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- PDB-4wb7: Crystal structure of a chimeric fusion of human DnaJ (Hsp40) and ... -

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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


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / channel activator activity / sperm head / HDL assembly / negative regulation of inclusion body assembly / negative regulation of cAMP-dependent protein kinase activity / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / channel activator activity / sperm head / HDL assembly / negative regulation of inclusion body assembly / negative regulation of cAMP-dependent protein kinase activity / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / 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 / intracellular potassium ion homeostasis / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / Loss of phosphorylation of MECP2 at T308 / cAMP-dependent protein kinase activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / protein localization to lipid droplet / PKA activation / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of interleukin-2 production / negative regulation of protein import into nucleus / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / Triglyceride catabolism / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / ATPase activator activity / : / mesoderm formation / cAMP/PKA signal transduction / RET signaling / Regulation of MECP2 expression and activity / sperm flagellum / Interleukin-3, Interleukin-5 and GM-CSF signaling / PKA activation in glucagon signalling / plasma membrane raft / DARPP-32 events / regulation of cardiac conduction / Regulation of HSF1-mediated heat shock response / HSF1-dependent transactivation / response to unfolded protein / regulation of macroautophagy / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / postsynaptic modulation of chemical synaptic transmission / Attenuation phase / vascular endothelial cell response to laminar fluid shear stress / transcription regulator inhibitor activity / renal water homeostasis / Hedgehog 'off' state / regulation of cellular response to heat / forebrain development / positive regulation of phagocytosis / Ion homeostasis / regulation of G2/M transition of mitotic cell cycle / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / cellular response to epinephrine stimulus / sperm midpiece / calcium channel complex / Mitochondrial protein degradation / positive regulation of gluconeogenesis / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / CD209 (DC-SIGN) signaling / Hsp70 protein binding / protein serine/threonine/tyrosine kinase activity / protein folding chaperone / cellular response to glucagon stimulus / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / FCGR3A-mediated IL10 synthesis / positive regulation of calcium-mediated signaling / regulation of heart rate / protein export from nucleus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / acrosomal vesicle / AURKA Activation by TPX2 / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / Regulation of insulin secretion / neural tube closure / Degradation of GLI1 by the proteasome / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Degradation of GLI2 by the proteasome
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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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
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: 3.13 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

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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

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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

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)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

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  • 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

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