[English] 日本語
Yorodumi
- PDB-4wb7: Crystal structure of a chimeric fusion of human DnaJ (Hsp40) and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wb7
TitleCrystal structure of a chimeric fusion of human DnaJ (Hsp40) and cAMP-dependent protein kinase A (catalytic alpha subunit)
Components
  • DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha
  • PKI (5-24)
KeywordsTRANSFERASE/TRANSFERASE inhibitor / chaperone / catalysis / protein kinase / adenosine triphosphate / phosphorylation / chimera / fusion / fibrolamellar hepatocellular carinoma / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


cAMP/PKA signal transduction / PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / channel activator activity / sperm head / negative regulation of inclusion body assembly / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process ...cAMP/PKA signal transduction / PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / channel activator activity / sperm head / negative regulation of inclusion body assembly / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / negative regulation of cAMP-dependent protein kinase activity / negative regulation of cAMP/PKA signal transduction / nucleotide-activated protein kinase complex / cell communication by electrical coupling involved in cardiac conduction / high-density lipoprotein particle assembly / Rap1 signalling / positive regulation of ATP-dependent activity / regulation of protein processing / protein localization to lipid droplet / transcription regulator inhibitor activity / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / regulation of osteoblast differentiation / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / cAMP-dependent protein kinase activity / Loss of phosphorylation of MECP2 at T308 / sperm capacitation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / cAMP-dependent protein kinase complex / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / negative regulation of interleukin-2 production / postsynaptic modulation of chemical synaptic transmission / Triglyceride catabolism / protein kinase A regulatory subunit binding / plasma membrane raft / protein kinase A catalytic subunit binding / PKA activation in glucagon signalling / ATPase activator activity / chaperone cofactor-dependent protein refolding / Regulation of MECP2 expression and activity / mesoderm formation / RET signaling / HSF1-dependent transactivation / response to unfolded protein / Interleukin-3, Interleukin-5 and GM-CSF signaling / DARPP-32 events / regulation of cardiac muscle contraction / Regulation of HSF1-mediated heat shock response / regulation of cardiac conduction / sperm flagellum / Attenuation phase / regulation of macroautophagy / renal water homeostasis / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / regulation of proteasomal protein catabolic process / regulation of cellular response to heat / negative regulation of smoothened signaling pathway / Ion homeostasis / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / forebrain development / Recruitment of mitotic centrosome proteins and complexes / positive regulation of gluconeogenesis / sperm midpiece / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / cellular response to glucagon stimulus / regulation of G2/M transition of mitotic cell cycle / protein folding chaperone / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / calcium channel complex / Mitochondrial protein degradation / cellular response to epinephrine stimulus / protein kinase A signaling / protein serine/threonine/tyrosine kinase activity / Hsp70 protein binding / protein export from nucleus / CD209 (DC-SIGN) signaling / positive regulation of calcium-mediated signaling / regulation of heart rate / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / Regulation of insulin secretion / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / neuromuscular junction
Similarity search - Function
: / DnaJ domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor ...: / DnaJ domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Helix Hairpins / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / cAMP-dependent protein kinase catalytic subunit alpha / DnaJ homolog subfamily B member 1 / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
Model detailsexon 1 of DnaJ fused to beginning of exon 2 of cAMP-dependent protein kinase A
AuthorsCheung, J. / Ginter, C. / Cassidy, M. / Franklin, M.C. / Rudolph, M.J. / Hendrickson, W.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural insights into mis-regulation of protein kinase A in human tumors.
Authors: Cheung, J. / Ginter, C. / Cassidy, M. / Franklin, M.C. / Rudolph, M.J. / Robine, N. / Darnell, R.B. / Hendrickson, W.A.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Feb 25, 2015Group: Derived calculations
Revision 1.4Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.5Sep 27, 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 / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha
B: DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha
I: PKI (5-24)
J: PKI (5-24)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,63221
Polymers99,6374
Non-polymers1,99517
Water17,979998
1
A: DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha
I: PKI (5-24)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,91412
Polymers49,8182
Non-polymers1,09610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-195 kcal/mol
Surface area20690 Å2
MethodPISA
2
B: DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha
J: PKI (5-24)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7189
Polymers49,8182
Non-polymers9007
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-138 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.233, 121.155, 173.672
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

-
Components

#1: Protein DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha / DnaJ protein homolog 1 / Heat shock 40 kDa protein 1 / Heat shock protein 40 / Human DnaJ protein 1 ...DnaJ protein homolog 1 / Heat shock 40 kDa protein 1 / Heat shock protein 40 / Human DnaJ protein 1 / hDj-1 / PKA C-alpha


Mass: 47591.945 Da / Num. of mol.: 2
Fragment: UNP P25685 residues 2-70,UNP P17612 residues 16-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJB1, DNAJ1, HDJ1, HSPF1, PRKACA, PKACA / Plasmid: pLATE11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2
References: UniProt: P25685, UniProt: P17612, cAMP-dependent protein kinase
#2: Protein/peptide PKI (5-24)


