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- PDB-1z1c: Structural Determinants of Tissue Tropism and In Vivo Pathogenici... -

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Basic information

Entry
Database: PDB / ID: 1z1c
TitleStructural Determinants of Tissue Tropism and In Vivo Pathogenicity for the Parvovirus Minute virus of Mice
Components
  • 5'-D(*AP*CP*AP*CP*CP*AP*AP*AP*A)-3'
  • 5'-D(*AP*TP*CP*CP*TP*CP*TP*AP*TP*CP*AP*C)-3'
  • Coat protein VP2
KeywordsVirus/DNA / Immunosuppressive strain / MVMi / Minute virus of Mice / 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 / T=1 icosahedral viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / structural molecule activity / virion attachment to host cell / 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
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / DNA / DNA (> 10) / Capsid protein VP1
Similarity search - Component
Biological speciesMurine minute virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKontou, M. / Govindasamy, L. / Nam, H.J. / Bryant, N. / Llamas-Saiz, A.L. / Foces-Foces, C. / Hernando, E. / Rubio, M.P. / McKenna, R. / Almendral, J.M. / Agbandje-McKenna, M.
Citation
Journal: J.Virol. / Year: 2005
Title: Structural determinants of tissue tropism and in vivo pathogenicity for the parvovirus minute virus of mice.
Authors: Kontou, M. / Govindasamy, L. / Nam, H.J. / Bryant, N. / Llamas-Saiz, A.L. / Foces-Foces, C. / Hernando, E. / Rubio, M.P. / McKenna, R. / Almendral, J.M. / Agbandje-McKenna, M.
History
DepositionMar 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
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_assembly_gen / 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_z ..._atom_site.Cartn_x / _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][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_peptide_omega.omega / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _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_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
Revision 2.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE THE AUTHORS VERIFIED WITH THEIR COLLABORATORS THAT THE THIS DIFFERENCE BETWEEN THE CRYSTAL ...SEQUENCE THE AUTHORS VERIFIED WITH THEIR COLLABORATORS THAT THE THIS DIFFERENCE BETWEEN THE CRYSTAL COORDINATES AND SEQUENCE DATABASE IS DUE TO AN ERROR IN THE DEPOSITED SEQUENCE OR A POSSIBLE DIFFERENCE IN AN EARLIER VARIANT OF THE VIRUS. RESIDUE 366 IS A METHONINE AND THE RESIDUE 455 IS A THEORNINE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*AP*TP*CP*CP*TP*CP*TP*AP*TP*CP*AP*C)-3'
C: 5'-D(*AP*CP*AP*CP*CP*AP*AP*AP*A)-3'
A: Coat protein VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4166
Polymers71,0053
Non-polymers4113
Water1,820101
1
B: 5'-D(*AP*TP*CP*CP*TP*CP*TP*AP*TP*CP*AP*C)-3'
C: 5'-D(*AP*CP*AP*CP*CP*AP*AP*AP*A)-3'
A: Coat protein VP2
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,284,969360
Polymers4,260,286180
Non-polymers24,683180
Water3,243180
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
B: 5'-D(*AP*TP*CP*CP*TP*CP*TP*AP*TP*CP*AP*C)-3'
C: 5'-D(*AP*CP*AP*CP*CP*AP*AP*AP*A)-3'
A: Coat protein VP2
hetero molecules
x 5


