[English] 日本語
Yorodumi
- PDB-9bla: KIR3DL1*086 in complex with HLA-A*24:02 presenting the NEF peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bla
TitleKIR3DL1*086 in complex with HLA-A*24:02 presenting the NEF peptide
Components
  • Beta-2-microglobulin
  • C-terminal core peptide
  • Killer cell immunoglobulin-like receptor 3DL1
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / immunoglobulin fold / natural killer cell receptor / Kir
Function / homology
Function and homology information


: / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...: / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / Immunoglobulin / Immunoglobulin domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein ...: / Immunoglobulin / Immunoglobulin domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / KIR3DL1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFaoro, C. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2008981 Australia
CitationJournal: Cell / Year: 2024
Title: An archaic HLA class I receptor allele diversifies natural killer cell-driven immunity in First Nations peoples of Oceania.
Authors: Loh, L. / Saunders, P.M. / Faoro, C. / Font-Porterias, N. / Nemat-Gorgani, N. / Harrison, G.F. / Sadeeq, S. / Hensen, L. / Wong, S.C. / Widjaja, J. / Clemens, E.B. / Zhu, S. / Kichula, K.M. ...Authors: Loh, L. / Saunders, P.M. / Faoro, C. / Font-Porterias, N. / Nemat-Gorgani, N. / Harrison, G.F. / Sadeeq, S. / Hensen, L. / Wong, S.C. / Widjaja, J. / Clemens, E.B. / Zhu, S. / Kichula, K.M. / Tao, S. / Zhu, F. / Montero-Martin, G. / Fernandez-Vina, M. / Guethlein, L.A. / Vivian, J.P. / Davies, J. / Mentzer, A.J. / Oppenheimer, S.J. / Pomat, W. / Ioannidis, A.G. / Barberena-Jonas, C. / Moreno-Estrada, A. / Miller, A. / Parham, P. / Rossjohn, J. / Tong, S.Y.C. / Kedzierska, K. / Brooks, A.G. / Norman, P.J.
History
DepositionApr 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: C-terminal core peptide
G: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0246
Polymers78,5824
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.682, 61.790, 67.473
Angle α, β, γ (deg.)93.726, 100.679, 108.337
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein MHC class I antigen


Mass: 31778.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Details (production host): pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A411J078
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Details (production host): pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide C-terminal core peptide


Mass: 1040.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Protein Killer cell immunoglobulin-like receptor 3DL1


Mass: 33884.242 Da / Num. of mol.: 1 / Fragment: residues 1-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR3DL1 / Production host: Homo sapiens (human) / References: UniProt: I6LEK9
#5: 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


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
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 14% PEG 3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 3→46.96 Å / Num. obs: 14821 / % possible obs: 97.9 % / Redundancy: 2.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.045 / Net I/σ(I): 5.8
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2422 / CC1/2: 0.965

