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- PDB-4boh: Madanins (MEROPS I53) are cleaved by thrombin and factor Xa -

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Basic information

Entry
Database: PDB / ID: 4boh
TitleMadanins (MEROPS I53) are cleaved by thrombin and factor Xa
Components
  • THROMBIN HEAVY CHAIN
  • THROMBIN INHIBITOR MADANIN 1
  • THROMBIN LIGHT CHAIN
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / COAGULATION INHIBITOR / PROTEASE / MACROMOLECULAR RECOGNITION
Function / homology
Function and homology information


molecular function inhibitor activity / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway ...molecular function inhibitor activity / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thrombin inhibitor Madanin / Thrombin inhibitor Madanin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily ...Thrombin inhibitor Madanin / Thrombin inhibitor Madanin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Prothrombin / Thrombin inhibitor madanin 1
Similarity search - Component
Biological speciesHAEMAPHYSALIS LONGICORNIS (longhorned tick)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.595 Å
AuthorsFigueiredo, A.C. / deSanctis, D. / Pereira, P.J.B.
CitationJournal: Plos One / Year: 2013
Title: The Tick-Derived Anticoagulant Madanin is Processed by Thrombin and Factor Xa.
Authors: Figueiredo, A.C. / De Sanctis, D. / Pereira, P.J.
History
DepositionMay 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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 "HB" 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THROMBIN HEAVY CHAIN
B: THROMBIN LIGHT CHAIN
H: THROMBIN HEAVY CHAIN
L: THROMBIN LIGHT CHAIN
M: THROMBIN INHIBITOR MADANIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,50314
Polymers74,5355
Non-polymers9699
Water1,65792
1
H: THROMBIN HEAVY CHAIN
L: THROMBIN LIGHT CHAIN
M: THROMBIN INHIBITOR MADANIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0947
Polymers40,6583
Non-polymers4364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-39.6 kcal/mol
Surface area13020 Å2
MethodPISA
2
A: THROMBIN HEAVY CHAIN
B: THROMBIN LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4097
Polymers33,8772
Non-polymers5325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-54 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.071, 78.578, 155.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.327063, 0.611687, -0.720326), (0.640479, -0.41699, -0.644908), (-0.69485, -0.672279, -0.25539)28.6372, 13.0298, 89.3278
2given(-0.326757, 0.645208, -0.690606), (0.610181, -0.413999, -0.675488), (-0.72174, -0.642115, -0.258417)62.8492, 48.1413, 51.9672

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Components

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Protein , 2 types, 3 molecules AHM

#1: Protein THROMBIN HEAVY CHAIN / / ALPHA-THROMBIN / COAGULATION FACTOR II /


Mass: 29780.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: PLASMA / References: UniProt: P00734, thrombin
#3: Protein THROMBIN INHIBITOR MADANIN 1 / MADANIN-1


Mass: 6781.231 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-79
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAEMAPHYSALIS LONGICORNIS (longhorned tick)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / References: UniProt: Q86FP9

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Protein/peptide / Sugars , 2 types, 4 molecules BL

#2: Protein/peptide THROMBIN LIGHT CHAIN / / ALPHA-THROMBIN / COAGULATION FACTOR II


Mass: 4096.534 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: PLASMA / References: UniProt: P00734, thrombin
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 99 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.18 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1M TRIS-HCL PH 8.5, 0.2M LITHIUM SULFATE, 25% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→44 Å / Num. obs: 20364 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 46.73 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / % possible all: 86.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U69

