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- PDB-2yns: rImp_alpha_B54NLS -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2yns
TitlerImp_alpha_B54NLS
Components
  • B54NLS
  • IMPORTIN SUBUNIT ALPHA-1A
KeywordsTRANSPORT PROTEIN / NUCLEAR LOCALIZATION SIGNAL
Function / homology
Function and homology information


nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / perinuclear region of cytoplasm / nucleus
Similarity search - Function
Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Leucine-rich Repeat Variant ...Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1a
Similarity search - Component
Biological speciesORYZA SATIVA (Asian cultivated rice)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChang, C.-W. / Counago, R.L.M. / Williams, S.J. / Boden, M. / Kobe, B.
CitationJournal: Plant Cell / Year: 2012
Title: Crystal Structure of Rice Importin-Alpha and Structural Basis of its Interaction with Plant-Specific Nuclear Localization Signals.
Authors: Chang, C.-W. / Counago, R.L.M. / Williams, S.J. / Boden, M. / Kobe, B.
History
DepositionOct 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMPORTIN SUBUNIT ALPHA-1A
B: IMPORTIN SUBUNIT ALPHA-1A
C: B54NLS
D: B54NLS


Theoretical massNumber of molelcules
Total (without water)108,8754
Polymers108,8754
Non-polymers00
Water2,954164
1
A: IMPORTIN SUBUNIT ALPHA-1A
C: B54NLS


Theoretical massNumber of molelcules
Total (without water)54,4382
Polymers54,4382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint1.7 kcal/mol
Surface area18790 Å2
MethodPISA
2
B: IMPORTIN SUBUNIT ALPHA-1A
D: B54NLS


Theoretical massNumber of molelcules
Total (without water)54,4382
Polymers54,4382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint1.9 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.242, 141.405, 73.325
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 73:494 )
211CHAIN B AND (RESSEQ 73:494 )

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Components

#1: Protein IMPORTIN SUBUNIT ALPHA-1A


Mass: 53026.848 Da / Num. of mol.: 2 / Fragment: NLS BINDING DOMAIN, RESIDUES 73-526
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYZA SATIVA (Asian cultivated rice) / Strain: JAPONICA GROUP / Plasmid: PET30A_IMPALPHA_DIBB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q71VM4
#2: Protein/peptide B54NLS


