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- PDB-6c5x: Crystal Structure of SOCS1 in complex with ElonginB and ElonginC -

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Basic information

Entry
Database: PDB / ID: 6c5x
TitleCrystal Structure of SOCS1 in complex with ElonginB and ElonginC
Components
  • Elongin-B
  • Elongin-C
  • GP130 peptide fragment
  • Suppressor of Cytokine Signalling 1
KeywordsSIGNALING PROTEIN / Complex / Ubiquitination / Cytokine signalling / SOCS
Function / homology
Function and homology information


oncostatin-M receptor activity / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / interleukin-6 receptor activity / triglyceride mobilization / interleukin-6 binding / Interleukin-6 signaling ...oncostatin-M receptor activity / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / interleukin-6 receptor activity / triglyceride mobilization / interleukin-6 binding / Interleukin-6 signaling / Interleukin-35 Signalling / oncostatin-M receptor complex / oncostatin-M-mediated signaling pathway / regulation of type II interferon-mediated signaling pathway / ciliary neurotrophic factor receptor activity / ciliary neurotrophic factor receptor binding / negative regulation of interleukin-6-mediated signaling pathway / leukemia inhibitory factor signaling pathway / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / interleukin-6 receptor binding / regulation of Notch signaling pathway / interleukin-11-mediated signaling pathway / positive regulation of astrocyte differentiation / negative regulation of receptor signaling pathway via JAK-STAT / intestinal epithelial cell development / target-directed miRNA degradation / elongin complex / VCB complex / cytokine receptor activity / regulation of growth / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / neuronal cell body membrane / glycogen metabolic process / interleukin-6-mediated signaling pathway / cytokine binding / positive regulation of Notch signaling pathway / protein tyrosine kinase activator activity / negative regulation of cytosolic calcium ion concentration / positive regulation of smooth muscle cell migration / growth factor binding / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / positive regulation of osteoblast differentiation / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / coreceptor activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / RNA Polymerase II Pre-transcription Events / transcription corepressor binding / response to cytokine / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Regulation of expression of SLITs and ROBOs / cytokine-mediated signaling pathway / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cell body / Neddylation / ubiquitin-dependent protein catabolic process / scaffold protein binding / protein-containing complex assembly / negative regulation of neuron apoptotic process / protein ubiquitination / receptor complex / intracellular signal transduction / membrane raft / external side of plasma membrane / dendrite / neuronal cell body / ubiquitin protein ligase binding / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / signal transduction / extracellular space / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Suppressor of cytokine signalling 1 / SOCS1, SH2 domain / SOCS box / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin C; Chain C, domain 1 ...Suppressor of cytokine signalling 1 / SOCS1, SH2 domain / SOCS box / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin C; Chain C, domain 1 / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Immunoglobulin-like fold / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Suppressor of cytokine signaling / Interleukin-6 receptor subunit beta / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.105 Å
AuthorsKershaw, N.J. / Laktyushin, A. / Babon, J.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Cancer Council Victoria1065180 Australia
CitationJournal: Nat Commun / Year: 2018
Title: The molecular basis of JAK/STAT inhibition by SOCS1.
Authors: Liau, N.P.D. / Laktyushin, A. / Lucet, I.S. / Murphy, J.M. / Yao, S. / Whitlock, E. / Callaghan, K. / Nicola, N.A. / Kershaw, N.J. / Babon, J.J.
History
DepositionJan 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Elongin-B
C: Elongin-C
E: Elongin-B
F: Elongin-C
D: Suppressor of Cytokine Signalling 1
A: Suppressor of Cytokine Signalling 1
G: GP130 peptide fragment


Theoretical massNumber of molelcules
Total (without water)87,1277
Polymers87,1277
Non-polymers00
Water181
1
B: Elongin-B
C: Elongin-C
A: Suppressor of Cytokine Signalling 1
G: GP130 peptide fragment


Theoretical massNumber of molelcules
Total (without water)44,1654
Polymers44,1654
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-48 kcal/mol
Surface area16360 Å2
MethodPISA
2
E: Elongin-B
F: Elongin-C
D: Suppressor of Cytokine Signalling 1


