[English] 日本語
Yorodumi
- PDB-6lhd: Crystal structure of p53/BCL-xL fusion complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lhd
TitleCrystal structure of p53/BCL-xL fusion complex
Componentsfusion protein of Bcl-2-like protein 1 and Isoform 6 of Cellular tumor antigen p53
KeywordsPROTEIN BINDING / complex / interaction
Function / homology
Function and homology information


apoptotic process in bone marrow cell / dendritic cell apoptotic process / The NLRP1 inflammasome / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ...apoptotic process in bone marrow cell / dendritic cell apoptotic process / The NLRP1 inflammasome / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / regulation of mitochondrial membrane permeability / negative regulation of execution phase of apoptosis / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / oligodendrocyte apoptotic process / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / fertilization / regulation of growth / mRNA transcription / bone marrow development / circadian behavior / positive regulation of programmed necrotic cell death / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / RUNX3 regulates CDKN1A transcription / germ cell nucleus / homolactic fermentation / TP53 Regulates Transcription of Death Receptors and Ligands / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Activation of PUMA and translocation to mitochondria / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / Regulation of TP53 Activity through Association with Co-factors / regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / thymocyte apoptotic process / ER overload response / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / B cell lineage commitment / entrainment of circadian clock by photoperiod / hepatocyte apoptotic process / negative regulation of mitophagy / negative regulation of release of cytochrome c from mitochondria / cellular response to alkaloid / negative regulation of DNA replication / Zygotic genome activation (ZGA) / negative regulation of intrinsic apoptotic signaling pathway / Association of TriC/CCT with target proteins during biosynthesis / PI5P Regulates TP53 Acetylation / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / necroptotic process / positive regulation of release of cytochrome c from mitochondria / germ cell development / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / apoptotic mitochondrial changes / TFIID-class transcription factor complex binding / negative regulation of reproductive process / negative regulation of developmental process / cellular response to actinomycin D / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of reactive oxygen species metabolic process / rRNA transcription / Transcriptional Regulation by VENTX / negative regulation of anoikis / cellular response to UV-C / BH3 domain binding / viral process / replicative senescence / general transcription initiation factor binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of RNA polymerase II transcription preinitiation complex assembly / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Pyroptosis
Similarity search - Function
Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Immunoglobulin-like - #720 / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Blc2-like ...Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Immunoglobulin-like - #720 / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Blc2-like / Apoptosis Regulator Bcl-x / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / : / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / p53-like transcription factor, DNA-binding / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Cellular tumor antigen p53 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsWei, H. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81372904, 81570537, 81974074 and 31900880 China
CitationJournal: Nat Commun / Year: 2021
Title: Structural insight into the molecular mechanism of p53-mediated mitochondrial apoptosis.
Authors: Wei, H. / Qu, L. / Dai, S. / Li, Y. / Wang, H. / Feng, Y. / Chen, X. / Jiang, L. / Guo, M. / Li, J. / Chen, Z. / Chen, L. / Zhang, Y. / Chen, Y.
History
DepositionDec 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: fusion protein of Bcl-2-like protein 1 and Isoform 6 of Cellular tumor antigen p53
B: fusion protein of Bcl-2-like protein 1 and Isoform 6 of Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8504
Polymers83,7192
Non-polymers1312
Water1,892105
1
A: fusion protein of Bcl-2-like protein 1 and Isoform 6 of Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9252
Polymers41,8601
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: fusion protein of Bcl-2-like protein 1 and Isoform 6 of Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9252
Polymers41,8601
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.221, 68.850, 75.028
Angle α, β, γ (deg.)90.000, 110.270, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein fusion protein of Bcl-2-like protein 1 and Isoform 6 of Cellular tumor antigen p53 / Bcl2-L-1 / Apoptosis regulator Bcl-X / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 41859.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCLX, P53 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07817, UniProt: P04637
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M sodium malonate pH 7.0, 20%(w/v) polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.499→50 Å / Num. obs: 23478 / % possible obs: 97 % / Redundancy: 3.4 % / CC1/2: 0.899 / Rmerge(I) obs: 0.1158 / Rrim(I) all: 0.1386 / Net I/σ(I): 7.89
Reflection shellResolution: 2.499→2.599 Å / Rmerge(I) obs: 0.6334 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 2185 / CC1/2: 0.766 / Rrim(I) all: 0.7549

