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- PDB-2xbo: Equine Rhinitis A Virus in Complex with its Sialic Acid Receptor -

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Basic information

Entry
Database: PDB / ID: 2xbo
TitleEquine Rhinitis A Virus in Complex with its Sialic Acid Receptor
Components(P1) x 4
KeywordsVIRUS / CAPSID
Function / homology
Function and homology information


icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / cytoplasm
Similarity search - Function
Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Jelly Rolls - #20 / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
3'-sialyl-alpha-lactose / Genome polyprotein
Similarity search - Component
Biological speciesEQUINE RHINITIS A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 4 Å
AuthorsFry, E.E. / Tuthill, T.J. / Harlos, K. / Walter, T.S. / Rowlands, D.J. / Stuart, D.I.
CitationJournal: J.Gen.Virol. / Year: 2010
Title: The Crystal Structure of Equine Rhinitis a Virus in Complex with its Sialic Acid Receptor.
Authors: Fry, E.E. / Tuthill, T.J. / Harlos, K. / Walter, T.S. / Rowlands, D.J. / Stuart, D.I.
History
DepositionApr 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: P1
2: P1
3: P1
4: P1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9025
Polymers85,2694
Non-polymers6341
Water00
1
1: P1
2: P1
3: P1
4: P1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,154,140300
Polymers5,116,127240
Non-polymers38,01360
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: P1
2: P1
3: P1
4: P1
hetero molecules
x 5


