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- PDB-3ei4: Structure of the hsDDB1-hsDDB2 complex -

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Basic information

Entry
Database: PDB / ID: 3ei4
TitleStructure of the hsDDB1-hsDDB2 complex
Components
  • DNA damage-binding protein 1
  • DNA damage-binding protein 2
KeywordsDNA BINDING PROTEIN / UV-damage / DDB / nucleotide excision repair / xeroderma pigmentosum / Disease mutation / DNA damage / DNA repair / DNA-binding / Nucleus / Phosphoprotein / WD repeat
Function / homology
Function and homology information


positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / site of DNA damage / cullin family protein binding / viral release from host cell / pyrimidine dimer repair / ectopic germ cell programmed cell death / proteasomal protein catabolic process / positive regulation of viral genome replication / protein autoubiquitination / response to UV / positive regulation of gluconeogenesis / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / cell junction / protein-macromolecule adaptor activity / Neddylation / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome, telomeric region / damaged DNA binding / Ub-specific processing proteases / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / protein-containing complex binding / chromatin / nucleolus / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Helix Hairpins - #3280 / DNA damage-binding protein 2 / DNA polymerase; domain 1 - #910 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...Helix Hairpins - #3280 / DNA damage-binding protein 2 / DNA polymerase; domain 1 - #910 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / DNA polymerase; domain 1 / Helix Hairpins / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA damage-binding protein 1 / DNA damage-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsScrima, A. / Pavletich, N.P. / Thoma, N.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex.
Authors: Scrima, A. / Konickova, R. / Czyzewski, B.K. / Kawasaki, Y. / Jeffrey, P.D. / Groisman, R. / Nakatani, Y. / Iwai, S. / Pavletich, N.P. / Thoma, N.H.
History
DepositionSep 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
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_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA damage-binding protein 1
B: DNA damage-binding protein 2
C: DNA damage-binding protein 1
D: DNA damage-binding protein 2
E: DNA damage-binding protein 1
F: DNA damage-binding protein 2


Theoretical massNumber of molelcules
Total (without water)534,9636
Polymers534,9636
Non-polymers00
Water00
1
A: DNA damage-binding protein 1
B: DNA damage-binding protein 2


Theoretical massNumber of molelcules
Total (without water)178,3212
Polymers178,3212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-27 kcal/mol
Surface area60250 Å2
MethodPISA
2
C: DNA damage-binding protein 1
D: DNA damage-binding protein 2


Theoretical massNumber of molelcules
Total (without water)178,3212
Polymers178,3212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-28 kcal/mol
Surface area60280 Å2
MethodPISA
3
E: DNA damage-binding protein 1
F: DNA damage-binding protein 2


Theoretical massNumber of molelcules
Total (without water)178,3212
Polymers178,3212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-27 kcal/mol
Surface area60330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)268.500, 268.500, 471.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12A
22C
32E
13A
23C
33E
14A
24C
34E
15B
25D
35F
16B
26D
36F

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETPROPROAA1 - 1219 - 30
211METMETPROPROCC1 - 1219 - 30
311METMETPROPROEE1 - 1219 - 30
121LEULEUARGARGAA356 - 391374 - 409
221LEULEUARGARGCC356 - 391374 - 409
321LEULEUARGARGEE356 - 391374 - 409
131HISHISASPASPAA711 - 1099729 - 1117
231HISHISASPASPCC711 - 1099729 - 1117
331HISHISASPASPEE711 - 1099729 - 1117
112THRTHRASNASNAA13 - 35531 - 373
212THRTHRASNASNCC13 - 35531 - 373
312THRTHRASNASNEE13 - 35531 - 373
113ASNASNLEULEUAA392 - 710410 - 728
213ASNASNLEULEUCC392 - 710410 - 728
313ASNASNLEULEUEE392 - 710410 - 728
114ILEILELEULEUAA1100 - 11361118 - 1154
214ILEILELEULEUCC1100 - 11361118 - 1154
314ILEILELEULEUEE1100 - 11361118 - 1154
115TRPTRPSERSERBB54 - 10063 - 109
215TRPTRPSERSERDD54 - 10063 - 109
315TRPTRPSERSERFF54 - 10063 - 109
116TYRTYRGLUGLUBB101 - 421110 - 430
216TYRTYRGLUGLUDD101 - 421110 - 430
316TYRTYRGLUGLUFF101 - 421110 - 430

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein DNA damage-binding protein 1 / hsDDB1 / Damage-specific DNA-binding protein 1 / UV-damaged DNA-binding factor / DDB p127 subunit / ...hsDDB1 / Damage-specific DNA-binding protein 1 / UV-damaged DNA-binding factor / DDB p127 subunit / DNA damage-binding protein a / DDBa / UV-damaged DNA-binding protein 1 / UV-DDB 1 / Xeroderma pigmentosum group E-complementing protein / XPCe / XPE-binding factor / XPE-BF / HBV X-associated protein 1 / XAP-1