  • icosahedral pentamer
  • 357 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)357,08130
Polymers355,02415
Non-polymers2,05715
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
B: 5'-D(*AP*TP*CP*CP*TP*CP*TP*AP*TP*CP*AP*C)-3'
C: 5'-D(*AP*CP*AP*CP*CP*AP*AP*AP*A)-3'
A: Coat protein VP2
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 428 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)428,49736
Polymers426,02918
Non-polymers2,46818
Water32418
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
B: 5'-D(*AP*TP*CP*CP*TP*CP*TP*AP*TP*CP*AP*C)-3'
C: 5'-D(*AP*CP*AP*CP*CP*AP*AP*AP*A)-3'
A: Coat protein VP2
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 4.28 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)4,284,969360
Polymers4,260,286180
Non-polymers24,683180
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
transform to crystal frame1
point symmetry operation29
Unit cell
Length a, b, c (Å)448.700, 416.700, 305.300
Angle α, β, γ (deg.)90.00, 95.80, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.31411193, -0.83619076, 0.44959871), (0.7734491, 0.5, 0.38956017), (-0.55044306, 0.22521296, 0.80392206)
3generate(-0.79556319, -0.57949741, 0.17692003), (0.41524345, -0.30901699, 0.85569782), (-0.44122329, 0.75393553, 0.48654619)
4generate(-0.79549205, 0.41533856, -0.44120338), (-0.57958892, -0.30901699, 0.75422656), (0.1767213, 0.85549111, 0.48647505)
5generate(0.31422704, 0.77348766, -0.55054597), (-0.83622349, 0.5, 0.22537623), (0.44941229, 0.38953332, 0.80380695)
6generate(-0.97939006, -0.20189452), (-1), (-0.20206154, 0.97939006)
7generate(-0.19650666, 0.77348766, -0.60263997), (-0.7734491, -0.5, -0.38956017), (-0.6025684, 0.38953332, 0.69650666)
8generate(0.86824723, 0.41533856, -0.27150472), (-0.41524345, 0.30901699, -0.85569782), (-0.27137698, 0.85549111, 0.44076976)
9generate(0.74341794, -0.57949741, 0.33389356), (0.57958892, 0.30901699, -0.75422656), (0.33381743, 0.75393553, 0.56559906)
10generate(-0.39848471, -0.83619076, 0.37691504), (0.83622349, -0.5, -0.22537623), (0.37665673, 0.22521296, 0.8984847)
11generate(-0.10104657, -0.10145575, 0.98984984), (0.99483237, 0.10147126), (-0.01031511, 0.99468037, 0.10104657)
12generate(-0.65506676, 0.25669335, 0.7108086), (0.25663456, -0.80901699, 0.52885034), (0.71047416, 0.52872259, 0.46408376)
13generate(-0.39848471, 0.83619076, 0.37691504), (-0.83622349, -0.5, 0.22537623), (0.37665673, -0.22521296, 0.8984847)
14generate(0.31411193, 0.83619076, 0.44959871), (-0.7734491, 0.5, -0.38956017), (-0.55044306, -0.22521296, 0.80392206)
15generate(0.4979388, 0.25669335, 0.82841326), (0.35820565, 0.80901699, -0.46613765), (-0.78960481, 0.52872259, 0.31107819)
16generate(-0.10104657, 0.10145575, 0.98984984), (-0.99483237, -0.10147126), (-0.01031511, -0.99468037, 0.10104657)
17generate(-0.49812505, 0.35814909, 0.78985484), (-0.25663456, 0.80901699, -0.52885034), (-0.82819513, -0.46595779, -0.31089194)
18generate(-0.31422704, 0.77348766, 0.55054597), (0.83622349, 0.5, -0.22537623), (-0.44941229, 0.38953332, -0.80380695)
19generate(0.19650666, 0.77348766, 0.60263997), (0.7734491, -0.5, 0.38956017), (0.6025684, 0.38953332, -0.69650666)
20generate(0.32825944, 0.35814909, 0.87414469), (-0.35820565, -0.80901699, 0.46613765), (0.87394537, -0.46595779, -0.13727642)
21generate(-0.10093146, 0.99483597, -0.01029484), (-0.10157109, 0.99498799), (0.98954023, 0.10155557, 0.10093146)
22generate(0.74341794, 0.57949741, 0.33389356), (-0.57958892, 0.30901699, 0.75422656), (0.33381743, -0.75393553, 0.56559906)