-
Processing

Software
NameVersionClassification
PHENIX1.21rc1_5058refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→46.96 Å / SU ML: 0.4568 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 32.2443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2477 737 4.97 %
Rwork0.2 14084 -
obs0.2024 14821 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.69 Å2
Refinement stepCycle: LAST / Resolution: 3→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4993 0 28 0 5021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00255170
X-RAY DIFFRACTIONf_angle_d0.53227037
X-RAY DIFFRACTIONf_chiral_restr0.0409746
X-RAY DIFFRACTIONf_plane_restr0.0047916
X-RAY DIFFRACTIONf_dihedral_angle_d11.17511810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.230.32931330.2792836X-RAY DIFFRACTION98.25
3.23-3.560.31251600.2332832X-RAY DIFFRACTION98.62
3.56-4.070.24721430.20872809X-RAY DIFFRACTION97.75
4.07-5.130.23591520.17712845X-RAY DIFFRACTION98.17
5.13-46.960.2171490.18282762X-RAY DIFFRACTION96.26
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)
10.175138863756-0.2637968070980.09422642888890.382140979811-0.5000159372811.657431032890.006654236646240.3332143628890.230932243411-0.04530430351580.239641530006-0.1309497271890.153861708906-0.1060278104320.00806159088310.3683986040370.05888018383130.1106886712690.423346010311-0.1767161475650.4940218911925.4875.571-9.124
20.02654845654750.081345080479-0.1015210422930.597502932035-0.490248398430.2668575783750.3387572262430.166130703679-0.0888162986722-1.105547689410.1055879078960.186352753053-0.266286835516-0.07507480892070.01332076191890.5316534097490.1159668834670.08522307247560.599319927990.02769801980810.641664081563-1.45614.411-15.037
30.379280479526-0.00862014488085-0.1355995655220.320048480656-0.4206237030581.39373422319-0.00548160450333-0.113444574051-0.2468168554380.4001618032050.599753846910.3325905370220.548492302946-0.7777039249520.07876296359650.580390361966-0.15457192945-0.04003173280930.7579699486710.1032292892690.683912558637-11.635.431-9.605
40.06332896075880.0954370732447-0.2531697580860.767058651957-0.820477252340.887933182397-0.01037578748160.314336494804-0.135353329683-0.6062133782830.4743397373880.2537905022650.755330759135-0.6819378052760.1201248933770.59706399294-0.0438133293042-0.09266786674750.7964691572380.09496341565870.726131599322-9.5152.648-19.212
50.4548578234780.00311729688327-0.0310942400751-0.00245170156884-0.1219287956640.1666968491860.120734343531-0.345408831552-0.571015030149-0.138887903010.1695602198080.1036595553030.1783990939121.05170779698-0.0005434631609511.07396753959-0.0559033428306-0.1283036579020.760026659414-0.02112435007380.7584561677716.154-15.6849.812
61.73002840150.686166538287-0.8714143836340.382463342951-0.3820824248040.5274808570130.136895908858-0.2057936951880.0869982695909-0.2954187824490.0835100476329-0.07071669993840.27520560452-0.5225607838590.000161345932860.792400774436-0.0853538743863-0.06690255500110.6119784445720.03930315197590.585987880565-0.845-16.46214.542
70.6198211956020.7225221150590.2799403646882.40801887626-1.076232797261.25472393420.1972404172520.157285830719-0.0737415958791-0.2695528286080.6546957610110.08429907375230.652057056779-0.3486197941860.299734614860.608525544156-0.09108403420270.07698827083260.779554544408-0.02531465832930.380552195842-1.4125.50710.988
80.3461340771270.6349055009350.02578271968571.183253278440.04476116328660.001453397697260.191584027330.175573333492-0.356297700529-0.2570061611350.810051928192-0.7592454337980.5434921918050.702687095458-0.02415227408280.7955462757690.199985807741-0.2787882489411.073515873390.0845260507771.1088125468618.818-8.90813.758
90.7298617580340.5096093308140.2111819472020.4199284424370.05650586647990.2145666138281.17858379094-0.141892077685-0.4928865999840.341034755064-0.596816403345-0.0445170025465-0.01809853885510.1692736831280.1722836933270.5748621091380.1003439088990.004106690292120.471191935028-0.000265816082930.5172127899458.8440.9069.402
100.1640810352260.181504338367-0.2041237036370.163329244595-0.2391937368790.234978115595-0.0490629400243-0.03539624996570.2229852467630.794875332377-0.487745946597-0.244078269296-0.760835179838-0.09980199999190.000303607211980.9765286654150.108199858797-0.2407199625350.708000697144-0.01451806090750.9024658340256.07411.189.977