  • icosahedral pentamer
  • 430 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)429,51225
Polymers426,34420
Non-polymers3,1685
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: P1
2: P1
3: P1
4: P1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 515 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)515,41430
Polymers511,61324
Non-polymers3,8016
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
Length a, b, c (Å)344.800, 531.400, 488.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1, -1.0E-5), (1, -0.00019), (1.0E-5, -0.00019, -1)0.0025, 0.0371, 244.1952
3generate(0.30951, -0.8144, 0.49088), (0.80041, 0.50183, 0.32789), (-0.51337, 0.29142, 0.80717)43.9791, 23.4199, -13.6881
4generate(-0.30947, 0.81438, -0.49092), (0.80051, 0.50177, 0.32774), (0.51324, -0.29156, -0.8072)-43.9678, 23.4607, 257.8788
5generate(-0.8086, -0.51719, 0.2805), (0.48051, -0.30538, 0.8221), (-0.33952, 0.79953, 0.49545)31.8233, 66.0929, -40.5505
6generate(0.80862, 0.51713, -0.28056), (0.48056, -0.30545, 0.82205), (0.33941, -0.79955, -0.4955)-31.7975, 66.1176, 284.7175
7generate(-0.80773, 0.48189, -0.33964), (-0.51798, -0.30496, 0.79918), (0.28154, 0.82145, 0.49594)-20.0364, 68.8944, -43.3725
8generate(0.80774, -0.48186, 0.33967), (-0.51801, -0.305, 0.79915), (-0.28148, -0.82146, -0.49596)20.0222, 68.9087, 287.5307
9generate(0.31006, 0.80055, -0.51282), (-0.81418, 0.5021, 0.29155), (0.49089, 0.32713, 0.80747)-39.5281, 27.8937, -18.2152
10generate(-0.31003, -0.80052, 0.51288), (-0.81427, 0.50205, 0.2914), (-0.49076, -0.32728, -0.80749)39.5092, 27.9352, 262.4031
11generate(-0.02272, 0.99974, -0.00361), (-0.02245, 0.0031, 0.99974), (0.99949, 0.02279, 0.02237)-127.0456, 5.1679, 116.4412
12generate(0.02293, -0.99973, 0.00364), (-0.02268, 0.00312, 0.99974), (-0.99948, -0.02301, -0.0226)127.0364, 5.1654, 127.8049
13generate(0.79523, 0.51887, 0.31366), (-0.51757, 0.3115, 0.79692), (0.31579, -0.79608, 0.51627)-104.4354, -9.4054, 160.6084
14generate(-0.79516, -0.519, -0.31363), (-0.51768, 0.31163, 0.7968), (-0.3158, 0.79594, -0.51647)104.4586, -9.4113, 83.6157
15generate(0.5003, -0.29571, 0.81379), (-0.31975, 0.81034, 0.49103), (-0.80465, -0.50587, 0.31086)-61.5975, -35.6726, 148.6568
16generate(-0.50039, 0.29571, -0.81374), (-0.31953, 0.81044, 0.491), (0.80468, 0.50571, -0.31105)61.5893, -35.6918, 95.5704
17generate(-0.49977, -0.31836, 0.80553), (0.29756, 0.81029, 0.50486), (-0.81344, 0.49201, -0.31023)-57.6973, -37.3554, 97.2348
18generate(0.49967, 0.31839, -0.80558), (0.29782, 0.81016, 0.50492), (0.81341, -0.49221, 0.30999)57.7021, -37.3394, 147.009
19generate(-0.82306, 0.48212, 0.30022), (0.48132, 0.3115, 0.81933), (0.3015, 0.81886, -0.48843)-98.0845, -12.1504, 77.278
20generate(0.8231, -0.48202, -0.30028), (0.48127, 0.31136, 0.81941), (-0.30148, -0.81897, 0.48826)98.073, -12.1345, 166.9344
21generate(-0.02497, -0.02063, 0.99948), (0.99969, 0.00167, 0.02501), (-0.00219, 0.99979, 0.02058)-119.4797, 124.2427, -8.0728
22generate(0.02494, 0.02076, -0.99947), (0.99969, 0.00165, 0.02498), (0.00217, -0.99978, -0.02072)119.4483, 124.2524, 252.2513
23generate(-0.53727, 0.30115, 0.78782), (0.29699, -0.8067, 0.51091), (0.78939, 0.50847, 0.34398)-134.7267, 168.1755, 15.0616
24generate(0.53745, -0.30107, -0.78772), (0.29704, -0.80665, 0.51097), (-0.78925, -0.5086, -0.3441)134.689, 168.1501, 229.1452
25generate(-0.32851, 0.81835, 0.47158), (-0.81661, -0.49697, 0.29355), (0.47458, -0.28866, 0.83153)-162.111, 155.1688, 57.3798
26generate(0.32866, -0.81841, -0.47137), (-0.81659, -0.497, 0.29355), (-0.47451, 0.28844, -0.83165)162.0825, 155.1744, 186.8472
27generate(0.31211, 0.81546, 0.48746), (-0.80126, 0.50162, -0.32612), (-0.51046, -0.2888, 0.80996)-163.5611, 103.3617, 60.0384
28generate(-0.31224, -0.81551, -0.48728), (-0.80124, 0.50165, -0.32613), (0.51041, 0.2886, -0.81006)163.5397, 103.3578, 184.1799
29generate(0.49955, 0.29748, 0.81361), (0.32034, 0.80918, -0.49255), (-0.80488, 0.50669, 0.30893)-137.3079, 84.4707, 19.7362
30generate(-0.49976, -0.29736, -0.81352), (0.32039, 0.80914, -0.49258), (0.80473, -0.50682, -0.30911)137.2653, 84.4865, 224.4821
31generate(0.99887, 0.00061, 0.04753), (0.00048, -1, 0.00293), (0.04753, -0.00291, -0.99887)-5.9375, 255.1501, 244.6808
32generate(-0.99887, -0.00061, -0.04753), (0.00048, -1, 0.00274), (-0.04753, 0.00272, 0.99887)5.9375, 255.187, -0.4859
33generate(0.28421, -0.80049, 0.52767), (-0.80286, -0.49954, -0.32539), (0.52406, -0.33117, -0.78465)37.8581, 231.2894, 260.4532
34generate(-0.28424, 0.8005, -0.52764), (-0.80276, -0.4996, -0.32553), (-0.5242, 0.33104, 0.78462)-37.868, 231.3314, -16.2636
35generate(-0.82384, -0.47865, 0.3036), (-0.48192, 0.30953, -0.81972), (0.29839, -0.82163, -0.48568)24.0596, 188.2263, 286.5046
36generate(0.82383, 0.47871, -0.30355), (-0.48188, 0.30947, -0.81977), (-0.29849, 0.82163, 0.48563)-24.0825, 188.2504, -42.3399
37generate(-0.79432, 0.51945, -0.31501), (0.51839, 0.3092, -0.79729), (-0.31675, -0.7966, -0.51488)-27.8346, 185.5161, 286.8183
38generate(0.79431, -0.51949, 0.31497), (0.51836, 0.30917, -0.79732), (0.31683, 0.79658, 0.51486)27.8528, 185.5304, -42.6588
39generate(0.3313, 0.8161, -0.47352), (0.81693, -0.49921, -0.28881), (-0.47208, -0.29115, -0.83209)-46.4312, 226.6581, 261.1058
40generate(-0.33133, -0.81613, 0.47345), (0.81685, -0.49925, -0.28896), (0.4722, 0.291, 0.83207)46.4514, 226.699, -16.9165
41generate(0.02413, 0.99971, 0.00149), (0.02249, 0.00094, -0.99975), (-0.99946, 0.02415, -0.02246)-127.9372, 249.6796, 121.7681
42generate(-0.02434, -0.9997, -0.00152), (0.02226, 0.00097, -0.99975), (0.99946, -0.02437, 0.02223)127.9432, 249.6756, 122.4791
43generate(0.80732, 0.48205, 0.34038), (0.52009, -0.3087, -0.79638), (-0.27882, 0.81996, -0.49993)-103.2986, 264.4203, 78.4181
44generate(-0.80739, -0.48191, -0.34041), (0.51999, -0.30857, -0.79649), (0.2788, -0.82009, 0.49973)103.2746, 264.4127, 165.8038
45generate(0.46106, -0.31783, 0.8285), (0.32164, -0.81031, -0.48985), (0.82702, 0.49233, -0.27137)-60.7378, 291.1739, 92.2677
46generate(-0.46097, 0.31783, -0.82855), (0.32187, -0.8102, -0.48987), (-0.82699, -0.4925, 0.27118)60.7461, 291.1533, 151.9604
47generate(-0.53701, -0.29372, 0.79079), (-0.29919, -0.81017, -0.50409), (0.78873, -0.5073, 0.34719)-59.1641, 292.9148, 144.503
48generate(0.53712, 0.29369, -0.79073), (-0.29895, -0.8103, -0.50402), (-0.78876, 0.50711, -0.34743)59.1581, 292.9299, 99.7408
49generate(-0.80632, 0.52109, 0.27984), (-0.48363, -0.30845, -0.81912), (-0.34052, -0.79581, 0.50073)-100.8404, 267.1745, 162.606
50generate(0.80627, -0.52119, -0.27978), (-0.48369, -0.30859, -0.81903), (0.34054, 0.79569, -0.5009)100.8524, 267.1885, 81.6077
51generate(-0.02089, 0.02618, 0.99944), (-0.99978, 0.00238, -0.02096), (-0.00293, -0.99965, 0.02613)-125.4227, 129.8073, 246.5454
52generate(0.02092, -0.02633, -0.99943), (-0.99978, 0.00236, -0.02098), (0.00291, 0.99965, -0.02627)125.4549, 129.8167, -2.3637
53generate(-0.49785, 0.32167, 0.8054), (-0.29692, 0.80933, -0.50678), (-0.81485, -0.49144, -0.30741)-139.3726, 86.1848, 222.3127
54generate(0.49765, -0.32175, -0.8055), (-0.29688, 0.80939, -0.50671), (0.81499, 0.4913, 0.30727)139.4093, 86.1598, 21.8979
55generate(-0.31016, 0.80154, 0.51121), (0.81568, 0.50058, -0.28999), (-0.48834, 0.32704, -0.80906)-164.6661, 99.0877, 179.1787
56generate(0.31, -0.80147, -0.51142), (0.8157, 0.50055, -0.28999), (0.4884, -0.32726, 0.80893)164.6917, 99.0942, 65.0506
57generate(0.28318, 0.80357, 0.52353), (0.80194, -0.49779, 0.33029), (0.52602, 0.32631, -0.78538)-166.5852, 150.7295, 176.3557
58generate(-0.28304, -0.80351, -0.5237), (0.80196, -0.49776, 0.33029), (-0.52607, -0.32651, 0.78527)166.6037, 150.7247, 67.8644
59generate(0.46232, 0.32402, 0.82539), (-0.3208, -0.80667, 0.49635), (0.82665, -0.49426, -0.26899)-142.272, 169.9761, 218.0908
60generate(-0.46209, -0.32414, -0.82547), (-0.32075, -0.80671, 0.49632), (-0.8268, 0.49412, 0.26881)142.3132, 169.9909, 26.1315

