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- PDB-9rkg: Mixed model refinement of beta-2 Adrenergic receptor with photoaz... -

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Basic information

Entry
Database: PDB / ID: 9rkg
TitleMixed model refinement of beta-2 Adrenergic receptor with photoazolol in dark state and Light state, 10 seconds after light activation, recorded at SwissFEL
ComponentsBeta-2 adrenergic receptor,Endolysin
KeywordsMEMBRANE PROTEIN / GPCR / 7TM / Beta 2 / ADRENERGIC / LIPIDIC CUBIC PHASE / LIPIDIC / PHOTO-SWITCHABLE COMPOUNDS / PHOTOAZOLOL-1 / TIME RESOLVE CRYSTALLOGRAPHY
Function / homology
Function and homology information


beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / AMPA selective glutamate receptor signaling pathway / heat generation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine binding / Adrenoceptors / negative regulation of smooth muscle contraction ...beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / AMPA selective glutamate receptor signaling pathway / heat generation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine binding / Adrenoceptors / negative regulation of smooth muscle contraction / positive regulation of cardiac muscle cell contraction / positive regulation of lipophagy / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / adrenergic receptor signaling pathway / diet induced thermogenesis / response to psychosocial stress / endosome to lysosome transport / positive regulation of cAMP/PKA signal transduction / smooth muscle contraction / negative regulation of cardiac muscle cell apoptotic process / adenylate cyclase binding / potassium channel regulator activity / bone resorption / positive regulation of bone mineralization / viral release from host cell by cytolysis / neuronal dense core vesicle / intercellular bridge / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / peptidoglycan catabolic process / positive regulation of cardiac muscle cell apoptotic process / receptor-mediated endocytosis / brown fat cell differentiation / response to cold / clathrin-coated endocytic vesicle membrane / cellular response to amyloid-beta / cell wall macromolecule catabolic process / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / lysozyme / lysozyme activity / mitotic spindle / Cargo recognition for clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / Clathrin-mediated endocytosis / microtubule cytoskeleton / transcription by RNA polymerase II / G alpha (s) signalling events / host cell cytoplasm / early endosome / positive regulation of MAPK cascade / cell surface receptor signaling pathway / lysosome / signaling receptor complex / defense response to bacterium / endosome / endosome membrane / apical plasma membrane / Ub-specific processing proteases / cilium / ciliary basal body / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme-like domain superfamily ...Beta 2 adrenoceptor / Adrenoceptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme-like domain superfamily / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
: / ACETAMIDE / CHOLESTEROL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PALMITIC ACID / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Tequatrovirus T4
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsBertrand, Q. / Stipp, R. / Glover, H. / Stierli, F. / Siedel, H.P. / Mous, S. / Kepa, M. / Weinert, T. / Standfuss, J.
Funding supportEuropean Union, Switzerland, 4items
OrganizationGrant numberCountry
Innosuisse42711.1 IP-LSEuropean Union
Swiss National Science Foundation310030_207462 Switzerland
Swiss National Science Foundation310030_197674 Switzerland
Swiss National Science FoundationCRSII5_213507 Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2026
Title: Structural Mechanism of an Efficacy Photoswitch Targeting the beta 2 -adrenergic Receptor.
Authors: Stipp, R. / Bertrand, Q. / Trabuco, M. / Duran-Corbera, A. / Ignazzitto, M.T. / Glover, H. / Stierli, F. / Catena, J. / Carrillo, M. / Hartmann, S. / Seidel, H.P. / Mulder, M. / Mason, T. / ...Authors: Stipp, R. / Bertrand, Q. / Trabuco, M. / Duran-Corbera, A. / Ignazzitto, M.T. / Glover, H. / Stierli, F. / Catena, J. / Carrillo, M. / Hartmann, S. / Seidel, H.P. / Mulder, M. / Mason, T. / Kondo, Y. / Wranik, M. / Appleby, M. / Sager, C. / Sierra, R. / Gate, G. / Schleissner, P. / Cheng, X. / Weinert, T. / Cheng, R. / Mous, S. / Beale, J.H. / Kepa, M. / Llebaria, A. / Hennig, M. / Rovira, X. / Standfuss, J.
History
DepositionJun 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.1May 6, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-2 adrenergic receptor,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,31827
Polymers50,5421
Non-polymers6,77626
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-82 kcal/mol
Surface area23830 Å2
Unit cell
Length a, b, c (Å)111.940, 172.230, 41.230
Angle α, β, γ (deg.)90.00, 106.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-2 adrenergic receptor,Endolysin / Beta-2 adrenoreceptor / Beta-2 adrenoceptor / Lysis protein / Lysozyme / Muramidase


Mass: 50542.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCE FWTSIDVLCVTASIWTLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAE ...Details: ADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCE FWTSIDVLCVTASIWTLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAE ETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPS LNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSL RMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQ DNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL(PZL),ADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCE FWTSIDVLCVTASIWTLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAE ETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPS LNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSL RMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQ DNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL(PZL),ADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCE FWTSIDVLCVTASIWTLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAE ETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPS LNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSL RMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQ DNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL(PZL),ADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCE FWTSIDVLCVTASIWTLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAE ETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPS LNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSL RMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQ DNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL(PZL),ADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCE FWTSIDVLCVTASIWTLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAE ETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPS LNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSL RMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQ DNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL(PZL),ADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCE FWTSIDVLCVTASIWTLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAE ETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPS LNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSL RMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQ DNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL(PZL),ADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCE FWTSIDVLCVTASIWTLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAE ETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPS LNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSL RMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQ DNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL(PZL),ADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCE FWTSIDVLCVTASIWTLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAE ETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPS LNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSL RMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQ DNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL(PZL),ADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCE FWTSIDVLCVTASIWTLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAE ETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPS LNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSL RMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQ DNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL(PZL)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Tequatrovirus T4
Gene: ADRB2, ADRB2R, B2AR / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P07550, UniProt: P00720, lysozyme

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Non-polymers , 11 types, 30 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACM / ACETAMIDE


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO
#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#6: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#7: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-A1JHU / ~{N}-[4-[(~{E})-[2-[(2~{S})-2-oxidanyl-3-(propan-2-ylamino)propoxy]phenyl]diazenyl]phenyl]ethanamide


Mass: 370.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N4O3 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.78 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 289 K / Method: lipidic cubic phase
Details: 100 mM tri-sodium citrate (pH= 6.2), 245 mM Li2SO4, 32% PEG 350 MME, 10 uM photoazolol-1

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESC / Wavelength: 1.0294 Å
DetectorType: PSI JUNGFRAU 8M / Detector: PIXEL / Date: Feb 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0294 Å / Relative weight: 1
ReflectionResolution: 2.45→53.75 Å / Num. obs: 27481 / % possible obs: 100 % / Redundancy: 467 % / CC star: 0.998 / R split: 0.08 / Net I/σ(I): 8.27
Reflection shellResolution: 2.45→2.54 Å / Mean I/σ(I) obs: 0.74 / Num. unique obs: 2741 / CC star: 0.669 / R split: 1.42

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Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
PHENIX(1.20_4459)refinement
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→53.75 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2169 --
Rwork0.1831 --
obs-27481 100 %
Refinement stepCycle: LAST / Resolution: 2.45→53.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 364 4 3924

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