Mass: 1410.753 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PGEX2T-B54NLS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.3 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growDetails: 0.1 M BIS-TRISPROPANE PH 7.0, 15-17% PEG 3350 AND 0.2 M NAF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: SILICON MIRRORS (ADAPTIVE AND U-BENT)
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR (SI111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.1→19.95 Å / Num. obs: 73652 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B8P
Resolution: 2.1→19.908 Å / σ(F): 1.34 / Phase error: 20.36 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1974 3719 5.1 %
Rwork0.1769 --
obs0.1748 73622 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.31 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6612 0 0 164 6776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146722
X-RAY DIFFRACTIONf_angle_d1.6819142
X-RAY DIFFRACTIONf_dihedral_angle_d16.4472482
X-RAY DIFFRACTIONf_chiral_restr0.0651092
X-RAY DIFFRACTIONf_plane_restr0.011180
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3231X-RAY DIFFRACTIONPOSITIONAL
12B3231X-RAY DIFFRACTIONPOSITIONAL0.563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1011-2.13730.28541770.27263505X-RAY DIFFRACTION95
2.1373-2.17610.28941930.25433460X-RAY DIFFRACTION95
2.1761-2.21790.2631750.24633527X-RAY DIFFRACTION95
2.2179-2.26310.2441870.23133398X-RAY DIFFRACTION95
2.2631-2.31220.23482020.22963522X-RAY DIFFRACTION94
2.3122-2.36590.22431820.22073457X-RAY DIFFRACTION95
2.3659-2.4250.22731720.21413484X-RAY DIFFRACTION95
2.425-2.49050.26041710.19993528X-RAY DIFFRACTION95
2.4905-2.56360.23071930.20463449X-RAY DIFFRACTION95
2.5636-2.64620.24711820.19663461X-RAY DIFFRACTION95
2.6462-2.74050.2041780.18143528X-RAY DIFFRACTION95
2.7405-2.84990.20541800.18773496X-RAY DIFFRACTION95
2.8499-2.97920.19521780.18253474X-RAY DIFFRACTION95
2.9792-3.13570.22161860.17973509X-RAY DIFFRACTION95
3.1357-3.33130.19621620.16753514X-RAY DIFFRACTION96
3.3313-3.58710.19771920.16263476X-RAY DIFFRACTION95
3.5871-3.94550.1642030.14583485X-RAY DIFFRACTION94
3.9455-4.51060.15262010.13143491X-RAY DIFFRACTION95
4.5106-5.66090.17061880.14993529X-RAY DIFFRACTION95
5.6609-19.82560.17252100.15683516X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-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)
10.01660.01940.01640.02350.02130.015-0.04040.00490.02330.0304-0.02040.0124-0.07190.0254-0.1660.7002-0.2150.03450.1536-0.08480.172154.570334.474725.0399
20.00390.01440.00670.04430.02320.00980.01030.0192-0.04570.01960.00090.018-0.0356-0.0080.02610.8357-0.14990.00140.1494-0.05880.242747.494130.122131.5449
30.0162-0.0116-0.00780.0090.00430.00270.0417-0.0136-0.06580.01680.005-0.0904-0.14980.1670.00110.5722-0.21430.05460.3662-0.02290.298855.246122.004626.5058
40.0063-0.0010.00110.002-0.00510.01510.01340.0089-0.031-0.00410.0244-0.00490.02990.04950.05361.27540.48010.16380.71020.03070.495254.4418-104.420211.8442
50.0123-0.03280.02390.0882-0.06160.0452-0.0272-0.02940.02350.0257-0.04850.0280.0468-0.0397-0.06341.2990.18240.04730.3919-0.17240.415248.9357-101.03825.4388
60.0180.00970.02740.01070.00880.0412-0.0259-0.0063-0.00670.1065-0.00390.1323-0.03150.01540.00610.94930.0502-0.14770.172-0.07750.438537.9231-99.964810.5143
70.01750.0185-0.01320.0441-0.02140.0108-0.02080.03640.0155-0.02150.02090.0876-0.0009-0.02950.04360.4608-0.14550.07930.0992-0.00510.216940.93521.451827.1222
80.03290.0146-0.03770.0057-0.01580.03910.0327-0.0728-0.0323-0.1105-0.00060.0593-0.08960.13210.00730.3651-0.04580.08980.1894-0.00950.265744.057116.651419.1897
