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- PDB-4ove: X-ray Crystal Structure of Mouse Netrin-1 -

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Basic information

Entry
Database: PDB / ID: 4ove
TitleX-ray Crystal Structure of Mouse Netrin-1
ComponentsNetrin-1
KeywordsAPOPTOSIS / similar to laminin gamma-1 / domain VI: beta-sandwich jelly-roll / domains V-1 / V-2 / V-3: laminin-type epidermal growth factor / structural calcium / axon guidance cue / survival factor / neogenin / DCC / UNC5A / UNC5B / UNC5C / UNC5D / DSCAM / extracellular matrix
Function / homology
Function and homology information


regulation of glial cell migration / chemorepulsion of axon / anterior/posterior axon guidance / Cdc42 protein signal transduction / motor neuron migration / tissue development / negative regulation of axon extension / mammary gland development / substrate-dependent cell migration, cell extension / mammary gland duct morphogenesis ...regulation of glial cell migration / chemorepulsion of axon / anterior/posterior axon guidance / Cdc42 protein signal transduction / motor neuron migration / tissue development / negative regulation of axon extension / mammary gland development / substrate-dependent cell migration, cell extension / mammary gland duct morphogenesis / motor neuron axon guidance / nuclear migration / positive regulation of cell motility / inner ear morphogenesis / regulation of synapse assembly / dendrite development / basement membrane / glial cell proliferation / positive regulation of axon extension / positive regulation of glial cell proliferation / regulation of cell migration / axonogenesis / axon guidance / cell periphery / animal organ morphogenesis / neuron migration / cell-cell adhesion / actin cytoskeleton / collagen-containing extracellular matrix / Ras protein signal transduction / cell population proliferation / glutamatergic synapse / synapse / apoptotic process / extracellular region / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
: / Laminin, N-terminal / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain ...: / Laminin, N-terminal / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Galactose-binding domain-like / EGF-like domain signature 1. / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.64 Å
AuthorsMeier, M. / Nikodemus, D. / Reuten, R. / Patel, T.R. / Orriss, G. / Okun, N. / Koch, M. / Stetefeld, J.
CitationJournal: Cancer Cell / Year: 2016
Title: Structural Decoding of the Netrin-1/UNC5 Interaction and its Therapeutical Implications in Cancers.
Authors: Grandin, M. / Meier, M. / Delcros, J.G. / Nikodemus, D. / Reuten, R. / Patel, T.R. / Goldschneider, D. / Orriss, G. / Krahn, N. / Boussouar, A. / Abes, R. / Dean, Y. / Neves, D. / Bernet, A. ...Authors: Grandin, M. / Meier, M. / Delcros, J.G. / Nikodemus, D. / Reuten, R. / Patel, T.R. / Goldschneider, D. / Orriss, G. / Krahn, N. / Boussouar, A. / Abes, R. / Dean, Y. / Neves, D. / Bernet, A. / Depil, S. / Schneiders, F. / Poole, K. / Dante, R. / Koch, M. / Mehlen, P. / Stetefeld, J.
History
DepositionFeb 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Derived calculations
Revision 1.2Feb 17, 2016Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: Netrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6266
Polymers48,9941
Non-polymers1,6325
Water1,74797
1
A: Netrin-1
hetero molecules

A: Netrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,25212
Polymers97,9892
Non-polymers3,26410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6770 Å2
ΔGint-9 kcal/mol
Surface area46900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.754, 69.754, 334.802
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsNetrin-1 without C-terminal domain forms monomers, dimers, and higher order oligomers in solution, as evidenced by dynamic light scattering (DLS), size exclusion chromatography (SEC), and small angle X-ray scattering (SAXS). In the presence of glycine and high concentrations of sodium chloride, the dimeric form can be stabilized. The asymmetric unit contains one monomer. A dimer that resembles the shape model obtained from SAXS can be obtained by applying the following crystallographic symmetry operation: x-y, -y, -z+1/3.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Netrin-1


Mass: 48994.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ntn1 / Plasmid: pCEP-Pu / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: O09118