Theoretical massNumber of molelcules
Total (without water)42,9623
Polymers42,9623
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-41 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.122, 79.996, 132.747
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 70:72 or (resid 73 and (name...
21(chain D and (resseq 70:74 or (resid 75 and (name...
12(chain E and (resseq 1:48 or resseq 50:100))
22(chain B and (resseq 1:18 or (resid 19 and (name...
13(chain F and (resseq 17:28 or (resid 29 and (name...
23(chain C and (resseq 17:28 or (resid 29 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRSERSER(chain A and (resseq 70:72 or (resid 73 and (name...AF70 - 7223 - 25
121METMETMETMET(chain A and (resseq 70:72 or (resid 73 and (name...AF7326
131ARGARGILEILE(chain A and (resseq 70:72 or (resid 73 and (name...AF59 - 21112 - 164
141ARGARGILEILE(chain A and (resseq 70:72 or (resid 73 and (name...AF59 - 21112 - 164
151ARGARGILEILE(chain A and (resseq 70:72 or (resid 73 and (name...AF59 - 21112 - 164
161ARGARGILEILE(chain A and (resseq 70:72 or (resid 73 and (name...AF59 - 21112 - 164
211THRTHRLEULEU(chain D and (resseq 70:74 or (resid 75 and (name...DE70 - 7423 - 27
221ASPASPASPASP(chain D and (resseq 70:74 or (resid 75 and (name...DE7528
231THRTHRGLNGLN(chain D and (resseq 70:74 or (resid 75 and (name...DE70 - 21023 - 163
241THRTHRGLNGLN(chain D and (resseq 70:74 or (resid 75 and (name...DE70 - 21023 - 163
251THRTHRGLNGLN(chain D and (resseq 70:74 or (resid 75 and (name...DE70 - 21023 - 163
261THRTHRGLNGLN(chain D and (resseq 70:74 or (resid 75 and (name...DE70 - 21023 - 163
271THRTHRGLNGLN(chain D and (resseq 70:74 or (resid 75 and (name...DE70 - 21023 - 163
281THRTHRGLNGLN(chain D and (resseq 70:74 or (resid 75 and (name...DE70 - 21023 - 163
112METMETASPASP(chain E and (resseq 1:48 or resseq 50:100))EC1 - 481 - 48
122LEULEUPROPRO(chain E and (resseq 1:48 or resseq 50:100))EC50 - 10050 - 100
212METMETALAALA(chain B and (resseq 1:18 or (resid 19 and (name...BA1 - 181 - 18
222LYSLYSLYSLYS(chain B and (resseq 1:18 or (resid 19 and (name...BA1919
232METMETPROPRO(chain B and (resseq 1:18 or (resid 19 and (name...BA1 - 1001 - 100
242METMETPROPRO(chain B and (resseq 1:18 or (resid 19 and (name...BA1 - 1001 - 100
252METMETPROPRO(chain B and (resseq 1:18 or (resid 19 and (name...BA1 - 1001 - 100
262METMETPROPRO(chain B and (resseq 1:18 or (resid 19 and (name...BA1 - 1001 - 100
113METMETGLUGLU(chain F and (resseq 17:28 or (resid 29 and (name...FD17 - 281 - 12
123PHEPHEPHEPHE(chain F and (resseq 17:28 or (resid 29 and (name...FD2913
133METMETASPASP(chain F and (resseq 17:28 or (resid 29 and (name...FD17 - 1111 - 95
143METMETASPASP(chain F and (resseq 17:28 or (resid 29 and (name...FD17 - 1111 - 95
153METMETASPASP(chain F and (resseq 17:28 or (resid 29 and (name...FD17 - 1111 - 95
163METMETASPASP(chain F and (resseq 17:28 or (resid 29 and (name...FD17 - 1111 - 95
173METMETASPASP(chain F and (resseq 17:28 or (resid 29 and (name...FD17 - 1111 - 95
183METMETASPASP(chain F and (resseq 17:28 or (resid 29 and (name...FD17 - 1111 - 95
193METMETASPASP(chain F and (resseq 17:28 or (resid 29 and (name...FD17 - 1111 - 95
1103METMETASPASP(chain F and (resseq 17:28 or (resid 29 and (name...FD17 - 1111 - 95
213METMETGLUGLU(chain C and (resseq 17:28 or (resid 29 and (name...CB17 - 281 - 12
223PHEPHEPHEPHE(chain C and (resseq 17:28 or (resid 29 and (name...CB2913
233METMETCYSCYS(chain C and (resseq 17:28 or (resid 29 and (name...CB17 - 1121 - 96
243METMETCYSCYS(chain C and (resseq 17:28 or (resid 29 and (name...CB17 - 1121 - 96
253METMETCYSCYS(chain C and (resseq 17:28 or (resid 29 and (name...CB17 - 1121 - 96
263METMETCYSCYS(chain C and (resseq 17:28 or (resid 29 and (name...CB17 - 1121 - 96
273METMETCYSCYS(chain C and (resseq 17:28 or (resid 29 and (name...CB17 - 1121 - 96
283METMETCYSCYS(chain C and (resseq 17:28 or (resid 29 and (name...CB17 - 1121 - 96
293METMETCYSCYS(chain C and (resseq 17:28 or (resid 29 and (name...CB17 - 1121 - 96
2103METMETCYSCYS(chain C and (resseq 17:28 or (resid 29 and (name...CB17 - 1121 - 96

