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- PDB-5oob: COMPLEX OF HUMAN NUCLEAR CAP-BINDING COMPLEX WITH M7GTP AND NELF-... -

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Basic information

Entry
Database: PDB / ID: 5oob
TitleCOMPLEX OF HUMAN NUCLEAR CAP-BINDING COMPLEX WITH M7GTP AND NELF-E C-TERMINAL PEPTIDE
Components
  • Negative elongation factor E
  • Nuclear cap-binding protein subunit 1
  • Nuclear cap-binding protein subunit 2
KeywordsNUCLEAR PROTEIN / Complex nuclear cap-binding complex m7GTP C-terminal peptide from ARS2
Function / homology
Function and homology information


snRNA export from nucleus / nuclear cap binding complex / NELF complex / positive regulation of protein modification process / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation ...snRNA export from nucleus / nuclear cap binding complex / NELF complex / positive regulation of protein modification process / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs / snRNA binding / positive regulation of RNA binding / RNA cap binding / alternative mRNA splicing, via spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of mRNA processing / primary miRNA processing / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated post-transcriptional gene silencing / : / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / mRNA 3'-end processing / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA cis splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / RNA catabolic process / Transport of Mature mRNA derived from an Intron-Containing Transcript / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / regulation of translational initiation / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Signaling by FGFR2 IIIa TM / spliceosomal complex assembly / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / negative regulation of transcription elongation by RNA polymerase II / 7-methylguanosine mRNA capping / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / localization / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of HIV elongation complex in the absence of HIV Tat / translation elongation factor activity / mRNA export from nucleus / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / mRNA transcription by RNA polymerase II / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / snRNP Assembly / positive regulation of cell growth / defense response to virus / positive regulation of ERK1 and ERK2 cascade / molecular adaptor activity / nuclear body / ribonucleoprotein complex / mRNA binding / chromatin binding / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Negative elongation factor E / Negative elongation factor E, RNA recognition motif / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 ...Negative elongation factor E / Negative elongation factor E, RNA recognition motif / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / Negative elongation factor E / Negative elongation factor E / Nuclear cap-binding protein subunit 2 / Nuclear cap-binding protein subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsCusack, S. / Schulze, W.M.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for mutually exclusive co-transcriptional nuclear cap-binding complexes with either NELF-E or ARS2.
Authors: Schulze, W.M. / Cusack, S.
History
DepositionAug 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity_name_com / pdbx_entity_src_syn ...entity_name_com / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.2Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear cap-binding protein subunit 1
B: Nuclear cap-binding protein subunit 2
C: Nuclear cap-binding protein subunit 1
D: Nuclear cap-binding protein subunit 2
E: Negative elongation factor E
F: Nuclear cap-binding protein subunit 1
G: Nuclear cap-binding protein subunit 2
I: Nuclear cap-binding protein subunit 1
J: Nuclear cap-binding protein subunit 2
K: Negative elongation factor E
Z: Negative elongation factor E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,43315
Polymers439,27611
Non-polymers2,1574
Water0
1
A: Nuclear cap-binding protein subunit 1
B: Nuclear cap-binding protein subunit 2
Z: Negative elongation factor E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9854
Polymers110,4463
Non-polymers5391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-15 kcal/mol
Surface area39590 Å2
MethodPISA
2
C: Nuclear cap-binding protein subunit 1
D: Nuclear cap-binding protein subunit 2
E: Negative elongation factor E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9854
Polymers110,4463
Non-polymers5391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-15 kcal/mol
Surface area39120 Å2
MethodPISA
3
F: Nuclear cap-binding protein subunit 1
G: Nuclear cap-binding protein subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4773
Polymers107,9382
Non-polymers5391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-9 kcal/mol
Surface area38540 Å2
MethodPISA
4
I: Nuclear cap-binding protein subunit 1
J: Nuclear cap-binding protein subunit 2
K: Negative elongation factor E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9854
Polymers110,4463
Non-polymers5391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-14 kcal/mol
Surface area38930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.800, 147.230, 153.880
Angle α, β, γ (deg.)90.00, 91.48, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22F
13A
23I
14B
24D
15B
25G
16B
26J
17C
27F
18C
28I
19D
29G
110D
210J
111E
211K
112E
212Z
113F
213I
114G
214J
115K
215Z

