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- PDB-4dpv: PARVOVIRUS/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 4dpv
TitlePARVOVIRUS/DNA COMPLEX
Components
  • DNA (5'-D(*AP*TP*AP*CP*CP*TP*CP*TP*TP*GP*C)-3')
  • PROTEIN (PARVOVIRUS COAT PROTEIN)
KeywordsVirus/DNA / COMPLEX (VIRUS-DNA) / FULL CAPSID / SINGLE-STRANDED DNA / VIRUS / Icosahedral virus / Virus-DNA complex
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / T=1 icosahedral viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Beta Complex / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Capsid protein VP1
Similarity search - Component
Biological speciesCanine parvovirus
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsChapman, M.S. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Canine parvovirus capsid structure, analyzed at 2.9 A resolution.
Authors: Xie, Q. / Chapman, M.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structural Refinement of the DNA-Containing Capsid of Canine Parvovirus Using a New Restrained Real Space Method
Authors: Chapman, M.S. / Rossmann, M.G.
#2: Journal: Structure / Year: 1995
Title: Single-Stranded DNA-Protein Interactions in Canine Parvovirus
Authors: Chapman, M.S. / Rossmann, M.G.
#3: Journal: Acta Crystallogr.,Sect.A / Year: 1995
Title: Restrained Real-Space Macromolecular Atomic Refinement Using a New Resolution- Dependent Electron Density Function
Authors: Chapman, M.S.
#4: Journal: Virology / Year: 1993
Title: Structure, Sequence, and Function Correlations Among Parvoviruses
Authors: Chapman, M.S. / Rossmann, M.G.
#5: Journal: Acta Crystallogr.,Sect.A / Year: 1992
Title: Ab Initio Phase Determination for Spherical Viruses: Parameter Determination for Spherical-Shell Models
Authors: Chapman, M.S. / Tsao, J. / Rossmann, M.G.
#6: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure Determination of Monoclinic Canine Parvovirus
Authors: Tsao, J. / Chapman, M.S. / Wu, H. / Agbandje, M. / Keller, W. / Rossmann, M.G.
#7: Journal: Science / Year: 1991
Title: The Three-Dimensional Structure of Canine Parvovirus and its Functional Implications
Authors: Tsao, J. / Chapman, M.S. / Agbandje, M. / Keller, W. / Smith, K. / Wu, H. / Luo, M. / Smith, T.J. / Rossmann, M.G. / Compans, R.W. / al., et
#8: Journal: J.Mol.Biol. / Year: 1988
Title: Preliminary X-Ray Crystallographic Analysis of Canine Parvovirus Crystals
Authors: Luo, M. / Tsao, J. / Rossmann, M.G. / Basak, S. / Compans, R.W.
History
DepositionFeb 1, 1996Processing site: NDB
SupersessionApr 1, 1997ID: 3DPV
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_peptide_omega.omega / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_angle.linker_flag / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Remark 700SHEET THE STRUCTURE OF CANINE PARVOVIRUS FOLLOWS THE CANONICAL PICORNA-VIRUS LIKE "JELLY ROLL" ...SHEET THE STRUCTURE OF CANINE PARVOVIRUS FOLLOWS THE CANONICAL PICORNA-VIRUS LIKE "JELLY ROLL" BARREL. THE SHEET IDENTIFIED AS "BDG" IS THAT REFERRED TO AS "BIDG" IN THE LITERATURE WITH STRANDS 1 TO 5 CORRESPONDING TO STRANDS A, B, I, D, AND G. THE SHEET IDENTIFIED AS "CHF" IS THE SO-CALLED CHEF SHEET WITH STRANDS 1 TO 4 CORRESPONDING TO STRANDS C, H, E, AND F. THESE TWO SHEETS ARE LOOSELY CONNECTED TOGETHER BY HYDROGEN BONDS BETWEEN STRAND 4 OF "CHF" AND RESIDUE 45 IMMEDIATELY PRECEDING STRAND 1 OF "BDG" OF A FIVE-FOLD