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KMD, 2YXJ

3kmd

2yxj


Resolution: 2.499→49.217 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 1210 5.16 %
Rwork0.2018 22237 -
obs0.2048 23447 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.58 Å2 / Biso mean: 58.2423 Å2 / Biso min: 18.78 Å2
Refinement stepCycle: final / Resolution: 2.499→49.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5007 0 2 105 5114
Biso mean--40.61 42.2 -
Num. residues----644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045123
X-RAY DIFFRACTIONf_angle_d0.5926954
X-RAY DIFFRACTIONf_chiral_restr0.043758
X-RAY DIFFRACTIONf_plane_restr0.004908
X-RAY DIFFRACTIONf_dihedral_angle_d8.4443043
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4995-2.59960.33451350.2617228992
2.5996-2.71790.29731430.2545244997
2.7179-2.86110.2631280.2352252599
2.8611-3.04040.34031360.2324249699
3.0404-3.27510.28081630.2148249799
3.2751-3.60460.30681290.2088239495
3.6046-4.12590.21981370.1915247297
4.1259-5.19730.21251050.1612573100
5.1973-49.20.23491340.1911254297
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)
12.1012-3.1659-1.82845.91354.14034.72140.37650.48940.7027-0.8199-0.4709-0.1882-0.621-0.12150.0630.42960.075-0.03730.4830.04350.428748.67518.308138.115
26.3229-0.058-5.90516.0643-1.67917.1228-0.8399-0.825-0.6191.4669-0.2585-0.0568-0.12570.08350.970.60950.1988-0.1050.7251-0.0090.705850.7998.617146.624
35.383-3.6766-2.30116.95144.60545.0709-0.8032-0.94930.33781.73341.0634-0.76040.1930.80210.01860.96570.1722-0.25990.74470.07050.878762.9989.166151.253
48.8509-5.0835-3.10065.87382.48733.588-0.3365-0.54170.4260.60230.3226-0.45570.38790.39450.00160.54560.057-0.1480.4034-0.02460.308457.64412.983142.875
58.5376-5.6150.23593.7194-0.24362.1763-0.4935-1.96190.55451.63320.5847-0.1573-0.30940.3937-0.31080.73790.0510.05221.0405-0.10890.649314.42417.87172.013
66.8992-0.2876-6.7110.75350.10977.8297-0.4878-2.14770.31180.50390.7320.1576-0.2682-0.2002-0.16250.58130.238-0.01711.49890.09490.63614.34513.578175.122
76.67661.3876-2.1182.0123-0.71682.26760.0451-0.7052-0.5113-0.22540.63880.60520.6327-0.1457-0.64090.90360.2068-0.25840.9171-0.00610.88593.3749.515161.932
86.27942.8855-5.59563.2659-1.89047.1478-0.4407-0.9101-0.6990.2589-0.1197-1.04690.04540.63290.48260.50230.1443-0.06940.75740.07880.6319.10510.991167.56
96.3691.9099-4.17747.3004-1.2937.5749-0.0919-0.03560.64850.2756-0.0020.5027-0.4631-0.9443-0.01870.50130.1126-0.07780.6574-0.03760.64869.49218.783161.258
103.06980.9759-1.99520.643-0.54241.86440.6694-0.29120.88510.68340.23320.8054-1.1289-1.3842-0.72410.84310.31580.35811.43470.04081.4674-3.30819.212178.63
111.6936-0.81741.46823.5996-0.78421.730.07750.14430.0154-0.051-0.0758-0.14270.06080.19370.01970.3994-0.0414-0.09030.2453-0.03730.326421.1624.469145.138