Mass: 2226.411 Da / Num. of mol.: 2 / Fragment: residues 5-24 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925*PLUS
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 998 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 70mM sodium cacodylate pH 6.5, 150mM magnesium acetate, 20mM zinc chloride, 5% glycerol, 11.5% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 25, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 97666 / % possible obs: 98.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 28.93 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.022 / Net I/av σ(I): 24.882 / Net I/σ(I): 9.7 / Num. measured all: 505754
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.933.30.56242320.83886.5
1.93-1.974.70.63245730.56593.5
1.97-2.014.70.49546890.57695.6
2.01-2.054.70.41647920.58696.6
2.05-2.094.80.32447800.60997.6
2.09-2.144.80.28447970.62497.7
2.14-2.194.90.24448480.65498.4
2.19-2.2550.20448450.67298.8
2.25-2.3250.17749050.72299.3
2.32-2.395.10.14449280.73299.8
2.39-2.485.30.12849420.752100
2.48-2.585.40.11349670.809100
2.58-2.75.50.10249700.855100
2.7-2.845.70.08749370.923100
2.84-3.025.70.0749711.079100
3.02-3.255.80.05849861.257100
3.25-3.585.80.0550191.482100
3.58-4.095.80.04450461.787100
4.09-5.165.70.03951081.842100
5.16-505.50.0453312.08299.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WB8
Resolution: 1.9→41.146 Å / FOM work R set: 0.8892 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 18.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1879 9133 4.98 %RANDOM
Rwork0.1499 174155 --
obs0.1518 183288 96.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.08 Å2 / Biso mean: 40.43 Å2 / Biso min: 13.22 Å2
Refinement stepCycle: final / Resolution: 1.9→41.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7034 0 77 998 8109
Biso mean--25.5 48.77 -
Num. residues----850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127323
X-RAY DIFFRACTIONf_angle_d1.2289896
X-RAY DIFFRACTIONf_chiral_restr0.0631014
X-RAY DIFFRACTIONf_plane_restr0.0061268
X-RAY DIFFRACTIONf_dihedral_angle_d14.9582774
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92030.30382180.3064362458072
1.9203-1.94290.30642860.26175169545587
1.9429-1.96660.27172820.24885363564589
1.9666-1.99150.28242810.23295524580591
1.9915-2.01770.25682580.21995642590092
2.0177-2.04530.23422940.20625592588693
2.0453-2.07460.22272900.1945614590494
2.0746-2.10550.2133000.19145703600394
2.1055-2.13840.23812800.18955743602395
2.1384-2.17350.23983200.18095769608996
2.1735-2.2110.2143390.17115772611196
2.211-2.25120.20243190.16275784610397
2.2512-2.29450.19413190.1675904622397
2.2945-2.34130.20773200.15685866618698
2.3413-2.39220.1743250.14355931625698
2.3922-2.44780.19783330.14485984631799
2.4478-2.5090.19712780.15025967624599
2.509-2.57690.21833060.14976063636999
2.5769-2.65270.18323350.151159826317100
2.6527-2.73830.20983260.156160316357100
2.7383-2.83610.21812930.156360636356100
2.8361-2.94970.18793400.152960146354100
2.9497-3.08390.18852990.146160446343100
3.0839-3.24640.19023150.151460266341100
3.2464-3.44970.19842870.147961196406100
3.4497-3.71590.17283390.139259936332100
3.7159-4.08950.15473040.122660306334100
4.0895-4.68060.15743370.111460316368100
4.6806-5.89430.14973280.124260366364100
5.8943-41.15530.15892820.141160346316100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.87210.1797-0.27710.66160.37022.15950.1923-0.58730.6152-0.0605-0.0395-0.3218-0.51720.7605-0.18560.0567-0.23350.15140.62930.12560.574114.8799-37.5839.7911
20.75440.6732-1.96520.4661-1.75215.9250.1326-0.1219-0.0738-0.1875-0.03690.23570.15550.02130.02730.265-0.03280.05650.22220.05080.250514.0152-39.3143-8.6247
30.7938-0.3228-0.03931.62510.20331.959-0.0007-0.0704-0.0211-0.01660.05790.1110.0964-0.1847-0.01660.04450.0227-0.02230.11480.0370.131116.0255-16.0049-21.622
43.6303-1.6608-1.40692.6610.35392.85020.0680.4730.0679-0.5629-0.04740.0799-0.3065-0.3358-0.01330.2840.0025-0.06220.20220.01960.16516.6457-10.504-41.1009
51.1330.47641.14050.68831.2251.82940.3691-0.4510.24080.2918-0.3715-0.2656-0.0035-0.16550.2950.6735-0.3944-0.22810.4151-0.090.297650.70636.7517-2.6542
60.8462-0.37120.2971.4603-0.73212.1237-0.04510.0237-0.0219-0.0506-0.019-0.0498-0.09280.1450.02880.0989-0.00150.02290.0861-0.01850.120444.598615.1068-26.3143
77.99630.9575-1.43045.2763-1.42910.56320.1806-0.70891.03890.2983-0.1740.3459-1.0931-0.7423-0.0130.44230.19380.01550.3881-0.07430.31937.71723.8334-11.0101
86.4933-1.6691.14557.34920.8686.79770.02880.03680.49010.09290.0862-0.4511-0.73220.44-0.070.15950.01290.01050.0970.03320.184318.6165-1.2279-22.6889
98.2959-2.63742.68433.3168-0.34073.0118-0.1262-0.3601-0.5774-0.0187-0.13750.3450.20260.15520.15480.09210.0459-0.01290.22890.07830.381850.5689-6.1508-15.8775
102.8366-2.2988-2.30326.0795-0.49046.78630.1430.4317-0.5656-0.223-0.09980.89410.1501-0.6917-0.00050.09810.0328-0.0030.1616-0.01260.269338.91132.9886-25.4665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 39 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 86 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 371 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 372 through 405 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 86 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 87 through 405 )B0
7X-RAY DIFFRACTION7chain 'I' and (resid 5 through 11 )I0
8X-RAY DIFFRACTION8chain 'I' and (resid 12 through 24 )I0
9X-RAY DIFFRACTION9chain 'J' and (resid 5 through 13 )J0
10X-RAY DIFFRACTION10chain 'J' and (resid 14 through 24 )J0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more