RELATED PROTOMER THAT IS GENERATED USING THE SYMMETRY OPERATORS LISTED BELOW. CPV CONTAINS SEVERAL LONG LOOPS BETWEEN STRANDS OF "BDG" AND "CHF" WITH LITTLE ORGANIZED SECONDARY STRUCTURE. THERE ARE STRANDS WITHIN THE LOOPS THAT ARE LOOSELY HYDROGEN-BONDED TOGETHER. WITH FEWER HYDROGEN BONDS AND LESS REGULAR SECONDARY STRUCTURE THEY MUST BE REGARDED MORE TENTATIVELY. THIS IS WHY THE SHEET "LP2" HAS BEEN IDENTIFIED SEPARATELY, ALTHOUGH IT COULD BE CONSIDERED TO BE AN EXTENSION OF SHEET "CHF", EXTENDING FROM STRAND 1. STRAND 1 OF "LP2" HAS A BULGE AND A CHANGE OF DIRECTION AT RESIDUE 107, AFTER WHICH IT BECOMES STRAND 1 OF "CHF". THE MIDDLE STRAND OF "LP2" CONTAINS TWO SEGMENTS THAT RUN IN THE SAME GENERAL DIRECTION, BUT ARE SEPARATED BY NON-BETA STRUCTURE. THE FIRST SEGMENT (206 - 211) HYDROGEN BONDS ON ONE SIDE ONLY, TO RESIDUES 103 - 111, AND THE SECOND SEGMENT (215 - 218) HYDROGEN BONDS ON THE OPPOSITE SIDE TO RESIDUES 230 - 235. IN ORDER TO REPRESENT THE BIFURCATED SHEET STRUCTURE IN THE *SHEET* RECORDS BELOW, TWO SHEETS, *BDG* AND *CDG* ARE DEFINED. STRANDS 1 - 4 OF THESE SHEETS ARE IDENTICAL. THE CHAIN DESIGNATORS IN THE SECONDARY STRUCTURE LIST REFER TO THE NON-CRYSTALLOGRAPHIC ICOSAHEDRAL SYMMETRY OPERATORS LABELED "A" TO "H" IN *REMARK 8*, AND ARE USED WHEN A SHEET SPANS TWO SUBUNITS. PDB FORMAT DOES NOT ALLOW STRANDS FROM ANOTHER ASYMMETRIC UNIT TO BE PRESENTED ON SHEET RECORDS. THE FOLLOWING STRANDS COME FROM OTHER ASYMMETRIC UNITS: CHF 6 GLY A 43 PHE A 45 -1 O GLY A 43 N LEU Z 254 GH1 4 TRP F 414 ASN F 417 -1 N TRP F 414 O PHE Z 345 GH1 4 ASN F 428 LEU F 430 -1 N LEU F 430 O ILE F 415 GH2 3 GLY F 315 THR F 317 -1 N THR F 317 O ARG Z 377

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: DNA (5'-D(*AP*TP*AP*CP*CP*TP*CP*TP*TP*GP*C)-3')
Z: PROTEIN (PARVOVIRUS COAT PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0876
Polymers67,9902
Non-polymers974
Water0
1
N: DNA (5'-D(*AP*TP*AP*CP*CP*TP*CP*TP*TP*GP*C)-3')
Z: PROTEIN (PARVOVIRUS COAT PROTEIN)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,085,216360
Polymers4,079,383120
Non-polymers5,833240
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
N: DNA (5'-D(*AP*TP*AP*CP*CP*TP*CP*TP*TP*GP*C)-3')
Z: PROTEIN (PARVOVIRUS COAT PROTEIN)
hetero molecules
x 5


  • icosahedral pentamer
  • 340 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)340,43530
Polymers339,94910
Non-polymers48620
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
N: DNA (5'-D(*AP*TP*AP*CP*CP*TP*CP*TP*TP*GP*C)-3')
Z: PROTEIN (PARVOVIRUS COAT PROTEIN)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 409 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)408,52236
Polymers407,93812
Non-polymers58324
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
6
N: DNA (5'-D(*AP*TP*AP*CP*CP*TP*CP*TP*TP*GP*C)-3')
Z: PROTEIN (PARVOVIRUS COAT PROTEIN)
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 4.09 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)4,085,216360
Polymers4,079,383120
Non-polymers5,833240
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)263.210, 349.010, 267.320
Angle α, β, γ (deg.)90.00, 90.82, 90.00
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.42068488, 0.85725203, -0.29687292), (-0.8822812, 0.31042008, -0.35387133), (-0.21120183, 0.41079762, 0.88692902)-57.82013, -81.56334, -21.39948
