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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 / Cul4B-RING E3 ubiquitin ligase complex / positive regulation of viral release from host cell / Cul4A-RING E3 ubiquitin ligase complex / UV-damage excision repair / histone H2A monoubiquitination / WD40-repeat domain binding / cullin-RING ubiquitin ligase complex / interaction with symbiont / Cul4-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / Cul4B-RING E3 ubiquitin ligase complex / positive regulation of viral release from host cell / Cul4A-RING E3 ubiquitin ligase complex / UV-damage excision repair / histone H2A monoubiquitination / WD40-repeat domain binding / cullin-RING ubiquitin ligase complex / interaction with symbiont / Cul4-RING E3 ubiquitin ligase complex / cullin family protein binding / nucleotide-excision repair, preincision complex stabilization / nucleotide-excision repair, DNA incision, 3'-to lesion / positive regulation of gluconeogenesis / positive regulation of viral genome replication / regulation of mitotic cell cycle phase transition / protein autoubiquitination / response to UV / pyrimidine dimer repair / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair, DNA duplex unwinding / proteasomal protein catabolic process / global genome nucleotide-excision repair / nucleotide-excision repair, preincision complex assembly / nucleotide-excision repair / DNA damage response, detection of DNA damage / nucleotide-excision repair, DNA incision, 5'-to lesion / nucleotide-excision repair, DNA incision / protein-macromolecule adaptor activity / positive regulation of protein catabolic process / regulation of circadian rhythm / transcription-coupled nucleotide-excision repair / rhythmic process / proteasome-mediated ubiquitin-dependent protein catabolic process / cell junction / post-translational protein modification / protein polyubiquitination / nuclear chromosome, telomeric region / ubiquitin-dependent protein catabolic process / Wnt signaling pathway / damaged DNA binding / protein ubiquitination / protein deubiquitination / DNA repair / cellular response to DNA damage stimulus / protein-containing complex binding / viral process / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytoplasm
WD40 repeat / WD40-repeat-containing domain superfamily / WD40 repeat, conserved site / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / WD40/YVTN repeat-like-containing domain superfamily / DNA damage-binding protein 2 / DNA damage-binding protein 1 / WD40-repeat-containing domain / Helix Hairpins - #3280 / DNA polymerase; domain 1 - #910 ...WD40 repeat / WD40-repeat-containing domain superfamily / WD40 repeat, conserved site / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / WD40/YVTN repeat-like-containing domain superfamily / DNA damage-binding protein 2 / DNA damage-binding protein 1 / WD40-repeat-containing domain / Helix Hairpins - #3280 / DNA polymerase; domain 1 - #910 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / DNA polymerase; domain 1 / Helix Hairpins / Orthogonal Bundle / Mainly Beta / Mainly Alpha
DNA damage-binding protein 2 / DNA damage-binding protein 1
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.
Validation Report
SummaryFull reportAbout validation report
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

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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
Water0
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
γ
α
β
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-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111AA1 - 121 - 12
211CC1 - 121 - 12
311EE1 - 121 - 12
121AA356 - 391356 - 391
221CC356 - 391356 - 391
321EE356 - 391356 - 391
131AA711 - 1099711 - 1099
231CC711 - 1099711 - 1099
331EE711 - 1099711 - 1099
112AA13 - 35513 - 355
212CC13 - 35513 - 355
312EE13 - 35513 - 355
113AA392 - 710392 - 710
213CC392 - 710392 - 710
313EE392 - 710392 - 710
114AA1100 - 11361100 - 1136
214CC1100 - 11361100 - 1136
314EE1100 - 11361100 - 1136
115BB54 - 10054 - 100
215DD54 - 10054 - 100
315FF54 - 10054 - 100
116BB101 - 421101 - 421
216DD101 - 421101 - 421
316FF101 - 421101 - 421

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
Refinement-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 / Refinement-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 / Refinement-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)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
IDRefinement-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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