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 99 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.8 Å3/Da / Density % sol: 74.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.1 M HEPES, 2.7-2.8 M NaCl, 0.02-0.2 M glycine, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCLSI 08B1-111.2544
SYNCHROTRONSLS X06SA21.25470, 1.25520, 1.24210
Detector
TypeIDDetectorDateDetails
RAYONIX MX-3001CCDOct 14, 2011vertical collimating mirror, toroidal focusing mirror
RAYONIX MX-2252CCDOct 12, 2005dynamically bendable mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromator (DCM) with water-cooled first crystalSINGLE WAVELENGTHMx-ray1
2liquid nitrogen cooled fixed-exit Si(111) monochromatorSIRASMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.25441
21.25471
31.25521
41.24211
ReflectionResolution: 2.5→50 Å / Num. all: 27279 / Num. obs: 27279 / % possible obs: 80.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 60.1 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 8.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.64→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.862 / SU B: 29.397 / SU ML: 0.267 / SU R Cruickshank DPI: 0.359 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The diffraction pattern of Netrin-1 crystals shows strong anisotropy. The resolution limits in direction a*/b* are 44.85 - 2.80 A and in ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The diffraction pattern of Netrin-1 crystals shows strong anisotropy. The resolution limits in direction a*/b* are 44.85 - 2.80 A and in direction c* 44.85 - 2.64 A. Completeness of the dataset in the resolution range of INF - 2.80 A is 0.999, in the range of INF - 2.64 A it is 0.896. The Wilson B-factor calculated from the linear range of the data is 68.0 A**2. The ellipsoidal outer shell in the range of 2.90 - 2.80 A (a*/b*) and 2.74 - 2.64 A (c*) contains 2564 reflections, has a completeness of 1.0, a redundancy of 10.8, I/sigmaI of 2.0, Rmeas of 1.344, Rmerge of 1.280 and Rpim of 0.406. For refinement, an ellipsoidal trunction (limit of 2.80 A in a*/b*, limit of 2.50 A in c*), anisotropic scaling and a negative isotropic B-factor correction of 50% of the B-factor in direction of the lowest fall-off (c*) was applied according to the procedure described by M. Strong, M.R. Sawaya, S. Wang, M. Phillips, D. Cascio, D. Eisenberg, Proc Natl Acad Sci USA. 103, 8060-8-65, 2006. After above anisotropy correction and conversion to amplitudes, the completeness of the refinement dataset is as follows: INF - 2.80 A: 0.996, INF - 2.50 A: 0.807. The Wilson B-factor calculated from the linear range of data is 60.1 A**2.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1308 5.1 %RANDOM
Rwork0.23 ---
obs0.233 24458 89.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.552 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0.42 Å2-0 Å2
2---0.84 Å20 Å2
3---2.72 Å2
Refinement stepCycle: LAST / Resolution: 2.64→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 105 97 3511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193662
X-RAY DIFFRACTIONr_bond_other_d0.0020.023265
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.9884985
X-RAY DIFFRACTIONr_angle_other_deg0.85737484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.2615.148440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25922.443176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.16415557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2431540
X-RAY DIFFRACTIONr_chiral_restr0.0860.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02897
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_it3.6214.681726
X-RAY DIFFRACTIONr_mcbond_other3.6224.6791724
X-RAY DIFFRACTIONr_mcangle_it5.9517.0132163
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8785.2571936
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refinement TLS params.Method: refined / Origin x: 29.0771 Å / Origin y: 15.8929 Å / Origin z: 3.8209 Å
111213212223313233
T0.0711 Å20.0258 Å20.0085 Å2-0.0822 Å20.0231 Å2--0.0237 Å2
L0.5237 °20.3001 °2-0.9402 °2-0.3894 °2-0.9701 °2--4.0219 °2
S-0.051 Å °0.1256 Å °0.0392 Å °-0.0033 Å °0.018 Å °-0.0184 Å °-0.027 Å °-0.2278 Å °0.0331 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 456
2X-RAY DIFFRACTION1A509
3X-RAY DIFFRACTION1A501 - 505
4X-RAY DIFFRACTION1A506 - 507
5X-RAY DIFFRACTION1A508
6X-RAY DIFFRACTION1A510
7X-RAY DIFFRACTION1A601 - 697

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