3generate(-0.51666147, 0.50478652, -0.69155208), (-0.57030188, -0.80534622, -0.16178213), (-0.63860948, 0.31081497, 0.7039737)-145.71159, -48.29596, -61.67362
4generate(-0.51665825, -0.57030117, -0.63860429), (0.50479313, -0.8053478, 0.31080687), (-0.69156009, -0.16177534, 0.70397206)-142.21138, 53.82775, -65.16492
5generate(0.42069009, -0.8822764, -0.2112016), (0.85725908, 0.31041752, 0.41079372), (-0.29687772, -0.35386955, 0.88692637)-52.15666, 83.67629, -27.04852
6generate(0.35568263, -0.05656871, -0.93289172), (-0.05656156, -0.99763985, 0.03892195), (-0.93289526, 0.03892701, -0.35804277)-104.14861, -1.15642, -151.27912
7generate(0.39656825, -0.09588011, -0.91298324), (0.8481839, -0.34218591, 0.40434874), (-0.35118021, -0.93472574, -0.05438234)-100.13689, 82.65191, -92.85208
8generate(0.44424723, -0.06485553, -0.89355249), (0.57332314, 0.78699149, 0.2279156), (0.68844039, -0.61354772, 0.38679526)-95.70884, 52.86678, 4.85631
9generate(0.43282882, -0.00636986, -0.9014521), (-0.50129561, 0.82940757, -0.2465529), (0.74924621, 0.55860396, 0.35579759)-96.98388, -49.34977, 6.81638
10generate(0.37809289, -0.00124833, -0.92576508), (-0.89058577, -0.27355525, -0.36335739), (-0.25279433, 0.96185553, -0.10453763)-102.19994, -82.73794, -89.68062
11generate(-0.35593434, 0.03415219, 0.93388505), (0.03415087, -0.99818912, 0.04951822), (0.93388841, 0.04952032, 0.35412345)-27.66827, 5.52497, 18.87972
12generate(-0.37710627, 0.08911386, 0.92187154), (0.88459191, -0.26024008, 0.38701119), (0.27439036, 0.96142291, 0.01931236)-29.85832, 83.90633, -46.73493
13generate(-0.43196735, 0.08309026, 0.89805243), (0.52000189, 0.83651773, 0.17273158), (-0.73689228, 0.54160014, -0.40455038)-35.04999, 45.70333, -141.43035
14generate(-0.44470143, 0.0244058, 0.89534492), (-0.55576816, 0.7764023, -0.29719348), (-0.70240128, -0.62976718, -0.33170088)-36.06856, -56.2888, -134.34069
15generate(-0.39771044, -0.00583958, 0.91749069), (-0.85604061, -0.35750889, -0.37334352), (0.33019798, -0.93388923, 0.13718534)-31.5064, -81.12039, -35.26362
16generate(-0.9997483, 0.02241651, -0.00099333), (0.02241069, 0.99582897, -0.08844017), (-0.00099315, -0.08844734, -0.99608068)-131.91501, -4.36855, -132.0122
17generate(-0.44014687, -0.85048577, 0.28798462), (-0.85049461, 0.29200591, -0.4374886), (0.28799168, -0.43749479, -0.85185904)-75.91654, -84.9949, -103.42511
18generate(0.50438159, -0.52302125, 0.68705214), (-0.52302314, -0.81816301, -0.23886505), (0.68706137, -0.23886739, -0.68621858)12.73855, -50.27414, -66.16394
19generate(0.52853085, 0.55226523, 0.64471148), (0.55227065, -0.80046207, 0.23293951), (0.64471516, 0.23293855, -0.72806878)11.53194, 51.81082, -71.72237
20generate(-0.40107254, 0.88936431, 0.21947599), (0.8893673, 0.32064662, 0.32590719), (0.21947407, 0.32590325, -0.91957408)-77.86887, 80.18204, -112.41884
21generate(-0.47008306, 0.54249723, -0.69621191), (-0.80262572, 0.06541085, 0.5928927), (0.36718292, 0.83750606, 0.40467221)-142.94857, -13.72757, -15.14343
22generate(-0.5293507, -0.52057982, -0.66990983), (-0.52058329, -0.42418877, 0.74098456), (-0.66991505, 0.74098538, -0.04646052)-145.11762, 14.65763, -113.34356
23generate(0.37809413, -0.89058276, -0.25279432), (-0.00124505, -0.27355309, 0.96185605), (-0.92576805, -0.36335516, -0.10454104)-57.71454, 63.49938, -134.052
24generate(0.99819353, -0.05618011, -0.02130482), (0.03768121, 0.30914449, 0.95027027), (-0.04679593, -0.94935449, 0.31069597)-1.52742, 65.30005, -48.65039