124.9183-1.04290.75353.4672-0.06833.09990.07860.126-0.23330.01590.00740.03130.0560.0801-0.07260.2872-0.0203-0.05720.1732-0.0070.191516.41-6.671142.769
137.5626-0.20330.14146.87094.60143.105-0.3033-0.4660.1198-0.5424-0.35181.91810.4054-1.08740.4770.6060.0126-0.19180.44360.01940.5987.52814.066136.423
142.451-0.0235-0.45864.1296-2.51271.75710.0909-0.25210.00360.725-0.04620.0747-0.4064-0.15810.13490.57670.0727-0.11170.2771-0.08910.392241.9659.996181.492
152.07140.36270.36215.33770.10081.7635-0.034-0.08520.27310.1031-0.0085-0.1403-0.08820.0490.02850.4058-0.0045-0.08530.2065-0.0280.2740.4055.751179.009
161.5277-0.7974-1.8612.47141.0577.379-0.1483-0.0795-0.11350.20240.10480.61550.6954-0.5504-0.08840.6119-0.1248-0.27980.40260.01270.65929.928-6.614171.209
173.05390.95152.67633.81243.76747.02160.55530.6849-0.4285-1.51620.16390.40120.70220.2825-0.67670.87330.1326-0.19390.44660.01910.470640.405-9.943167.913
189.1465-0.2867-1.36076.46061.79574.6710.0645-0.2413-0.36510.23610.00880.17080.08640.3118-0.04240.41740.0698-0.05550.1893-0.00070.208341.932-8.752178.35
195.28791.56153.78569.29492.9536.2685-0.07090.86130.43680.35840.2891-1.4502-0.46921.1066-0.22950.39960.0709-0.12560.417-0.01880.43152.2972.055181.948
202.76-0.17860.3454.499-0.63412.13970.15660.0028-0.0368-0.09720.02380.42730.3655-0.1636-0.19760.4843-0.0061-0.07520.1922-0.0260.278137.2082.128176.816
215.8639-5.5292-4.8415.93465.05454.8759-0.41850.2888-0.4639-0.7516-0.59262.2123-0.865-1.45110.6580.5331-0.0514-0.21220.60450.13140.596832.22519.106168.591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 3:44 )B3 - 44
2X-RAY DIFFRACTION2( CHAIN B AND RESID 45:81 )B45 - 81
3X-RAY DIFFRACTION3( CHAIN B AND RESID 82:96 )B82 - 96
4X-RAY DIFFRACTION4( CHAIN B AND RESID 97:155 )B97 - 155
5X-RAY DIFFRACTION5( CHAIN A AND RESID 3:20 )A3 - 20
6X-RAY DIFFRACTION6( CHAIN A AND RESID 21:58 )A21 - 58
7X-RAY DIFFRACTION7( CHAIN A AND RESID 59:96 )A59 - 96
8X-RAY DIFFRACTION8( CHAIN A AND RESID 97:116 )A97 - 116
9X-RAY DIFFRACTION9( CHAIN A AND RESID 117:136 )A117 - 136
10X-RAY DIFFRACTION10( CHAIN A AND RESID 137:149 )A137 - 149
11X-RAY DIFFRACTION11( CHAIN A AND RESID 162:221 )A162 - 221
12X-RAY DIFFRACTION12( CHAIN A AND RESID 222:341 )A222 - 341
13X-RAY DIFFRACTION13( CHAIN A AND RESID 342:355 )A342 - 355
14X-RAY DIFFRACTION14( CHAIN B AND RESID 163:189 )B163 - 189
15X-RAY DIFFRACTION15( CHAIN B AND RESID 190:234 )B190 - 234
16X-RAY DIFFRACTION16( CHAIN B AND RESID 235:246 )B235 - 246
17X-RAY DIFFRACTION17( CHAIN B AND RESID 247:260 )B247 - 260
18X-RAY DIFFRACTION18( CHAIN B AND RESID 261:279 )B261 - 279
19X-RAY DIFFRACTION19( CHAIN B AND RESID 280:295 )B280 - 295
20X-RAY DIFFRACTION20( CHAIN B AND RESID 296:343 )B296 - 343
21X-RAY DIFFRACTION21( CHAIN B AND RESID 344:355 )B344 - 355

+
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