23generate(0.4979388, -0.25669335, 0.82841326), (-0.35820565, 0.80901699, 0.46613765), (-0.78960481, -0.52872259, 0.31107819)
24generate(-0.49812505, -0.35814909, 0.78985484), (0.25663456, 0.80901699, 0.52885034), (-0.82819513, 0.46595779, -0.31089194)
25generate(-0.86824723, 0.41533856, 0.27150472), (0.41524345, 0.30901699, 0.85569782), (0.27137698, 0.85549111, -0.44076976)
26generate(0.10093146, 0.99483597, 0.01029484), (0.10157109, -0.99498799), (-0.98954023, 0.10155557, -0.10093146)
27generate(0.79549205, 0.41533856, 0.44120338), (0.57958892, -0.30901699, -0.75422656), (-0.1767213, 0.85549111, -0.48647505)
28generate(0.32825944, -0.35814909, 0.87414469), (0.35820565, -0.80901699, -0.46613765), (0.87394537, 0.46595779, -0.13727642)
29generate(-0.65506676, -0.25669335, 0.7108086), (-0.25663456, -0.80901699, -0.52885034), (0.71047416, -0.52872259, 0.46408376)
30generate(-0.79556319, 0.57949741, 0.17692003), (-0.41524345, -0.30901699, -0.85569782), (-0.44122329, -0.75393553, 0.48654619)
31generate(-0.72178669, -0.69210489), (1), (0.69208786, -0.72197079)-15.42624, 208.35, 151.86854
32generate(0.15424252, 0.44768037, -0.88091276), (0.7734491, 0.5, 0.38956017), (0.61479686, -0.74131465, -0.26924643)-15.42624, 208.35, 151.86854
33generate(0.87959972, -0.10352895, -0.46443952), (0.41524345, -0.30901699, 0.85569782), (-0.2320493, -0.94538256, -0.22882793)-15.42624, 208.35, 151.86854
34generate(0.4518659, -0.89187543, -0.01823703), (-0.57958892, -0.30901699, 0.75422656), (-0.678138, -0.33018882, -0.65657228)-15.42624, 208.35, 151.86854
35generate(-0.53784534, -0.82789102, -0.15894197), (-0.83622349, 0.5, 0.22537623), (-0.10698983, 0.25408974, -0.96135132)-15.42624, 208.35, 151.86854
36generate(0.84675849, -0.53211587), (-1), (-0.53194144, -0.84681976)-15.42624, 208.35, 151.86854
37generate(0.55887643, -0.82789102, -0.04707816), (-0.7734491, -0.5, -0.38956017), (0.29903691, 0.25408974, -0.91993727)-15.42624, 208.35, 151.86854
38generate(-0.43886796, -0.89187543, -0.10909042), (-0.41524345, 0.30901699, -0.85569782), (0.79682962, -0.33018882, -0.50612802)-15.42624, 208.35, 151.86854
39generate(-0.76762585, -0.10352895, -0.6324538), (0.57958892, 0.30901699, -0.75422656), (0.2735041, -0.94538256, -0.17726232)-15.42624, 208.35, 151.86854
40generate(0.02693499, 0.44768037, -0.89389792), (0.83622349, -0.5, -0.22537623), (-0.54772158, -0.74131465, -0.38782139)-15.42624, 208.35, 151.86854
41generate(0.0800732, -0.61519375, -0.78439527), (0.99483237, 0.10147126), (-0.06248589, -0.78834647, 0.61211039)-15.42624, 208.35, 151.86854
42generate(-0.01890417, -0.55120933, -0.83424683), (0.25663456, -0.80901699, 0.52885034), (-0.96630534, -0.20406792, 0.15688708)-15.42624, 208.35, 151.86854
43generate(0.02693499, -0.44768037, -0.89389792), (-0.83622349, -0.5, 0.22537623), (-0.54772158, 0.74131465, -0.38782139)-15.42624, 208.35, 151.86854
44generate(0.15424252, -0.44768037, -0.88091276), (-0.7734491, 0.5, -0.38956017), (0.61479686, 0.74131465, -0.26924643)-15.42624, 208.35, 151.86854
45generate(0.18708375, -0.55120933, -0.8132364), (0.35820565, 0.80901699, -0.46613765), (0.91468901, -0.20406792, 0.3487454)-15.42624, 208.35, 151.86854
46generate(0.0800732, 0.61519375, -0.78439527), (-0.99483237, -0.10147126), (-0.06248589, 0.78834647, 0.61211039)-15.42624, 208.35, 151.86854
47generate(0.93273793, 0.06398442, -0.35493687), (-0.25663456, 0.80901699, -0.52885034), (0.25318639, 0.58427855, 0.77110385)-15.42624, 208.35, 151.86854
48generate(0.53784534, -0.82789102, 0.15894197), (0.83622349, 0.5, -0.22537623), (0.10698983, 0.25408974, 0.96135132)-15.42624, 208.35, 151.86854