25generate(0.4739912, 0.82951202, -0.29535196), (-0.45759928, 0.51863573, 0.72223837), (0.75229172, -0.20718145, 0.62540706)-54.20494, 17.57117, 24.83915
26generate(0.45160793, -0.54172632, 0.70892528), (-0.84228655, 0.00322657, 0.53902786), (-0.29428685, -0.8405478, -0.4548345)10.7049, -19.90315, -115.57199
27generate(0.51821325, 0.5102039, 0.68639765), (-0.47102763, -0.49961889, 0.72698972), (0.71385937, -0.70004584, -0.01859435)13.60724, 16.99988, -20.26517
28generate(-0.37710728, 0.88458742, 0.27439599), (0.08910858, -0.26023547, 0.96142445), (0.92187428, 0.38701059, 0.01930877)-72.6584, 69.42814, -4.04463
29generate(-0.99705111, 0.06403894, 0.04229258), (0.06403289, 0.39055707, 0.9183512), (0.04228836, 0.91834646, -0.39350596)-128.87585, 64.92756, -89.32659
30generate(-0.48487695, -0.81747142, 0.31084645), (-0.51160096, 0.55338558, 0.65729574), (-0.70934056, 0.15967365, -0.68654261)-77.3545, 9.71778, -158.25429
31generate(-0.46433879, -0.59204584, -0.658685), (0.84161151, -0.06334359, -0.53636392), (0.27582724, -0.80340983, 0.52768237)-140.08919, 20.03474, -13.03546
32generate(0.46612608, -0.85242451, -0.23684919), (0.52322114, 0.48147303, -0.70315291), (0.71342225, 0.20382958, 0.67043488)-50.85631, -11.98292, 25.25284
33generate(0.9981933, 0.03768075, -0.04680003), (-0.05617618, 0.30913772, -0.94935642), (-0.02130613, 0.95026852, 0.31070297)-3.21274, -66.45908, -46.96931
34generate(0.39656405, 0.84817475, -0.35117901), (-0.09587305, -0.34218795, -0.93472956), (-0.91298824, 0.40435375, -0.0543761)-63.00028, -68.10953, -129.89334
35generate(-0.50733049, 0.45898232, -0.72934472), (0.45899025, -0.57239407, -0.67948615), (-0.72934973, -0.67947907, 0.07972455)-147.59458, -14.65341, -108.92107
36generate(0.48281392, 0.59127492, 0.64597163), (0.80330076, -0.00529383, -0.59555664), (-0.34872331, 0.80645157, -0.47752008)8.60098, 13.59598, -120.66073
37generate(-0.45498862, 0.86280043, 0.22036137), (0.46838979, 0.44233464, -0.76482137), (-0.75736657, -0.24476912, -0.60538)-81.3652, -19.67458, -156.0557
38generate(-0.99918015, -0.03168541, 0.02519836), (-0.03168735, 0.22465084, -0.97392407), (0.0251999, -0.97392394, -0.2254707)-130.1462, -66.46845, -79.34566
39generate(-0.39770647, -0.85603358, 0.33019125), (-0.00584105, -0.35751361, -0.9338919), (0.91749581, -0.37334571, 0.1371861)-70.32834, -62.11808, 3.45872
40generate(0.51821623, -0.47102292, 0.71385023), (0.51020998, -0.49962724, -0.70004796), (0.68639856, 0.72698686, -0.01858899)15.42214, -12.63554, -22.07539
41generate(-0.47008127, -0.80261524, 0.36718245), (0.5425004, 0.06540758, 0.83750639), (-0.69622165, 0.59289312, 0.4046737)-72.655, 91.13026, -85.25676
42generate(0.43282664, -0.50128833, 0.7492417), (-0.00636905, 0.82940903, 0.55860918), (-0.9014562, -0.24655249, 0.35579832)12.13163, 36.50576, -102.01928
43generate(0.46611967, 0.52321826, 0.71342128), (-0.85243064, 0.48148066, 0.20383342), (-0.23684563, -0.70314889, 0.67043365)11.9589, -42.7293, -37.40123
44generate(-0.41621202, 0.85507125, 0.30922378), (-0.826456, -0.49755234, 0.26346715), (0.37914085, -0.14589538, 0.91376436)-72.93448, -37.07476, 19.29746
45generate(-0.99481603, 0.03566109, 0.09523642), (0.03565879, -0.75469965, 0.65509858), (0.09523086, 0.65510264, 0.74951567)-125.22874, 45.65501, -10.27889
