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- PDB-6n1z: Importin-9 bound to H2A-H2B -

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Basic information

Entry
Database: PDB / ID: 6n1z
TitleImportin-9 bound to H2A-H2B
Components
  • Histone H2A
  • Histone H2B 1.1
  • Importin-9
KeywordsTRANSPORT PROTEIN / Importin-9 / karyopherin / histone / H2A / H2B / histone chaperone / Ran GTPase / nucleosome / NLS / nuclear pore complex.
Function / homology
Function and homology information


proteasome localization / histone chaperone activity / nuclear import signal receptor activity / small GTPase binding / structural constituent of chromatin / protein import into nucleus / nucleosome / nuclear envelope / histone binding / protein heterodimerization activity ...proteasome localization / histone chaperone activity / nuclear import signal receptor activity / small GTPase binding / structural constituent of chromatin / protein import into nucleus / nucleosome / nuclear envelope / histone binding / protein heterodimerization activity / DNA binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site ...Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Armadillo-like helical / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Histone H2A / Importin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsTomchick, D.R. / Chook, Y.M. / Padavannil, A.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM069909 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM98256-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM083960 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM109824 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112108 United States
Welch FoundationI-1532 United States
CitationJournal: Elife / Year: 2019
Title: Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone.
Authors: Padavannil, A. / Sarkar, P. / Kim, S.J. / Cagatay, T. / Jiou, J. / Brautigam, C.A. / Tomchick, D.R. / Sali, A. / D'Arcy, S. / Chook, Y.M.
History
DepositionNov 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin-9
B: Histone H2A
C: Histone H2B 1.1
D: Importin-9
E: Histone H2A
F: Histone H2B 1.1


Theoretical massNumber of molelcules
Total (without water)287,6556
Polymers287,6556
Non-polymers00
Water6,395355
1
A: Importin-9
B: Histone H2A
C: Histone H2B 1.1


Theoretical massNumber of molelcules
Total (without water)143,8283
Polymers143,8283
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-53 kcal/mol
Surface area49310 Å2
MethodPISA
2
D: Importin-9
E: Histone H2A
F: Histone H2B 1.1


Theoretical massNumber of molelcules
Total (without water)143,8283
Polymers143,8283
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-53 kcal/mol
Surface area47980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.424, 223.289, 131.833
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1172-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESID 15 THROUGH 233 OR RESID 236...
211(CHAIN D AND (RESID 15 THROUGH 617 OR RESID 619...
112(CHAIN B AND RESID 17 THROUGH 101)
212CHAIN E
113CHAIN C
213(CHAIN F AND (RESID 26 THROUGH 28 OR RESID 31 THROUGH 82 OR RESID 85 THROUGH 121))

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Importin-9 / Imp9 / Ran-binding protein 9 / RanBP9


Mass: 116062.320 Da / Num. of mol.: 2 / Fragment: IMPORTIN-9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IPO9, IMP9, KIAA1192, RANBP9, HSPC273 / Plasmid: pGEX-4T3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96P70
#2: Protein Histone H2A