49generate(-0.55887643, -0.82789102, 0.04707816), (0.7734491, -0.5, 0.38956017), (-0.29903691, 0.25408974, 0.91993727)-15.42624, 208.35, 151.86854
50generate(-0.84179516, 0.06398442, -0.53593632), (-0.35820565, -0.80901699, 0.46613765), (-0.40377866, 0.58427855, 0.70409449)-15.42624, 208.35, 151.86854
51generate(-0.61201465, -0.78834647, -0.06242448), (-0.10157109, 0.99498799), (-0.78427258, 0.61519375, -0.07999451)-15.42624, 208.35, 151.86854
52generate(-0.76762585, 0.10352895, -0.6324538), (-0.57958892, 0.30901699, 0.75422656), (0.2735041, 0.94538256, -0.17726232)-15.42624, 208.35, 151.86854
53generate(0.18708375, 0.55120933, -0.8132364), (-0.35820565, 0.80901699, 0.46613765), (0.91468901, 0.20406792, 0.3487454)-15.42624, 208.35, 151.86854
54generate(0.93273793, -0.06398442, -0.35493687), (0.25663456, 0.80901699, 0.52885034), (0.25318639, -0.58427855, 0.77110385)-15.42624, 208.35, 151.86854
55generate(0.43886796, -0.89187543, 0.10909042), (0.41524345, 0.30901699, 0.85569782), (-0.79682962, -0.33018882, 0.50612802)-15.42624, 208.35, 151.86854
56generate(0.61201465, -0.78834647, 0.06242448), (0.10157109, -0.99498799), (0.78427258, 0.61519375, 0.07999451)-15.42624, 208.35, 151.86854
57generate(-0.4518659, -0.89187543, 0.01823703), (0.57958892, -0.30901699, -0.75422656), (0.678138, -0.33018882, 0.65657228)-15.42624, 208.35, 151.86854
58generate(-0.84179516, -0.06398442, -0.53593632), (0.35820565, -0.80901699, -0.46613765), (-0.40377866, -0.58427855, 0.70409449)-15.42624, 208.35, 151.86854
59generate(-0.01890417, 0.55120933, -0.83424683), (-0.25663456, -0.80901699, -0.52885034), (-0.96630534, 0.20406792, 0.15688708)-15.42624, 208.35, 151.86854
60generate(0.87959972, 0.10352895, -0.46443952), (-0.41524345, -0.30901699, -0.85569782), (-0.2320493, 0.94538256, -0.22882793)-15.42624, 208.35, 151.86854

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Components

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DNA chain , 2 types, 2 molecules BC

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


Mass: 3557.343 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*CP*AP*CP*CP*AP*AP*AP*A)-3'


Mass: 2701.829 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#3: Protein Coat protein VP2


Mass: 64745.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine minute virus (STRAIN MVMI) / Genus: ParvovirusParvoviridae / Species: Minute virus of mice / Strain: MVMi / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Immunosuppressive strain / References: UniProt: P07302

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Non-polymers , 3 types, 104 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Deoxyadenosine monophosphate


Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 35

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Sample preparation

Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 10mM Tris-HCl, 8 mM CaCl2, PEG8000, virus 10mg/ml, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91 Å
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. all: 441933 / Num. obs: 437558 / % possible obs: 63.7 % / Rmerge(I) obs: 0.155

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: canine parvovirus model

Resolution: 3.5→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.329 -
Rwork0.325 -
all-441933
obs-437558
Displacement parametersBiso mean: 21.47 Å2
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 415 20 101 4864
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.619

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