46generate(-0.46434534, 0.84160616, 0.27582855), (-0.59204734, -0.06334013, -0.80341145), (-0.65868707, -0.53635671, 0.52768547)-78.31557, -92.14327, -74.65055
47generate(-0.99613185, -0.02349982, 0.08467162), (-0.02349959, -0.85723534, -0.51439185), (0.08466961, -0.51438478, 0.85336717)-126.01386, -35.55219, -4.11034
48generate(-0.41620696, -0.82644796, 0.3791382), (0.8550772, -0.49755908, -0.14590166), (0.30921853, 0.26346904, 0.91376604)-68.3126, 46.73326, 14.68738
49generate(0.47399284, -0.45759123, 0.7522855), (0.82951977, 0.51862828, -0.20718179), (-0.29535928, 0.72223721, 0.62541287)15.04704, 40.99738, -44.23521
50generate(0.44424168, 0.57332291, 0.68843662), (-0.06485238, 0.78699035, -0.61354518), (-0.89355784, 0.22791772, 0.38680196)8.86486, -44.83303, -99.44909
51generate(0.4828155, 0.80329049, -0.34871803), (0.59127673, -0.00528797, 0.80645253), (0.64597708, -0.59555739, -0.47752753)-57.15078, 92.29348, -55.07767
52generate(-0.43196502, 0.51999952, -0.73688446), (0.0830824, 0.83652046, 0.54160336), (0.89805656, 0.17272501, -0.40455544)-143.12391, 41.27942, -33.63365
53generate(-0.4848756, -0.51159499, -0.70933843), (-0.81748239, 0.55338468, 0.15967822), (0.31084964, 0.6572877, -0.68654306)-144.79159, -43.34385, -90.99015
54generate(0.39720438, -0.86586449, -0.3041476), (-0.86586771, -0.46341129, 0.18848466), (-0.30414368, 0.18848153, -0.9337931)-59.84914, -44.62985, -147.88243
55generate(0.99527037, -0.05322058, -0.08127194), (0.00479331, -0.80868997, 0.58821316), (-0.09702354, -0.58581932, -0.80461438)-5.68415, 39.19863, -125.68729
56generate(0.45161112, -0.8422814, -0.29429298), (-0.54172979, 0.00322052, -0.84054748), (0.70893164, 0.53902097, -0.45483164)-55.61053, -91.28048, -49.42662
57generate(0.99527023, 0.00478863, -0.09702885), (-0.05321377, -0.80869415, -0.5858207), (-0.08126997, 0.58821226, -0.80461005)-6.72574, -42.23299, -124.64833
58generate(0.43496289, 0.81482468, -0.38322104), (0.81483582, -0.53730626, -0.21760998), (-0.38322254, -0.21760785, -0.89765662)-62.5866, 39.33989, -150.70761
59generate(-0.4549852, 0.46838447, -0.75736167), (0.86280395, 0.44233535, -0.24477002), (0.22036211, -0.76482335, -0.60538413)-145.9953, 40.70722, -91.59142
60generate(-0.44469603, -0.55576341, -0.7024011), (0.02440029, 0.77639927, -0.62976656), (0.89535052, -0.29720103, -0.33170324)-141.68385, -40.02061, -28.99633

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Components

#1: DNA chain DNA (5'-D(*AP*TP*AP*CP*CP*TP*CP*TP*TP*GP*C)-3')


Mass: 3284.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Keywords: PART OF SS-DNA GENOME
#2: Protein PROTEIN (PARVOVIRUS COAT PROTEIN)


Mass: 64705.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canine parvovirus / Genus: ParvovirusParvoviridae / Cell line: CULTURED IN CANINE A72 CELL LINE / Species: Feline panleukopenia virus / Strain: D / References: UniProt: P17455
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Compound detailsVP3 IS A PROTEOLYTIC CLEAVAGE PRODUCT, MISSING THE 15 - 20 N-TERMINAL RESIDUES OF VP2. UP TO 20 ...VP3 IS A PROTEOLYTIC CLEAVAGE PRODUCT, MISSING THE 15 - 20 N-TERMINAL RESIDUES OF VP2. UP TO 20 PERCENT OF THE 60 COPIES OF VP2 IN EACH CAPSID ARE REPLACED BY VP1, THE PRODUCT OF ALTERATE TRANSCRIPTIONAL SPLICING, CONTAINING AN ADDITIONAL 153 N-TERMINAL AMINO ACIDS. NO EVIDENCE IS SEEN FOR THIS EXTENSION IN THE SIXTY-FOLD AVERAGED ELECTRON DENSITY MAP.