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 13147.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15370
#2: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10843.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369
#3: Protein Suppressor of Cytokine Signalling 1 / / SOCS1


Mass: 18971.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0LEJ4
#4: Protein/peptide GP130 peptide fragment


Mass: 1202.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q00560*PLUS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 1.86 Å3/Da / Density % sol: 33.96 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: 18% PEG3350, 200 mM sodium fluoride, 100 mM Tris, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→55.519 Å / Num. obs: 12239 / % possible obs: 99.1 % / Redundancy: 4.819 % / Biso Wilson estimate: 68.46 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.198 / Rrim(I) all: 0.222 / Χ2: 0.883 / Net I/σ(I): 6.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.184.711.1271.438320.5531.26591.5
3.18-3.274.960.911.928430.6691.01799.9
3.27-3.364.9740.772.298510.7620.861100
3.36-3.474.9070.72.528420.7720.78499.9
3.47-3.5850.5533.167870.8370.61799.9
3.58-3.714.8940.4483.827630.8660.50199.9
3.71-3.854.9060.3874.677630.9020.43399.7
3.85-44.9020.325.317130.9480.35899.7
4-4.184.9280.2386.756910.9710.26799.9
4.18-4.384.8690.1838.636730.9840.205100
4.38-4.624.7660.1659.526240.9750.18599.2
4.62-4.94.8270.169.065960.980.1899.7
4.9-5.244.8010.1579.075740.980.177100
5.24-5.664.7950.1768.025370.9740.19999.6
5.66-6.24.7310.1658.484950.9810.186100
6.2-6.934.630.1349.74510.9850.15299.8
6.93-84.4780.07814.154040.9950.08999.8
8-9.84.6310.04821.553500.9980.054100
9.8-13.864.4010.04425.82790.9980.0599.6
13.86-55.5193.8360.04424.521710.9960.0594.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2C9W

2c9w


Resolution: 3.105→55.519 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 27.68
RfactorNum. reflection% reflection
Rfree0.2714 581 4.76 %
Rwork0.2353 --
obs0.2371 12194 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.73 Å2 / Biso mean: 61.2479 Å2 / Biso min: 30.4 Å2
Refinement stepCycle: final / Resolution: 3.105→55.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5068 0 0 1 5069
Biso mean---41.53 -
Num. residues----665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025176
X-RAY DIFFRACTIONf_angle_d0.4837019
X-RAY DIFFRACTIONf_chiral_restr0.039829
X-RAY DIFFRACTIONf_plane_restr0.003882
X-RAY DIFFRACTIONf_dihedral_angle_d9.5163122
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1114X-RAY DIFFRACTION8.45TORSIONAL
12D1114X-RAY DIFFRACTION8.45TORSIONAL
21E924X-RAY DIFFRACTION8.45TORSIONAL
22B924X-RAY DIFFRACTION8.45TORSIONAL
31F722X-RAY DIFFRACTION8.45TORSIONAL
32C722X-RAY DIFFRACTION8.45TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.105-3.41740.35571430.29222782292597
3.4174-3.91180.29211410.255728783019100
3.9118-4.9280.25481520.207429013053100
4.928-55.52830.24441450.227830523197100

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