Mass: 14109.436 Da / Num. of mol.: 2 / Fragment: HISTONE H2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591, XELAEV_18003602mg / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) plysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#3: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2 / Fragment: HISTONE H2B 1.1 / Mutation: S33T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) plysS / References: UniProt: P02281
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 3.26 Å3/Da / Density % sol: 62.27 % / Mosaicity: 0.628 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.04 M MES, 0.11 M potassium acetate, 2 mM magnesium acetate, 2 mM DTT, 3.0 M potassium formate, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97938 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2015 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 103239 / % possible obs: 97.7 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 7
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 8.2 % / Rmerge(I) obs: 2.086 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→45.44 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.3
RfactorNum. reflection% reflection
Rfree0.238 1978 2.11 %
Rwork0.209 --
obs0.21 93883 90.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 57.12 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17795 0 0 355 18150
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A8758X-RAY DIFFRACTIONPOSITIONAL
12D8758X-RAY DIFFRACTIONPOSITIONAL
21B788X-RAY DIFFRACTIONPOSITIONAL
22E788X-RAY DIFFRACTIONPOSITIONAL
31C847X-RAY DIFFRACTIONPOSITIONAL
32F847X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.76760.374550.32186X-RAY DIFFRACTION31
2.7676-2.84240.26511070.29865010X-RAY DIFFRACTION70
2.8424-2.9260.29211530.26736878X-RAY DIFFRACTION96
2.926-3.02050.27561500.24917078X-RAY DIFFRACTION99
3.0205-3.12840.2921530.24667057X-RAY DIFFRACTION99
3.1284-3.25360.26891550.24377116X-RAY DIFFRACTION99
3.2536-3.40160.26691470.22887099X-RAY DIFFRACTION98
3.4016-3.58090.23081510.21397056X-RAY DIFFRACTION98
3.5809-3.80520.24491540.19757059X-RAY DIFFRACTION98
3.8052-4.09880.25711480.18877049X-RAY DIFFRACTION97
4.0988-4.51090.17461490.16757077X-RAY DIFFRACTION97
4.5109-5.16290.21721520.1687069X-RAY DIFFRACTION97
5.1629-6.50170.23131490.21537068X-RAY DIFFRACTION96
6.5017-45.4420.19031550.18947103X-RAY DIFFRACTION93
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)
11.03350.0311-0.30150.69810.23042.84040.37490.4393-0.1751-0.4444-0.21910.03910.34990.0723-0.09350.7197-0.0368-0.05190.5845-0.11020.270517.8375-2.0119-6.9845
22.56520.29470.25441.42030.04341.49390.0328-0.0362-0.0379-0.0279-0.11660.06590.0589-0.22680.07480.1853-0.0407-0.05110.17950.00420.073833.736811.974227.9147
31.0011-0.033-0.00541.483-1.03981.3565-0.06190.24890.5433-0.13980.0178-0.0661-0.0632-0.06290.0430.1506-0.0331-0.0630.19140.13220.401254.499142.559715.0766
40.9167-0.1443-0.07650.2577-0.14030.49370.06920.63010.7371-0.0615-0.0465-0.1916-0.2494-0.01640.16770.45480.0031-0.18950.47680.68961.028432.605563.7613-4.8527
52.3541-0.025-0.193.33880.38972.78660.2502-0.14920.67150.6334-0.1244-0.1011-0.0202-0.1805-0.03760.4781-0.0239-0.10210.42260.18670.641610.262159.76758.0042
64.46650.01091.05721.51290.04694.68560.042-0.59540.35780.6149-0.07620.4963-0.2076-0.5490.04670.8647-0.03410.18510.46160.0930.5627.122933.783615.496
74.9364-4.6293-1.25444.9306-0.48495.01390.2243-0.92460.27890.69710.0395-0.8287-0.33720.4691-0.22321.2474-0.1879-0.21630.69140.08270.631322.16135.402620.2223
81.67640.33980.07375.44871.89631.65790.17710.29220.0384-0.25840.02020.0503-0.43140.0042-0.15050.7707-0.09960.00520.35590.11870.336412.983526.2734-2.5838
95.78124.07690.25969.15833.99722.68060.2370.1089-0.1975-0.6350.2422-0.12980.78030.0737-0.41890.945-0.18970.2810.47020.07060.67624.132532.9113-4.9725
103.8834-2.3317-1.77371.40061.0660.81030.14610.36580.1497-0.1773-0.0565-0.0746-0.43710.1817-0.07751.03260.3056-0.06660.9510.04370.486524.910221.609914.0617
113.50811.49561.09153.69171.30826.31670.0555-0.01560.2596-0.12020.02610.6274-0.198-0.4822-0.06440.674-0.0496-0.05760.31470.12040.47097.075523.83746.6816
122.3106-1.0978-0.48344.57230.53794.14610.04990.07340.5003-0.2030.2719-0.5474-0.62920.8772-0.25790.7505-0.17660.00410.49040.07490.451420.283128.34925.966
132.0024-2.0351-1.56992.81610.18514.83780.203-0.25990.52080.4381-0.1034-0.4471-1.03010.5014-0.15681.4461-0.2380.20810.42260.05460.70416.735343.61427.2901
141.1718-0.33760.10861.4662-0.12572.97190.1854-0.37-0.2710.54360.01750.02860.4622-0.2064-0.11230.5678-0.0126-0.09110.51370.07560.2604109.4463-1.283676.8914