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Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal grow
*PLUS
Method: unknown

-
Data collection

DetectorDetector: FILM / Date: Jan 1, 1987
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.9 Å / Num. obs: 565088 / % possible obs: 43 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.66 % / Rmerge(I) obs: 0.122

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Processing

Software
NameVersionClassification
PURDUESOFTWAREdata collection
TNTrefinement
PURDUEDATA PROCESSING PACKAGEdata reduction
RefinementHighest resolution: 2.9 Å / σ(F): 3
Details: ELEVEN NUCLEOTIDES OF THE GENOMIC SINGLE-STRANDED DNA ARE BOUND TO EACH OF THE 60 PROTOMERS OF THE CAPSID, TOGETHER CONSTITUTING 13 PERCENT OF THE GENOME. THE ELECTRON DENSITY IS THE AVERAGE ...Details: ELEVEN NUCLEOTIDES OF THE GENOMIC SINGLE-STRANDED DNA ARE BOUND TO EACH OF THE 60 PROTOMERS OF THE CAPSID, TOGETHER CONSTITUTING 13 PERCENT OF THE GENOME. THE ELECTRON DENSITY IS THE AVERAGE OF UP TO 60 DIFFERENT REGIONS OF THE DNA SEQUENCE. THUS, THE ELECTRON DENSITY FOR EACH BASE IS EXPECTED TO BE BLURRED AS IT IS THE AVERAGE OF MANY BASES. HOWEVER, FOR MANY OF THE NUCLEOTIDES, THE ELECTRON DENSITY IS DISTINCTIVE FOR PURINE OR PYRIMIDINE, AND IN SOME CASES FOR INDIVIDUAL BASE-TYPE. THIS SHOWS THAT THERE IS SOME SEQUENCE PREFERENCE. THERE ARE 30+ REGIONS OF THE ENCAPSIDATED GENOMIC SEQUENCE THAT SATISFY THIS PREFERENCE (SEE *JRNL* REFERENCE), BUT THE HOMOLOGY BETWEEN THEM IS WEAK. THE BASE-TYPES OF THE DNA MODEL WERE CHOSEN TO FIT THE ELECTRON DENSITY AND STERIC CONSTRAINTS BEST, AND IS THEREFORE SIMILAR TO THE CONSENSUS OF THE VIRAL SEQUENCES THAT BIND. NOTE THAT THE SEQUENCE OF THE DNA IN THE GENBANK ENTRY PVCPVC IS THE NEGATIVE OF THE SEQUENCE THAT IS ENCAPSIDATED IN THE VIRION. STRONG ELECTRON DENSITY BEGINS AT THE 37TH RESIDUE OF VP2. DIFFUSE DENSITY CONNECTS GLY 37 ON THE INSIDE SURFACE TO GLY 22 ON THE OUTER SURFACE, PASSING ALONG THE FIVE-FOLD AXIS, SO THAT AT MOST ONE IN FIVE OF THE N-TERMINI ARE EXTERNAL. AN OCCUPANCY FOR RESIDUES 24 TO 34 WAS OPTIMIZED AGAINST THE ELECTRON DENSITY AND FREE R-FACTOR. 13% OF N-TERMINI ARE EXTERNAL, MEANING THAT 65% OF FIVE-FOLD PORES ARE OCCUPIED BY POLYPEPTIDES FROM ONE OF THE FIVE SURROUNDING PROTEINS. N-TERMINI FROM THE INSIDE OF THE CAPSID LIKELY JOIN AT RESIDUE 35, BUT THERE IS INADEQUATE ELECTRON DENSITY FOR MODELING OF THE ALTERNATIVE N-TERMINAL CONFORMATIONS. SEE CITATION IN *JRNL* RECORDS FOR ADDITIONAL DETAILS. REAL-SPACE R-FACTORS (CHAPMAN, MS (1995) ACTA CRYST A51:69) - A MEASURE OF LOCAL RELATIVE RELIABILITY (LOW IS GOOD). (5 BLOCKS, EACH WITH 3 COLUMNS: RESIDUE #; MAIN CHAIN R; SIDE CHAIN R). FOR DETAILS SEE *JRNL* CITATION. RESIDUE RESIDUE RESIDUE RESIDUE RESIDUE MAIN CHAIN MAIN CHAIN MAIN CHAIN MAIN CHAIN MAIN SIDE CHAIN SIDE CHAIN SIDE CHAIN SIDE CHAIN SIDE NUCLEIC ACID: PROTEIN: 1 28% 24% 125 20% 26% 240 29% 28% 355 25% 39% 470 28% 26% 2 28% 35% 126 19% 23% 241 24% 34% 356 19% 21% 471 32% 34% 3 35% 37% 127 20% 35% 242 19% 31% 357 19% 27% 472 28% 32% 4 24% 26% 128 21% 37% 243 17% 25% 358 18% 473 23% 29% 5 20% 25% 129 18% 23% 244 19% 28% 359 18% 474 23% 36% 6 23% 29% 130 21% 34% 245 22% 25% 360 16% 475 19% 23% 7 34% 33% 131 