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- PDB-1pov: ROLE AND MECHANISM OF THE MATURATION CLEAVAGE OF VP0 IN POLIOVIRU... -

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Basic information

Entry
Database: PDB / ID: 1pov
TitleROLE AND MECHANISM OF THE MATURATION CLEAVAGE OF VP0 IN POLIOVIRUS ASSEMBLY: STRUCTURE OF THE EMPTY CAPSID ASSEMBLY INTERMEDIATE AT 2.9 ANGSTROMS RESOLUTION
Components(POLIOVIRUS NATIVE EMPTY CAPSID (TYPE ...) x 3
KeywordsVIRUS / PICORNAVIRUS / Icosahedral virus
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A ...Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Few Secondary Structures / Irregular / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / SPHINGOSINE / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsBasavappa, R. / Filman, D.J. / Hogle, J.M.
Citation
Journal: Protein Sci. / Year: 1994
Title: Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly: structure of the empty capsid assembly intermediate at 2.9 A resolution.
Authors: Basavappa, R. / Syed, R. / Flore, O. / Icenogle, J.P. / Filman, D.J. / Hogle, J.M.
#1: Journal: Embo J. / Year: 1991
Title: Three-Dimensional Structure of a Mouse-Adapted Type 2(Slash)Type 1 Poliovirus Chimera
Authors: Yeates, T.O. / Jacobson, D.H. / Martin, A. / Wychowski, C. / Girard, M. / Filman, D.J. / Hogle, J.M.
#2: Journal: Embo J. / Year: 1989
Title: Structural Factors that Control Conformational Transitions and Serotype Specificity in Type 3 Poliovirus
Authors: Filman, D.J. / Syed, R. / Chow, M. / Macadam, A.J. / Minor, P.D. / Hogle, J.M.
#3: Journal: Nature / Year: 1987
Title: Myristylation of Picornavirus Capsid Protein Vp4 and its Structural Significance
Authors: Chow, M. / Newman, J.F.E. / Filman, D. / Hogle, J.M. / Rowlands, D.J. / Brown, F.
#4: Journal: Science / Year: 1985
Title: Three-Dimensional Structure of Poliovirus at 2.9 Angstroms Resolution
Authors: Hogle, J.M. / Chow, M. / Filman, D.J.
History
DepositionAug 10, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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_database_status / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_ref_seq_dif / 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[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _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.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_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.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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 SHEET RECORDS DO NOT LIST BETA INTERACTIONS BETWEEN SYMMETRY-RELATED PROTOMERS. THESE ...SHEET THE SHEET RECORDS DO NOT LIST BETA INTERACTIONS BETWEEN SYMMETRY-RELATED PROTOMERS. THESE INCLUDE FIVE-STRANDED BETA TUBES AROUND THE FIVE-FOLD AXES, AS WELL AS EXTENDED SIX-STRANDED SHEETS WHICH JOIN SHEET K FROM ONE PROTOMER WITH SHEET B FROM ANOTHER PROTOMER. HYDROGEN BONDING PATTERNS IN THE BETA TUBES ARE IDENTICAL TO THOSE DESCRIBED IN THE REMARKS OF ENTRY 2PLV.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
1: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
3: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
1: SPHINGOSINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0155
Polymers97,4873
Non-polymers5282
Water3,783210
1
0: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
1: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
3: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,880,883300
Polymers5,849,211180
Non-polymers31,672120
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
0: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
1: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
3: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
hetero molecules
x 5