90.04130.0493-0.06090.0538-0.06440.0736-0.0141-0.00210.0315-0.06680.1102-0.0565-0.04880.02490.00030.2352-0.04710.03380.2594-0.01030.231644.20749.676726.5513
100.00330.00280.0030.00210.00170.0018-0.0698-0.03340.0362-0.0480.0402-0.12070.02080.0085-00.2635-0.0072-0.09790.49020.02350.361649.8242.173538.1725
110.01040.0137-0.0120.0259-0.03640.04350.01760.1198-0.12330.16960.04870.15460.02240.00360.00010.2703-0.0340.03340.17540.00390.206636.81945.759431.3355
120.00510.0024-0.00410.0003-0.00010.00520.09040.0385-0.0993-0.2223-0.143-0.0912-0.0263-0.037600.29840.03910.03080.3389-0.00540.253839.0065-5.72925.9999
130.0114-0.0052-0.00570.01310.01210.0108-0.05950.025-0.0690.0966-0.151-0.005-0.11490.194500.2411-0.03340.0290.22260.040.160734.42320.719138.826
140.12740.0743-0.03530.05210.00220.08230.01820.0064-0.14210.094-0.0302-0.0324-0.0853-0.02330.01070.21810.00540.00150.16410.0060.17724.8595-8.046439.1444
150.00140.00320.00070.00380.0020.0004-0.0469-0.01540.03040.02620.01170.0399-0.05570.0435-00.2317-0.0057-0.01950.36080.10430.387513.8957-0.268239.0761
160.26790.0616-0.06560.1534-0.06110.0425-0.07720.031-0.1330.17130.00630.06690.0685-0.0296-0.0110.1975-0.00240.0140.0630.06480.272811.0849-13.476240.7505
170.00230.0014-0.00070.0006-0.0004-0.0001-0.00750.0236-0.02630.04440.0316-0.0006-0.06570.013400.23740.042-0.02760.23650.06210.29385.9761-1.105935.8172
180.6661-0.31120.11340.1463-0.03920.12270.18660.2382-0.25180.1311-0.0005-0.02450.1293-0.08950.08320.2137-0.022-0.02630.1680.06550.28311.4652-14.134334.7558
190.019-0.004-0.01610.00140.00260.01170.0215-0.02250.0235-0.04970.01190.00360.0302-0.04810.02350.2595-0.1359-0.10750.16370.07880.552-7.4454-29.612936.0652
200.0046-0.00710.00770.0173-0.01590.01530.05050.0021-0.025-0.03650.0665-0.0090.0213-0.07270.00820.218-0.06030.01330.4530.09260.4797-10.5915-18.794638.9372
210.02210.01530.01950.0387-0.01580.064-0.02330.1073-0.0555-0.10260.05010.1163-0.0035-0.00910.0310.17320.0407-0.06150.42570.06310.3455-9.3-9.105525.5207
220.00340.00510.00190.00260.00150.00060.10930.0848-0.0508-0.0936-0.09490.12210.0812-0.0055-00.36890.039-0.15990.3501-0.00010.3815-9.105-18.830523.9964
230.02760.01920.00360.0149-0.00950.0664-0.00080.00170.0105-0.0141-0.0236-0.02540.05530.0663-0.11650.88380.4645-0.01940.4754-0.01640.244954.4068-92.435110.213
240.004-0.00030.00580.027-0.02970.039-0.0303-0.04770.00380.05040.0417-0.00640.0102-0.02060.10840.84890.1793-0.16120.3447-0.18730.285540.1606-91.89959.5912
250.005-0.00540.00010.0037-0.0005-0.00110.0778-0.0698-0.0329-0.01390.12250.0490.0657-0.0772-00.453-0.0214-0.08310.2108-0.04490.327940.137-89.33919.1437
260.0226-0.0052-0.00460.0413-0.00430.01630.0835-0.0575-0.1575-0.1957-0.04750.02080.30640.24690.02030.38390.0874-0.03490.2466-0.01170.164346.6287-82.76617.5659
270.0216-0.01260.02330.0078-0.01180.0187-0.02150.04410.03930.0651-0.0517-0.1368-0.0686-0.0815-00.2160.0593-0.00240.1546-0.0260.17140.8186-75.346214.4156
280.2193-0.10240.02580.1897-0.04960.01350.15450.00710.029-0.1160.09850.01080.03130.08070.04380.26150.04950.05260.3796-0.06320.204644.379-76.2763-2.1423
290.0043-0.00560.00630.0066-0.00750.00790.03130.0390.00780.03480.0890.0849-0.01890.001500.22030.05540.02390.45290.0320.196431.6352-74.020510.9383
300.0305-0.03390.03520.0725-0.02180.0348-0.0231-0.0373-0.02570.05090.0308-0.09370.11090.166400.17030.0343-0.00620.28040.00190.191935.0541-69.19432.024
310.1246-0.0801-0.01030.0937-0.06090.09440.0147-0.17010.14770.04-0.02180.0246-0.05160.0493-0.00090.12890.0237-0.00290.2241-0.04620.169724.8418-61.6347-1.7772
32-0.00150.00160.00090.01080.00570.00190.0596-0.0852-0.0902-0.06420.05230.07840.0421-0.000400.3543-0.0207-0.01930.235-0.00310.238913.5595-71.8685-5.5748