24% 37% 246 23% 38% 361 19% 26% 476 23% 31% 8 24% 38% 132 22% 27% 247 20% 21% 362 24% 477 21% 23% 9 31% 32% 133 22% 33% 248 24% 32% 363 25% 478 22% 35% 10 28% 36% 134 21% 24% 249 25% 34% 364 25% 479 23% 42% 11 28% 35% 135 22% 24% 250 23% 31% 365 26% 32% 480 25% 31% PROTEIN: 136 21% 35% 251 18% 23% 366 24% 31% 481 19% 32% 22 35% 137 20% 28% 252 15% 28% 367 20% 25% 482 21% 29% 23 33% 48% 138 24% 46% 253 20% 17% 368 24% 29% 483 21% 35% 24 42% 139 25% 33% 254 24% 39% 369 21% 27% 484 18% 24% 25 49% 82% 140 27% 26% 255 29% 48% 370 25% 27% 485 26% 29% 26 28% 141 26% 32% 256 30% 39% 371 28% 486 30% 27 22% 50% 142 24% 29% 257 23% 25% 372 26% 487 25% 29% 28 23% 143 20% 23% 258 30% 373 20% 32% 488 28% 33% 29 25% 144 22% 36% 259 30% 36% 374 23% 489 29% 43% 30 34% 145 18% 27% 260 25% 32% 375 27% 31% 490 32% 45% 31 47% 146 22% 35% 261 24% 28% 376 29% 32% 491 26% 38% 32 69% 147 25% 40% 262 30% 377 26% 35% 492 24% 33% 33 73% 148 25% 44% 263 23% 36% 378 26% 33% 493 31% 50% 34 53% 149 20% 27% 264 27% 379 26% 494 30% 38% 35 51% 58% 150 22% 35% 265 23% 34% 380 31% 40% 495 27% 34% 36 54% 151 25% 36% 266 27% 43% 381 31% 496 28% 37 35% 152 25% 34% 267 27% 34% 382 26% 36% 497 25% 40% 38 24% 31% 153 24% 41% 268 25% 44% 383 26% 33% 498 20% 19% 39 27% 154 23% 32% 269 26% 38% 384 32% 40% 499 19% 34% 40 29% 49% 155 24% 24% 270 22% 39% 385 28% 500 18% 19% 41 27% 45% 156 271 19% 38% 386 29% 53% 501 21% 31% 42 28% 39% 157 272 20% 22% 387 27% 38% 502 20% 34% 43 25% 158 273 20% 34% 388 23% 32% 503 20% 44 19% 18% 159 274 26% 34% 389 23% 39% 504 17% 21% 45 23% 34% 160 25% 27% 275 27% 37% 390 27% 35% 505 20% 35% 46 27% 29% 161 29% 28% 276 33% 38% 391 23% 27% 506 23% 35% 47 30% 41% 162 27% 32% 277 37% 38% 392 22% 507 20% 26% 48 26% 34% 163 24% 28% 278 30% 45% 393 22% 34% 508 22% 22% 49 21% 34% 164 25% 35% 279 27% 30% 394 24% 33% 509 21% 25% 50 20% 30% 165 24% 30% 280 25% 41% 395 31% 30% 510 23% 34% 51 21% 28% 166 22% 25% 281 22% 32% 396 32% 23% 511 23% 25% 52 22% 36% 167 23% 28% 282 24% 30% 397 25% 32% 512 25% 30% 53 23% 30% 168 19% 30% 283 28% 38% 398 27% 38% 513 22% 27% 54 24% 40% 169 20% 32% 284 28% 399 28% 42% 514 28% 55 25% 32% 170 25% 28% 285 28% 44% 400 29% 31% 515 24% 36% 56 27% 29% 171 29% 286 23% 401 24% 38% 516 21% 57 27% 172 25% 33% 287 23% 41% 402 32% 517 21% 24% 58 28% 33% 173 26% 30% 288 23% 25% 403 28% 29% 518 22% 38% 59 23% 33% 174 22% 37% 289 23% 31% 404 31% 39% 519 19% 29% 60 22% 26% 175 18% 24% 290 17% 21% 405 24% 28% 520 18% 27% 61 17% 33% 176 18% 291 18% 31% 406 18% 30% 521 20% 42% 62 20% 31% 177 22% 40% 292 14% 24% 407 19% 522 21% 28% 63 28% 178 25% 30% 293 18% 24% 408 21% 32% 523 19% 28% 64 32% 43% 179 34% 49% 294 21% 39% 409 24% 28% 524 21% 30% 65 35% 43% 180 32% 35% 295 22% 29% 410 26% 27% 525 19% 22% 66 30% 41% 181 28% 35% 296 15% 24% 411 23% 26% 526 20% 25% 67 22% 34% 182 25% 39% 297 20% 31% 412 24% 527 21% 26% 68 20% 27% 183 23% 39% 298 24% 30% 413 25% 37% 528 22% 21% 69 21% 30% 184 20% 23% 299 25% 414 21% 19% 529 22% 24% 70 24% 30% 185 27% 41% 300 24% 415 25% 34% 530 27% 34% 71 24% 41% 186 27% 35% 301 23% 24% 416 26% 33% 531 33% 72 22% 27% 187 27% 34% 302 27% 35% 417 20% 26% 532 29% 43% 73 20% 27% 188 29% 303 23% 32% 418 19% 30% 533 23% 36% 74 22% 27% 189 29% 304 21% 419 16% 22% 534 21% 27% 75 19% 30% 