110.16626184352-0.0940304214153-0.1703213452980.04725750609490.09004786591810.143387919605-0.6930760322540.384946052270.756994686540.6174797301070.0634317892377-0.8143849466660.3675278530530.166200537808-0.001074463786570.808551990197-0.0460789191057-0.1547986235140.8282166388960.08782740231731.0162866100817.489.32811.604
120.2181495865880.0884165414541-0.03466627476430.121322864812-0.2390030692030.3431580750980.6391102336860.269028627841-0.03221842362560.0607500517374-0.419956459481-0.232789463636-0.03697908720630.229058087085-0.000496130006030.521814056771-0.0278262072451-0.04471013994950.584462825087-0.005714989260810.3740800355334.8063.6453.393
130.06500768759490.101792915111-0.1109118800490.159978858153-0.1707879635570.1885576799380.579815840959-0.197244854565-0.3724083562380.4761841630490.664721459027-0.206834258546-0.3090542138240.2991658820820.008594496127020.8331928046810.356678466389-0.3224905417061.8118169290.1511620542621.4592013023521.046-0.54723.265
143.400984996120.06303053749020.9960568529952.38225841957-1.256334601071.931601633190.303868455185-0.08905084404940.001371139969041.07104601673-0.255340007657-0.379398986924-0.79480533314-0.975519893012-0.1230373005781.158263258570.2726539534940.07305489376310.472508184409-0.1224784092630.4778802464024.43411.55215.78
15-0.001160982883360.02034841880220.008828606281240.05801788939420.0545781808280.05097290414410.682569904293-0.0870717002347-0.1782549823220.22766506744-0.7686708865050.520993956691-0.1572066666550.5244025506670.0008456354043671.049029476150.179825173721-0.04821941497490.7631946459920.01957660699720.7017244090829.221-1.2220.982
160.260932723912-0.1078405918860.1647443698590.0368579320343-0.04189605403220.0768769953716-0.4333767112370.965138412143-0.8541270111620.28910319413-0.08168551019331.02772819036-0.384550369450.325223092528-4.73142454974E-50.4354907292170.06150004725750.03660721143950.671970092891-0.03094597230180.646272230049-5.168.824-17.511
171.324382899351.123040615790.4582612469240.8774326584950.9741197194551.48507530008-0.058738249843-0.3048812912850.1417809443280.229078111827-0.0328041687199-0.189554716518-0.724523658107-0.0512913777452-0.00015577660730.6924214511890.0428690213773-0.014891150150.507638227455-0.01647788790520.6498651921529.23138.51-1.961
181.52547597004-1.002588136691.424679687011.33058293686-1.453119276741.63100507315-0.4150387371910.0470975380160.001160325933720.372618622840.0644664165553-0.367616576625-0.645080648923-0.0766682342814-0.06369013821580.5981092332610.01199490281360.02321250498260.604010513831-0.02112849897160.566400388408-3.0834.744-26.612
191.78435760716-0.2798599969360.7613670499030.8113693879270.6735948137883.553626527730.879977363156-0.42188772305-0.2875071123040.1634436469850.4542098185270.160603933821-0.440987657882-1.363496820253.54125188879-0.5046806353440.2020083087570.449952485381.250945914440.57944684070.787361089193-24.37623.916-27.522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:56 )A1 - 56
2X-RAY DIFFRACTION2( CHAIN A AND RESID 57:85 )A57 - 85
3X-RAY DIFFRACTION3( CHAIN A AND RESID 86:137 )A86 - 137
4X-RAY DIFFRACTION4( CHAIN A AND RESID 138:174 )A138 - 174
5X-RAY DIFFRACTION5( CHAIN A AND RESID 175:197 )A175 - 197
6X-RAY DIFFRACTION6( CHAIN A AND RESID 198:276 )A198 - 276
7X-RAY DIFFRACTION7( CHAIN B AND RESID 0:11 )B0 - 11
8X-RAY DIFFRACTION8( CHAIN B AND RESID 12:19 )B12 - 19
9X-RAY DIFFRACTION9( CHAIN B AND RESID 20:30 )B20 - 30
10X-RAY DIFFRACTION10( CHAIN B AND RESID 31:41 )B31 - 41
11X-RAY DIFFRACTION11( CHAIN B AND RESID 42:51 )B42 - 51
12X-RAY DIFFRACTION12( CHAIN B AND RESID 52:71 )B52 - 71
13X-RAY DIFFRACTION13( CHAIN B AND RESID 72:77 )B72 - 77
14X-RAY DIFFRACTION14( CHAIN B AND RESID 78:90 )B78 - 90
15X-RAY DIFFRACTION15( CHAIN B AND RESID 91:99 )B91 - 99
16X-RAY DIFFRACTION16( CHAIN C AND RESID 1:8 )C1 - 8
17X-RAY DIFFRACTION17( CHAIN G AND RESID 7:108 )G7 - 108
18X-RAY DIFFRACTION18( CHAIN G AND RESID 109:219 )G109 - 219
19X-RAY DIFFRACTION19( CHAIN G AND ( RESID 220:291 OR RESID 401:402 ) )G220 - 291
20X-RAY DIFFRACTION19( CHAIN G AND ( RESID 220:291 OR RESID 401:402 ) )G401 - 402

+
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