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Components

#1: Protein P1


Mass: 27501.094 Da / Num. of mol.: 1 / Fragment: CAPSID PROTEIN VP1, RESIDUES 537-784 / Source method: isolated from a natural source / Source: (natural) EQUINE RHINITIS A VIRUS / Strain: NM11/67 / References: UniProt: B9VV85
#2: Protein P1


Mass: 25269.607 Da / Num. of mol.: 1 / Fragment: CAPSID PROTEIN VP2, RESIDUES 81-310 / Source method: isolated from a natural source / Source: (natural) EQUINE RHINITIS A VIRUS / Strain: NM11/67 / References: UniProt: B9VV85
#3: Protein P1


Mass: 24387.523 Da / Num. of mol.: 1 / Fragment: CAPSID PROTEIN VP3, RESIDUES 311-536 / Source method: isolated from a natural source / Source: (natural) EQUINE RHINITIS A VIRUS / Strain: NM11/67 / References: UniProt: B9VV85
#4: Protein P1


Mass: 8110.563 Da / Num. of mol.: 1 / Fragment: CAPSID PROTEIN VP4, RESIDUES 1-80 / Source method: isolated from a natural source / Source: (natural) EQUINE RHINITIS A VIRUS / Strain: NM11/67 / References: UniProt: B9VV85
#5: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / 3'-sialyl-alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-alpha-lactose
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE

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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

CrystalDescription: NONE
Crystal growpH: 4.6 / Details: pH 4.6

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.87
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 4→25 Å / Num. obs: 28861 / % possible obs: 7.8 % / Observed criterion σ(I): 0 / Redundancy: 1.1 % / Rmerge(I) obs: 0.37
Reflection shellRedundancy: 1.1 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 4→20 Å / Cross valid method: NONE / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.247 --
obs0.247 28779 7.8 %
Refinement stepCycle: LAST / Resolution: 4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5372 0 43 0 5415
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.23
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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  • 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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