190 21% 41% 305 20% 23% 420 18% 30% 535 18% 27% 76 20% 27% 191 20% 28% 306 24% 41% 421 20% 25% 536 23% 46% 77 19% 32% 192 23% 34% 307 21% 422 20% 30% 537 28% 78 22% 20% 193 23% 22% 308 21% 28% 423 21% 20% 538 27% 41% 79 22% 27% 194 22% 33% 309 22% 30% 424 30% 43% 539 21% 37% 80 28% 40% 195 24% 38% 310 22% 32% 425 31% 40% 540 19% 29% 81 22% 22% 196 27% 311 20% 25% 426 30% 30% 541 21% 82 25% 37% 197 25% 39% 312 24% 38% 427 28% 30% 542 23% 29% 83 21% 28% 198 21% 30% 313 22% 35% 428 34% 33% 543 21% 26% 84 26% 39% 199 22% 23% 314 20% 27% 429 38% 51% 544 20% 28% 85 22% 29% 200 18% 23% 315 22% 430 34% 44% 545 20% 23% 86 22% 36% 201 20% 38% 316 22% 32% 431 28% 39% 546 23% 28% 87 26% 35% 202 17% 19% 317 23% 31% 432 25% 27% 547 25% 26% 88 23% 20% 203 19% 23% 318 20% 29% 433 19% 21% 548 27% 43% 89 27% 35% 204 21% 30% 319 25% 38% 434 25% 32% 549 26% 31% 90 28% 42% 205 20% 23% 320 21% 435 22% 20% 550 24% 35% 91 31% 206 22% 27% 321 22% 29% 436 19% 26% 551 25% 41% 92 28% 36% 207 21% 20% 322 21% 32% 437 19% 552 24% 22% 93 29% 46% 208 30% 33% 323 20% 24% 438 19% 553 24% 35% 94 29% 209 25% 22% 324 25% 28% 439 27% 38% 554 20% 23% 95 21% 28% 210 20% 25% 325 22% 33% 440 27% 27% 555 21% 27% 96 16% 33% 211 19% 29% 326 19% 28% 441 29% 556 21% 20% 97 13% 212 25% 31% 327 27% 37% 442 32% 41% 557 22% 28% 98 20% 34% 213 28% 39% 328 25% 443 23% 28% 558 25% 39% 99 26% 33% 214 29% 31% 329 24% 39% 444 16% 31% 559 18% 24% 100 27% 29% 215 34% 50% 330 24% 30% 445 23% 32% 560 21% 28% 101 25% 40% 216 34% 37% 331 22% 27% 446 24% 37% 561 22% 33% 102 25% 34% 217 25% 27% 332 21% 35% 447 19% 23% 562 24% 35% 103 32% 218 23% 39% 333 19% 23% 448 20% 39% 563 24% 26% 104 24% 28% 219 25% 27% 334 23% 449 21% 22% 564 25% 31% 105 24% 36% 220 22% 24% 335 24% 37% 450 24% 37% 565 27% 36% 106 26% 36% 221 34% 46% 336 24% 32% 451 26% 30% 566 28% 41% 107 29% 37% 222 31% 30% 337 25% 452 20% 567 29% 108 25% 29% 223 27% 36% 338 25% 20% 453 19% 18% 568 30% 109 28% 24% 224 27% 339 27% 38% 454 20% 29% 569 24% 27% 110 27% 36% 225 28% 39% 340 27% 455 22% 34% 570 22% 25% 111 29% 38% 226 21% 29% 341 26% 25% 456 21% 571 23% 39% 112 19% 22% 227 23% 342 24% 35% 457 20% 25% 572 18% 28% 113 18% 26% 228 20% 32% 343 21% 30% 458 20% 35% 573 22% 27% 114 18% 229 24% 33% 344 27% 36% 459 17% 25% 574 20% 28% 115 24% 29% 230 21% 22% 345 27% 30% 460 22% 36% 575 25% 31% 116 25% 231 26% 40% 346 31% 32% 461 22% 28% 576 28% 28% 117 24% 24% 232 25% 32% 347 31% 462 18% 24% 577 28% 49% 118 29% 233 16% 23% 348 23% 23% 463 21% 35% 578 24% 43% 119 27% 39% 234 19% 33% 349 30% 49% 464 22% 30% 579 31% 120 23% 29% 235 20% 350 32% 51% 465 28% 30% 580 29% 29% 121 27% 33% 236 24% 34% 351 29% 466 20% 33% 581 24% 41% 122 25% 25% 237 31% 26% 352 25% 24% 467 25% 582 21% 33% 123 25% 30% 238 28% 29% 353 27% 36% 468 28% 40% 583 24% 39% 124 22% 239 26% 22% 354 25% 35% 469 25% 29% 584 23% 28%
RfactorNum. reflection
Rfree0.283 -
obs-557776
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 212 4 0 4606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.7
X-RAY DIFFRACTIONt_dihedral_angle_d15.4
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.016
X-RAY DIFFRACTIONt_gen_planes0.024
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.11166

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