Mass: 129273.930 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Cell (production host): high five cells / Cell line (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531
#2: Protein DNA damage-binding protein 2 / hsDDB2 / Damage-specific DNA-binding protein 2 / DDB p48 subunit / DDBb / UV-damaged DNA-binding ...hsDDB2 / Damage-specific DNA-binding protein 2 / DDB p48 subunit / DDBb / UV-damaged DNA-binding protein 2 / UV-DDB 2


Mass: 49047.133 Da / Num. of mol.: 3 / Fragment: residues (-8)-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB2 / Cell (production host): high five cells / Cell line (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92466
Sequence detailsTHE FEATURE OF UNIPROT (DDB1_HUMAN Q16531) SHOWS CONFLICT AT THESE POSITIONS: 422 D -> Y (IN REF. 3; ...THE FEATURE OF UNIPROT (DDB1_HUMAN Q16531) SHOWS CONFLICT AT THESE POSITIONS: 422 D -> Y (IN REF. 3; AAA88883), 898-899 EL -> DV (IN REF. 3; AAA88883 AND 4; CAA05770)

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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: 3.05 Å3/Da / Density % sol: 59.71 % / Mosaicity: 0.45 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 200 mM (NH4)2SO4; 800 mM LiSO2; 100 mM Na-Citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 1.038 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 83678 / Num. obs: 85881 / % possible obs: 86.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.142 / Rsym value: 0.132 / Χ2: 1.007 / Net I/σ(I): 7.537
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1814 / Rsym value: 0.483 / Χ2: 0.871 / % possible all: 19