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALAAA26 - 7908 - 772
21GLUGLUALAALACC26 - 7908 - 772
12GLUGLUALAALAAA26 - 7908 - 772
22GLUGLUALAALAFF26 - 7908 - 772
13GLUGLUALAALAAA28 - 79010 - 772
23GLUGLUALAALAIH28 - 79010 - 772
14GLYGLYALAALABB4 - 1536 - 155
24GLYGLYALAALADD4 - 1536 - 155
15GLYGLYLYSLYSBB4 - 1516 - 153
25GLYGLYLYSLYSGG4 - 1516 - 153
16GLYGLYGLYGLYBB4 - 1506 - 152
26GLYGLYGLYGLYJI4 - 1506 - 152
17ALAALAALAALACC24 - 7906 - 772
27ALAALAALAALAFF24 - 7906 - 772
18GLUGLUGLNGLNCC28 - 78910 - 771
28GLUGLUGLNGLNIH28 - 78910 - 771
19GLYGLYLYSLYSDD4 - 1516 - 153
29GLYGLYLYSLYSGG4 - 1516 - 153
110GLYGLYGLYGLYDD4 - 1506 - 152
210GLYGLYGLYGLYJI4 - 1506 - 152
111LYSLYSPHEPHEEE361 - 3802 - 21
211LYSLYSPHEPHEKJ361 - 3802 - 21
112LYSLYSLYSLYSEE361 - 3732 - 14
212LYSLYSGLYGLYZK361 - 3792 - 20
113GLUGLUALAALAFF28 - 79010 - 772
213GLUGLUALAALAIH28 - 79010 - 772
114GLYGLYGLYGLYGG4 - 1506 - 152
214GLYGLYGLYGLYJI4 - 1506 - 152
115LYSLYSLYSLYSKJ361 - 3732 - 14
215LYSLYSGLYGLYZK361 - 3792 - 20

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Nuclear cap-binding protein subunit 1 / 80 kDa nuclear cap-binding protein / NCBP 80 kDa subunit


Mass: 89781.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CBP80 delta NLS Additional M at N-terminus. / Source: (gene. exp.) Homo sapiens (human) / Gene: NCBP1, CBP80, NCBP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q09161
#2: Protein
Nuclear cap-binding protein subunit 2 / 20 kDa nuclear cap-binding protein / Cell proliferation-inducing gene 55 protein / NCBP 20 kDa ...20 kDa nuclear cap-binding protein / Cell proliferation-inducing gene 55 protein / NCBP 20 kDa subunit / CBP20 / NCBP-interacting protein 1 / NIP1


Mass: 18156.260 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Additional GAM at N-terminus after TEV cleavage. / Source: (gene. exp.) Homo sapiens (human) / Gene: NCBP2, CBP20, PIG55 / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 / References: UniProt: P52298
#3: Protein/peptide Negative elongation factor E / NELF-E / RNA-binding protein RD


Mass: 2507.728 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P18615, UniProt: L9KL62*PLUS
#4: Chemical
ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H20N5O14P3

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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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 6 mg/ml of CBC were mixed with 500 microM m7GTP and 500 microM NELF-E peptide in 120 mM NaCl, 1 mM tris(2-carboxyethyl)phosphine, 20 mM HEPES pH 7.8. Crystals grew at 20 C in mother liquor ...Details: 6 mg/ml of CBC were mixed with 500 microM m7GTP and 500 microM NELF-E peptide in 120 mM NaCl, 1 mM tris(2-carboxyethyl)phosphine, 20 mM HEPES pH 7.8. Crystals grew at 20 C in mother liquor containing 0.2 M lithium citrate and 20% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.79→159 Å / Num. obs: 123434 / % possible obs: 98.4 % / Redundancy: 2.71 % / CC1/2: 0.995 / Rsym value: 0.108 / Net I/σ(I): 9.2
Reflection shellResolution: 2.79→2.87 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 0.91 / Num. unique obs: 8453 / CC1/2: 0.363 / Rsym value: 1.29 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H2T

1h2t


Resolution: 2.79→153.83 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 18.895 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 6345 5.1 %RANDOM
Rwork0.20189 ---
obs0.20331 117089 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.444 Å2
Baniso -1Baniso -2Baniso -3
1--4.25 Å20 Å2-0.06 Å2
2--4.79 Å20 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 2.79→153.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29164 0 132 0 29296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01929997
X-RAY DIFFRACTIONr_bond_other_d0.0010.0227642
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9640609
X-RAY DIFFRACTIONr_angle_other_deg0.922364202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.41853543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33524.0271470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.018155354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3615192
X-RAY DIFFRACTIONr_chiral_restr0.070.24431
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02132773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026227
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0527.22914241
X-RAY DIFFRACTIONr_mcbond_other4.0527.22914240
X-RAY DIFFRACTIONr_mcangle_it6.46610.83717761
X-RAY DIFFRACTIONr_mcangle_other6.46610.83717762
X-RAY DIFFRACTIONr_scbond_it4.0577.52615756
X-RAY DIFFRACTIONr_scbond_other4.0567.52615756
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.64411.12622848
X-RAY DIFFRACTIONr_long_range_B_refined9.19281.94733142
X-RAY DIFFRACTIONr_long_range_B_other9.19181.94233142
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A500400.02
12C500400.02
21A490020.03
22F490020.03
31A497800.03
32I497800.03
41B93300.03
42D93300.03
51B93100.02
52G93100.02
61B92660.02
62J92660.02
71C490060.03
72F490060.03
81C495040.03
82I495040.03
91D92620.03
92G92620.03
101D92040.03
102J92040.03
111E6780.09
112K6780.09
121E5160.05
122Z5160.05
131F490140.02
132I490140.02
141G92640.01
142J92640.01
151K5200.01
152Z5200.01
LS refinement shellResolution: 2.794→2.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 391 -
Rwork0.389 8035 -
obs--91.33 %

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