330.0941-0.0688-0.02910.04410.01910.06870.0782-0.06530.2154-0.0463-0.01860.0171-0.0025-0.03970.00440.14170.02960.01920.26460.00520.197810.2602-57.1218-4.0657
340.0043-0.0029-0.00220.00140.00160.00030.03-0.04040.022-0.01180.0780.03040.0956-0.023100.2310.02630.08830.35620.10760.35215.0972-69.29440.8174
350.07290.00890.00010.08260.11650.15160.146-0.16720.25460.03660.01080.1822-0.1268-0.30310.0190.16820.04010.04760.38610.0120.27520.7603-56.72091.6962
360.032-0.03210.03540.093-0.01320.05290.01930.06850.05610.03590.05440.0083-0.0188-0.02020.03820.28140.10970.16280.4244-0.06680.56-4.8369-43.40012.4527
370.00770.00270.02250.01130.02890.11180.0333-0.06530.1395-0.0312-0.04890.0259-0.0217-0.21060.01050.20120.0980.05650.65090.09430.4369-12.4978-52.84671.3302
380.003-0.0012-0.00390.0051-0.00160.00540.0282-0.0315-0.0220.01520.0874-0.0121-0.0099-0.061900.3147-0.08610.04520.8567-0.01990.3046-7.2123-61.850717.5197
390.0051-0.00720.00950.0071-0.01140.01560.0692-0.00150.03920.0177-0.01790.027-0.0867-0.02040.03040.39070.02910.18460.464-0.17980.3937-10.0471-50.832811.9901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 73 THROUGH 88 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 89 THROUGH 102 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 118 THROUGH 135 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 74 THROUGH 88 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 89 THROUGH 99 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 100 THROUGH 117 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 136 THROUGH 148 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 149 THROUGH 165 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 166 THROUGH 204 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 205 THROUGH 214 )
11X-RAY DIFFRACTION11CHAIN A AND (RESID 215 THROUGH 235 )
12X-RAY DIFFRACTION12CHAIN A AND (RESID 236 THROUGH 246 )
13X-RAY DIFFRACTION13CHAIN A AND (RESID 247 THROUGH 269 )
14X-RAY DIFFRACTION14CHAIN A AND (RESID 270 THROUGH 340 )
15X-RAY DIFFRACTION15CHAIN A AND (RESID 341 THROUGH 348 )
16X-RAY DIFFRACTION16CHAIN A AND (RESID 349 THROUGH 381 )
17X-RAY DIFFRACTION17CHAIN A AND (RESID 382 THROUGH 389 )
18X-RAY DIFFRACTION18CHAIN A AND (RESID 390 THROUGH 439 )
19X-RAY DIFFRACTION19CHAIN A AND (RESID 440 THROUGH 455 )
20X-RAY DIFFRACTION20CHAIN A AND (RESID 456 THROUGH 463 )
21X-RAY DIFFRACTION21CHAIN A AND (RESID 464 THROUGH 481 )
22X-RAY DIFFRACTION22CHAIN A AND (RESID 482 THROUGH 494 )
23X-RAY DIFFRACTION23CHAIN B AND (RESID 118 THROUGH 135 )
24X-RAY DIFFRACTION24CHAIN B AND (RESID 136 THROUGH 148 )
25X-RAY DIFFRACTION25CHAIN B AND (RESID 149 THROUGH 160 )
26X-RAY DIFFRACTION26CHAIN B AND (RESID 161 THROUGH 188 )
27X-RAY DIFFRACTION27CHAIN B AND (RESID 189 THROUGH 207 )
28X-RAY DIFFRACTION28CHAIN B AND (RESID 208 THROUGH 224 )
29X-RAY DIFFRACTION29CHAIN B AND (RESID 225 THROUGH 234 )
30X-RAY DIFFRACTION30CHAIN B AND (RESID 235 THROUGH 268 )
31X-RAY DIFFRACTION31CHAIN B AND (RESID 269 THROUGH 336 )
32X-RAY DIFFRACTION32CHAIN B AND (RESID 337 THROUGH 347 )
33X-RAY DIFFRACTION33CHAIN B AND (RESID 348 THROUGH 381 )
34X-RAY DIFFRACTION34CHAIN B AND (RESID 382 THROUGH 389 )
35X-RAY DIFFRACTION35CHAIN B AND (RESID 390 THROUGH 436 )
36X-RAY DIFFRACTION36CHAIN B AND (RESID 437 THROUGH 449 )
37X-RAY DIFFRACTION37CHAIN B AND (RESID 450 THROUGH 473 )
38X-RAY DIFFRACTION38CHAIN B AND (RESID 474 THROUGH 482 )
39X-RAY DIFFRACTION39CHAIN B AND (RESID 483 THROUGH 494 )

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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

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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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