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0062refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
SHARPphasing
RefinementResolution: 3.3→25 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.846 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 72.519 / SU ML: 0.541 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.649 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2125 2.5 %RANDOM
Rwork0.254 ---
obs0.255 83678 80.2 %-
all-85881 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 142.29 Å2 / Biso mean: 64.131 Å2 / Biso min: 23.12 Å2
Baniso -1Baniso -2Baniso -3
1--6.99 Å2-3.49 Å20 Å2
2---6.99 Å20 Å2
3---10.48 Å2
Refinement stepCycle: LAST / Resolution: 3.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35241 0 0 0 35241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02236003
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.95748870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40454518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15424.4471599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.517156135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.63415192
X-RAY DIFFRACTIONr_chiral_restr0.1010.25562
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02127117
X-RAY DIFFRACTIONr_mcbond_it1.0571.2522485
X-RAY DIFFRACTIONr_mcangle_it1.9531.7536369
X-RAY DIFFRACTIONr_scbond_it1.755213518
X-RAY DIFFRACTIONr_scangle_it2.971312501
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3381TIGHT POSITIONAL0.020.03
1C3381TIGHT POSITIONAL0.010
1E3381TIGHT POSITIONAL0.020
1A3381TIGHT THERMAL3.4810
1C3381TIGHT THERMAL2.720
1E3381TIGHT THERMAL2.30
2A2689TIGHT POSITIONAL0.010.03
2C2689TIGHT POSITIONAL0.010
2E2689TIGHT POSITIONAL0.010
2A2689TIGHT THERMAL1.9910
2C2689TIGHT THERMAL2.190
2E2689TIGHT THERMAL1.980
3A2473TIGHT POSITIONAL0.020.03
3C2473TIGHT POSITIONAL0.010
3E2473TIGHT POSITIONAL0.020
3A2473TIGHT THERMAL2.9610
3C2473TIGHT THERMAL2.150
3E2473TIGHT THERMAL2.440
4A288TIGHT POSITIONAL0.010.03
4C288TIGHT POSITIONAL0.010
4E288TIGHT POSITIONAL0.010
4A288TIGHT THERMAL2.3410
4C288TIGHT THERMAL1.390.03
4E288TIGHT THERMAL1.420
5B364TIGHT POSITIONAL0.020.03
5D364TIGHT POSITIONAL0.020
5F364TIGHT POSITIONAL0.020
5B364TIGHT THERMAL2.1110
5D364TIGHT THERMAL1.80.03
5F364TIGHT THERMAL1.930
6B2521TIGHT POSITIONAL0.020.03
6D2521TIGHT POSITIONAL0.020
6F2521TIGHT POSITIONAL0.020
6B2521TIGHT THERMAL310
6D2521TIGHT THERMAL2.440
6F2521TIGHT THERMAL2.410
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 102 -
Rwork0.38 3912 -
all-4014 -
obs--51.49 %
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)
13.86910.30011.07393.14030.42452.91440.2463-0.0710.15480.3178-0.0484-0.2518-0.0456-0.1642-0.198-0.38660.0589-0.0011-0.6005-0.0533-0.5645-31.806140.94857.044
22.2533-0.575-0.43784.4003-0.71282.7253-0.261-0.7096-0.22280.77090.19750.0033-0.02240.0320.0635-0.26820.0818-0.03820.0125-0.0386-0.25374.3634.68554.208
35.2254-0.6067-0.6882.94140.67062.78150.1304-0.9244-0.14010.5258-0.01830.0312-0.06460.0518-0.1121-0.2147-0.1158-0.0116-0.22960.0407-0.4747-105.60957.53551.578
42.6230.0449-1.13593.01420.0262.98610.30470.83270.3206-0.9935-0.2657-0.0849-0.0344-0.1266-0.0390.10580.361-0.04090.11040.2148-0.4381-35.043142.15521
52.8868-0.4650.54242.77340.49813.21830.10950.8189-0.0634-0.5624-0.2239-0.40140.04950.10530.1145-0.2283-0.05880.27810.108-0.0162-0.26997.22935.82118.099
63.83980.00730.25843.0845-1.07442.9167-0.30770.809-0.3521-0.93730.24970.20530.0744-0.04260.05810.1184-0.1563-0.1068-0.1131-0.3218-0.3556-106.28753.7915.533
74.0838-1.6949-0.91777.6301-0.75073.0111-0.3348-0.2598-0.38161.07240.40980.93730.0017-0.2787-0.0749-0.29760.12880.0818-0.2990.0128-0.4363-58.686181.73261.107
87.156-0.24270.58984.75261.61753.18960.0616-1.12670.84630.32330.0117-0.198-0.2229-0.0611-0.0732-0.2885-0.0401-0.08-0.0298-0.1191-0.286453.60335.82457.693
94.98842.26621.60275.6637-0.76614.28440.5414-0.3701-0.70980.5291-0.2701-0.88340.1320.1659-0.2712-0.1515-0.0782-0.1107-0.30950.1971-0.037-127.57112.9953.732
1018.23012.5951-0.758416.69012.53449.80361.34-0.45120.65020.8594-0.42542.04640.9684-1.8738-0.91470.13080.0309-0.15520.4282-0.3160.4386-70.094146.02852.473
115.9773-2.8331-0.88786.6329-0.79723.0575-0.04440.18450.65710.8421.0325-1.083-1.06040.935-0.98810.4948-0.2686-0.13320.4988-0.01030.855928.57964.6349.292
1216.4301-2.6456-3.64266.0048-3.19966.7521-0.5183-2.1202-2.2717-0.05830.58860.52761.29070.662-0.07020.43560.21070.16470.44230.13630.9008-90.79721.97547.118
132.0109-3.7135-0.541517.0823-4.26475.22280.27770.55720.5989-0.8913-0.3986-1.31810.17540.10360.121-0.4534-0.0171-0.0275-0.40270.0479-0.4156-23.659129.1845.696
1419.0646-8.5305-4.25416.40153.36951.7808-0.56670.4753-1.787-0.08320.10520.26510.5372-0.33090.4615-0.2854-0.01520.0224-0.3048-0.1427-0.2797-9.84133.7942.699
1517.945713.55955.820517.02672.44822.6062-0.279-0.5750.6011-0.48720.45910.6741-0.5714-0.2667-0.1801-0.36410.0292-0.1406-0.3118-0.0612-0.4571-99.75770.41939.832
164.07210.2535-1.05552.8450.35513.3980.00570.3067-0.5394-0.0268-0.26250.47680.2975-0.19970.2567-0.39530.0194-0.026-0.5009-0.168-0.3862-35.552101.44744.584
173.21380.53060.03484.36920.47963.1950.0012-0.00780.38240.0124-0.04550.2888-0.2752-0.13990.0444-0.3902-0.02810.1267-0.3292-0.1564-0.3756-26.68558.73640.633
183.6058-0.94930.36433.3993-0.8672.8062-0.07930.14520.0311-0.0864-0.1723-0.6707-0.06370.3880.2515-0.2971-0.1229-0.0628-0.3011-0.0509-0.268-69.85573.27437.248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 12
2X-RAY DIFFRACTION1A356 - 391
3X-RAY DIFFRACTION1A711 - 1099
4X-RAY DIFFRACTION2C1 - 12
5X-RAY DIFFRACTION2C356 - 391
6X-RAY DIFFRACTION2C711 - 1099
7X-RAY DIFFRACTION3E1 - 12
8X-RAY DIFFRACTION3E356 - 391
9X-RAY DIFFRACTION3E711 - 1099
10X-RAY DIFFRACTION4A13 - 355
11X-RAY DIFFRACTION5C13 - 355
12X-RAY DIFFRACTION6E13 - 355
13X-RAY DIFFRACTION7A392 - 710
14X-RAY DIFFRACTION8C392 - 710
15X-RAY DIFFRACTION9E392 - 710
16X-RAY DIFFRACTION10A1100 - 1136
17X-RAY DIFFRACTION11C1100 - 1136
18X-RAY DIFFRACTION12E1100 - 1136
19X-RAY DIFFRACTION13B67 - 100
20X-RAY DIFFRACTION14D67 - 100
21X-RAY DIFFRACTION15F67 - 100
22X-RAY DIFFRACTION16B101 - 416
23X-RAY DIFFRACTION17D101 - 416
24X-RAY DIFFRACTION18F101 - 416

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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

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