523.7431189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.898155003
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.90415220
X-RAY DIFFRACTIONr_chiral_restr0.0660.24160
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0219918
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1790.212722
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.218153
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2656
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0050.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.35→3.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.342 129
Rwork0.306 2580

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