150.8836-0.60860.92871.30890.24431.82930.15970.4548-0.21290.05450.1048-0.37770.30420.6951-0.21390.25050.0901-0.02190.5036-0.02680.1975108.27412.530245.9297
164.0026-0.598-0.49520.9247-0.02351.7179-0.0495-0.13220.25940.2061-0.0264-0.06240.12740.44590.01660.2090.01660.00370.279-0.00860.072990.846412.692545.6096
170.9861-0.2696-0.09931.09440.45530.9902-0.0582-0.02580.4928-0.1219-0.0981-0.00390.05680.147-0.0020.0252-0.0497-0.06840.2122-0.05090.296876.081133.831846.0013
181.27860.51660.15450.9781-0.0170.7878-0.1128-0.61620.85120.2789-0.05050.2644-0.39640.0327-0.0260.3024-0.0365-0.08930.5265-0.44610.958887.540864.421270.5938
191.62640.64110.70411.5093-0.21531.835-0.0024-0.25380.7556-0.04030.0053-0.06310.0111-0.0378-0.16120.1743-0.0905-0.05960.3493-0.33840.8368111.647360.472766.4603
203.0248-0.2941-0.12763.78180.07514.78090.03570.56750.8034-0.71460.15750.18440.06360.1733-0.04930.344-0.0398-0.05160.3754-0.01760.5281117.133160.400752.0819
215.5991.00051.90082.25051.88641.80050.0560.7120.2652-0.7640.1692-0.5797-0.27860.5252-0.16750.73510.01140.3020.4135-0.04920.4537120.321832.821452.1061
223.02153.04041.10853.07841.39484.64560.21820.8384-0.7724-0.42990.08230.220.48660.0105-0.25190.89750.19670.04130.4281-0.03450.4479108.439731.177547.7416
235.6107-3.26183.07162.6605-0.44844.0214-0.08581.3871.5707-0.80410.29591.3046-0.6525-0.9208-0.22431.00270.2758-0.14460.72310.18381.0749100.874738.566246.6442
241.7203-0.0647-0.21893.3509-0.05272.96460.2933-0.00680.16530.19030.0016-0.2746-0.31180.1136-0.22110.57430.07650.06010.287-0.12490.2104115.674130.566666.8329
258.0162-1.0887-4.07872.5562-0.75332.81950.0174-1.07070.2110.8158-0.0272-0.8828-0.26450.36840.01990.6816-0.0013-0.13970.4428-0.06640.3386118.875915.405775.652
264.7787-1.6071-0.63953.6807-0.90539.16630.1839-0.61970.30650.82970.13820.5303-0.7498-0.674-0.30750.49910.13260.14060.46830.11750.298109.172523.732277.1478
270.98770.4628-0.01080.2173-0.0050.00020.0581-0.64780.19081.39910.3519-0.08910.58670.1252-0.3170.99830.28790.23490.4873-0.01010.6421103.907933.797672.8319
284.7771.87430.96610.73540.37840.19510.1526-0.89780.05580.4354-0.21240.9680.3377-0.81930.06560.851-0.21780.07860.731-0.01860.7934100.928621.084954.3764
290.1168-0.2431-0.36595.4029-1.09481.85530.24130.01610.16110.05990.25160.3095-0.8679-0.6116-0.37350.49320.1570.11220.42490.04340.341111.122126.40962.313
305.9742-2.611-0.01611.1541-0.00660.01450.08790.51461.8366-0.3582-0.19280.3926-1.2992-0.58690.08481.64120.47660.08040.87470.21840.975399.290847.117650.2162
311.05260.9145-1.32521.4920.05313.75310.26020.19030.4242-0.1873-0.0033-0.06-1.0824-0.491-0.41561.17920.18170.29290.3965-0.02960.5913112.900942.77261.2154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 15 THROUGH 228 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 229 THROUGH 491 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 492 THROUGH 706 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 707 THROUGH 852 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 853 THROUGH 1040 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 17 THROUGH 27 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 28 THROUGH 45 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 46 THROUGH 91 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 92 THROUGH 102 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 26 THROUGH 35 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 36 THROUGH 46 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 47 THROUGH 80 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 81 THROUGH 121 )
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 15 THROUGH 228 )
15X-RAY DIFFRACTION15CHAIN 'D' AND (RESID 229 THROUGH 308 )
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 309 THROUGH 397 )
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 398 THROUGH 706 )
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 707 THROUGH 795 )
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 796 THROUGH 909 )
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESID 910 THROUGH 1041 )
21X-RAY DIFFRACTION21CHAIN 'E' AND (RESID 17 THROUGH 27 )
22X-RAY DIFFRACTION22CHAIN 'E' AND (RESID 28 THROUGH 37 )
23X-RAY DIFFRACTION23CHAIN 'E' AND (RESID 38 THROUGH 45 )
24X-RAY DIFFRACTION24CHAIN 'E' AND (RESID 46 THROUGH 74 )
25X-RAY DIFFRACTION25CHAIN 'E' AND (RESID 75 THROUGH 80 )
26X-RAY DIFFRACTION26CHAIN 'E' AND (RESID 81 THROUGH 91 )
27X-RAY DIFFRACTION27CHAIN 'E' AND (RESID 92 THROUGH 101 )
28X-RAY DIFFRACTION28CHAIN 'F' AND (RESID 25 THROUGH 35 )
29X-RAY DIFFRACTION29CHAIN 'F' AND (RESID 36 THROUGH 79 )
30X-RAY DIFFRACTION30CHAIN 'F' AND (RESID 80 THROUGH 88 )
31X-RAY DIFFRACTION31CHAIN 'F' AND (RESID 89 THROUGH 121 )

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