  • icosahedral pentamer
  • 490 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)490,07425
Polymers487,43415
Non-polymers2,63910
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
0: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
1: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
3: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 588 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)588,08830
Polymers584,92118
Non-polymers3,16712
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
0: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
1: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
3: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.94 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)2,940,441150
Polymers2,924,60690
Non-polymers15,83660
Water1,62190
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)322.900, 358.000, 380.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO 0 152
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30928879, -0.8162167, 0.48798633), (0.80181729, 0.4997282, 0.32765947), (-0.51130183, 0.28993456, 0.80901699)46.32068, 31.10212, -18.1285
3generate(-0.80830541, -0.51884908, 0.2782768), (0.48115092, -0.30972858, 0.82009864), (-0.33931724, 0.79678356, 0.5)26.41461, 77.84547, -47.46104
4generate(-0.8083054, 0.48115093, -0.33931714), (-0.51884908, -0.30972858, 0.7967833), (0.27827689, 0.8200989, 0.5)-32.20869, 75.63233, -47.46104
5generate(0.30928879, 0.80181729, -0.51130167), (-0.8162167, 0.4997282, 0.28993447), (0.48798649, 0.32765957, 0.80901699)-48.53382, 27.52118, -18.1285
6generate(-0.99715365, -0.0753963), (-0.0753963, 0.99715365), (-1)-189.84416
7generate(-0.36886251, 0.7762158, -0.51130167), (0.7762158, 0.55984552, 0.28993447), (0.51130183, -0.28993456, -0.80901699)-48.53382, 27.52118, -171.71566
8generate(0.76972768, 0.54072464, -0.33931714), (0.54072464, -0.26972768, 0.7967833), (0.33931724, -0.79678356, -0.5)-32.20869, 75.63233, -142.38312
9generate(0.84512398, -0.45642901, 0.2782768), (-0.45642901, -0.34512398, 0.82009864), (-0.27827689, -0.8200989, -0.5)26.41461, 77.84547, -142.38312
10generate(-0.24686873, -0.83721269, 0.48798633), (-0.83721269, 0.43785174, 0.32765947), (-0.48798649, -0.32765957, -0.80901699)46.32068, 31.10212, -171.71566
11generate(-0.03769815, -0.00142318, 0.999288), (0.99857683, 0.03769815, 0.037725), (-0.03772501, 0.99928832)94.8545, 3.58094, -94.92208
12generate(-0.52373853, 0.31978679, 0.78957847), (0.31978679, -0.78527847, 0.53016417), (0.78957872, 0.53016433, 0.30901699)74.94843, 50.32429, -65.58954
13generate(-0.30928879, 0.8162167, 0.48798633), (-0.80181729, -0.4997282, 0.32765947), (0.51130183, -0.28993456, 0.80901699)46.32068, 31.10212, -18.1285
14generate(0.30928879, 0.80181729, 0.51130167), (-0.8162167, 0.4997282, -0.28993447), (-0.48798649, -0.32765957, 0.80901699)48.53382, -27.52118, -18.1285
15generate(0.47714105, 0.29648805, 0.82730347), (0.29648805, 0.83187594, -0.46912383), (-0.82730373, 0.46912399, 0.30901699)78.52937, -44.53021, -65.58954
16generate(0.03769815, 0.00142318, 0.999288), (-0.99857683, -0.03769815, 0.037725), (0.03772501, -0.99928832)94.8545, 3.58094, -94.92208
17generate(-0.49813704, 0.25966947, 0.82730347), (-0.35836451, 0.80715403, -0.46912383), (-0.78957872, -0.53016433, -0.30901699)78.52937, -44.53021, -124.25462
18generate(-0.36886251, 0.7762158, 0.51130167), (0.7762158, 0.55984552, -0.28993447), (-0.51130183, 0.28993456, -0.80901699)48.53382, -27.52118, -171.71566
19generate(0.24686873, 0.83721269, 0.48798633), (0.83721269, -0.43785174, 0.32765947), (0.48798649, 0.32765957, -0.80901699)46.32068, 31.10212, -171.71566
20generate(0.49813704, 0.35836451, 0.78957847), (-0.25966947, -0.80715403, 0.53016417), (0.82730373, -0.46912399, -0.30901699)74.94843, 50.32429, -124.25462
21generate(-0.03769815, 0.99857683, -0.037725), (-0.00142318, 0.03769815, 0.999288), (0.99928832, 0.03772501)-3.58094, 94.8545, -94.92208
22generate(0.80830541, 0.51884908, 0.2782768), (-0.48115092, 0.30972858, 0.82009864), (0.33931724, -0.79678356, 0.5)26.41461, 77.84547, -47.46104
23generate(0.52373853, -0.31978679, 0.78957847), (-0.31978679, 0.78527847, 0.53016417), (-0.78957872, -0.53016433, 0.30901699)74.94843, 50.32429, -65.58954
24generate(-0.49813704, -0.35836451, 0.78957847), (0.25966947, 0.80715403, 0.53016417), (-0.82730373, 0.46912399, -0.30901699)74.94843, 50.32429, -124.25462
25generate(-0.84512398, 0.45642901, 0.2782768), (0.45642901, 0.34512398, 0.82009864), (0.27827689, 0.8200989, -0.5)26.41461, 77.84547, -142.38312
26generate(0.03769815, -0.99857683, -0.037725), (0.00142318, -0.03769815, 0.999288), (-0.99928832, -0.03772501)-3.58094, 94.8545, -94.92208
27generate(-0.76972768, -0.54072464, -0.33931714), (-0.54072464, 0.26972768, 0.7967833), (-0.33931724, 0.79678356, -0.5)-32.20869, 75.63233, -142.38312
28generate(-0.49813704, 0.25966947, -0.82730347), (-0.35836451, 0.80715403, 0.46912383), (0.78957872, 0.53016433, -0.30901699)-78.52937, 44.53021, -124.25462
29generate(0.47714105, 0.29648805, -0.82730347), (0.29648805, 0.83187594, 0.46912383), (0.82730373, -0.46912399, 0.30901699)-78.52937, 44.53021, -65.58954
30generate(0.8083054, -0.48115093, -0.33931714), (0.51884908, 0.30972858, 0.7967833), (-0.27827689, -0.8200989, 0.5)-32.20869, 75.63233, -47.46104

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Components

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POLIOVIRUS NATIVE EMPTY CAPSID (TYPE ... , 3 types, 3 molecules 013

#1: Protein POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)


Mass: 37450.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#2: Protein POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)


Mass: 33488.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#3: Protein POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)


Mass: 26547.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300

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Non-polymers , 3 types, 212 molecules 1

#4: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#5: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsPOLIOVIRUS EMPTY CAPSID PRODUCED BY INFECTING HELA CELLS WITH P1/MAHONEY POLIOVIRUS AND INHIBITING ...POLIOVIRUS EMPTY CAPSID PRODUCED BY INFECTING HELA CELLS WITH P1/MAHONEY POLIOVIRUS AND INHIBITING POLIOVIRUS RNA SYNTHESIS PART WAY IN THE INFECTION CYCLE (SEE BASAVAPPA ET AL. FOR DETAILS).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlcapsid11
20.8 M11NaCl
310 mMPIPES11
45 mM11MgCl2
51 mM11CaCl2
60.05 M12NaCl
710 mMPIPES12
85 mM12MgCl2
91 mM12CaCl2

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Data collection

ReflectionNum. obs: 610509 / % possible obs: 61.7 %
Reflection
*PLUS
Num. measured all: 1885617 / Rmerge(I) obs: 0.189

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→30 Å /
RfactorNum. reflection
obs0.281 607564
Displacement parametersBiso mean: 18.86 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6035 0 36 210 6281
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.015
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.7
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.51.5
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it22
X-RAY DIFFRACTIONo_scangle_it

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