3u69


Resolution: 2.595→43.98 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 26.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2386 1035 5.1 %
Rwork0.1908 --
obs0.1932 20308 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54 Å2
Refinement stepCycle: LAST / Resolution: 2.595→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4618 0 55 92 4765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044798
X-RAY DIFFRACTIONf_angle_d0.8556480
X-RAY DIFFRACTIONf_dihedral_angle_d15.0931802
X-RAY DIFFRACTIONf_chiral_restr0.034670
X-RAY DIFFRACTIONf_plane_restr0.004824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.595-2.73180.36511320.2842367X-RAY DIFFRACTION86
2.7318-2.90290.36081460.27892694X-RAY DIFFRACTION98
2.9029-3.1270.34011570.28442789X-RAY DIFFRACTION100
3.127-3.44160.29141570.2282762X-RAY DIFFRACTION100
3.4416-3.93930.24441590.18312806X-RAY DIFFRACTION100
3.9393-4.9620.15771470.13542852X-RAY DIFFRACTION100
4.962-43.98610.17921370.1593003X-RAY DIFFRACTION100
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)
13.3268-3.66060.96566.48651.31062.8547-0.1982-0.468-0.29670.62640.35931.18130.9958-1.4634-0.2070.7242-0.2470.24920.90540.00860.862515.03626.01245.4603
20.67150.18160.43238.0616-4.2752.70910.4024-0.0104-0.08090.5014-0.15180.0252-0.0795-0.4535-0.2140.508-0.0834-0.05180.2769-0.03220.343824.3571-3.017345.8166
36.09763.3875-6.41682.1901-3.86637.3409-0.1925-0.0947-0.74150.6186-0.0061-0.48520.97810.92480.26640.60050.0866-0.08380.3979-0.0010.390332.4746-8.031144.4661
42.50740.17461.7321.723.48047.82030.37020.3361-1.49880.26090.9271-1.75250.26531.2433-0.88880.35340.0696-0.0670.4746-0.15350.708540.77981.434740.1922
55.2589-0.64821.59154.02380.14533.55050.20680.4083-0.1951-0.2842-0.20110.25450.3907-0.0429-0.01860.30680.0320.04210.248-0.05780.239416.6036-1.091825.1193
64.07080.40450.26112.35760.55514.84950.15550.044-0.0975-0.1602-0.05130.1361-0.0092-0.3199-0.09310.30840.02920.03960.2122-0.03220.269819.14752.946731.149
73.883-0.22320.18422.3090.96464.17860.13890.63260.0763-0.40530.2344-0.4002-0.31930.747-0.32860.3257-0.00410.05880.4259-0.04820.328732.50333.592724.4143
84.4428-0.80890.93112.1825-1.53558.56140.2758-0.2590.21340.1801-0.31050.4211-1.0086-0.5053-0.00770.60430.11070.04290.2781-0.04510.464315.181215.624134.2028
94.4407-4.1491-5.17824.763.59037.8081-0.1007-0.7748-1.13880.5108-0.07740.3710.6265-0.43430.08030.3741-0.1439-0.0090.67270.05330.5244-12.9307-0.143162.9273
108.99825.1456-0.3669.23921.11518.1466-0.94180.62520.4167-0.21730.37651.47250.3437-1.08570.46760.42980.03330.07870.7510.02190.4428-18.45796.409860.9817
112.7667-1.5013-3.9452.92024.33877.92830.087-0.09040.4478-0.6826-0.42060.5019-1.0331-2.00260.26540.39130.1549-0.04830.5415-0.0520.3653-12.775912.617949.7559
122.5903-0.0622-0.25525.5241-0.27735.43970.2901-0.6753-0.11670.3886-0.2571-0.2443-0.08730.0469-0.05810.3891-0.04950.050.70550.08810.2899-1.40910.10971.6447
132.1191-1.85440.73983.3521-0.09476.7495-0.0299-0.8681-0.34890.2157-0.3485-0.71520.12551.61770.17840.48430.1312-0.04541.01650.18560.483310.5175.386972.6084
143.7539-1.06770.1282.80550.59964.4990.0512-0.7980.03260.48060.0501-0.36950.36180.80260.02710.46780.1401-0.02970.83590.07070.42866.05745.555870.8303
151.95210.4467-0.62953.0001-0.95794.3358-0.0282-0.4904-0.49820.15250.12290.0540.5246-0.0279-0.06060.36570.01260.05660.53650.12160.3726-2.81541.924561.0178
166.1672-0.1418-1.78845.1562.32089.29360.1986-0.71590.4140.2978-0.06430.08-0.7272-0.451-0.11560.28680.0948-0.01980.35410.02340.3262-2.653719.077764.7009
171.7473-0.70691.1088.0101-0.98878.76640.0690.05490.2531-0.51910.3584-0.7772-0.35990.9936-0.45280.3851-0.07070.14130.62810.01440.404713.08716.954349.714
187.5439-3.76141.43058.3894-2.9536.50970.0147-0.28150.59810.2505-0.1564-0.5459-0.87040.28940.1470.2497-0.05110.01860.3466-0.06060.28921.093520.357157.0361
192.5551.00080.2064.42491.25714.3760.1487-0.137-0.0520.0253-0.1896-0.2316-0.09760.11020.07540.27740.05580.03640.45990.00270.28440.488711.517656.5693
206.8103-0.16664.57413.3018-0.60046.50390.70680.4901-0.61350.1662-0.3857-0.01021.63351.2081-0.22070.7250.31190.0660.6961-0.06320.64959.1808-5.37858.7043
216.0308-1.0323-2.65340.25190.5761.36530.4650.262-0.2356-0.0158-0.26270.1934-0.681-0.3115-0.10281.0526-0.19170.11790.6184-0.24410.689127.02395.208814.5396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN L AND (RESID 287 THROUGH 291 )
2X-RAY DIFFRACTION2CHAIN L AND (RESID 292 THROUGH 301 )
3X-RAY DIFFRACTION3CHAIN L AND (RESID 302 THROUGH 308 )
4X-RAY DIFFRACTION4CHAIN L AND (RESID 309 THROUGH 318 )
5X-RAY DIFFRACTION5CHAIN H AND (RESID 321 THROUGH 383 )
6X-RAY DIFFRACTION6CHAIN H AND (RESID 384 THROUGH 460 )
7X-RAY DIFFRACTION7CHAIN H AND (RESID 461 THROUGH 563 )
8X-RAY DIFFRACTION8CHAIN H AND (RESID 564 THROUGH 579 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 291 THROUGH 299 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 300 THROUGH 308 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 309 THROUGH 318 )
12X-RAY DIFFRACTION12CHAIN A AND (RESID 321 THROUGH 354 )
13X-RAY DIFFRACTION13CHAIN A AND (RESID 355 THROUGH 383 )
14X-RAY DIFFRACTION14CHAIN A AND (RESID 384 THROUGH 420 )
15X-RAY DIFFRACTION15CHAIN A AND (RESID 421 THROUGH 460 )
16X-RAY DIFFRACTION16CHAIN A AND (RESID 461 THROUGH 489 )
17X-RAY DIFFRACTION17CHAIN A AND (RESID 490 THROUGH 504 )
18X-RAY DIFFRACTION18CHAIN A AND (RESID 505 THROUGH 527 )
19X-RAY DIFFRACTION19CHAIN A AND (RESID 528 THROUGH 563 )
20X-RAY DIFFRACTION20CHAIN A AND (RESID 564 THROUGH 577 )
21X-RAY DIFFRACTION21CHAIN M AND (RESID 51 THROUGH 54 )

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  • 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

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