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- PDB-1ar8: P1/MAHONEY POLIOVIRUS, MUTANT P1095S -

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Basic information

Entry
Database: PDB / ID: 1ar8
TitleP1/MAHONEY POLIOVIRUS, MUTANT P1095S
Components(P1/MAHONEY POLIOVIRUS) x 5
KeywordsVIRUS / PICORNAVIRUS / POLIOVIRUS / COAT PROTEIN / 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 RIG-I activity / 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 MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / 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 RIG-I activity / 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 MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / 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 / virion attachment to host cell / structural molecule activity / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / SPHINGOSINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWien, M.W. / Curry, S. / Filman, D.J. / Hogle, J.M.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Structural studies of poliovirus mutants that overcome receptor defects.
Authors: Wien, M.W. / Curry, S. / Filman, D.J. / Hogle, J.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: A Pseudo-Cell Based Approach to Efficient Crystallographic Refinement of Viruses
Authors: Jacobson, D.H. / Hogle, J.M. / Filman, D.J.
#2: Journal: J.Virol. / Year: 1995
Title: Poliovirus Variants Selected on Mutant Receptor-Expressing Cells Identify Capsid Residues that Expand Receptor Recognition
Authors: Colston, E.M. / Racaniello, V.R.
#3: Journal: Science / Year: 1985
Title: Three-Dimensional Structure of Poliovirus at 2.9 A Resolution
Authors: Hogle, J.M. / Chow, M. / Filman, D.J.
History
DepositionAug 11, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_ncs_oper
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_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_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
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: P1/MAHONEY POLIOVIRUS
1: P1/MAHONEY POLIOVIRUS
2: P1/MAHONEY POLIOVIRUS
3: P1/MAHONEY POLIOVIRUS
4: P1/MAHONEY POLIOVIRUS
1: SPHINGOSINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6877
Polymers98,1605
Non-polymers5282
Water9,062503
1
0: P1/MAHONEY POLIOVIRUS
1: P1/MAHONEY POLIOVIRUS
2: P1/MAHONEY POLIOVIRUS
3: P1/MAHONEY POLIOVIRUS
4: P1/MAHONEY POLIOVIRUS
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,921,245420
Polymers5,889,573300
Non-polymers31,672120
Water5,405300
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: P1/MAHONEY POLIOVIRUS
1: P1/MAHONEY POLIOVIRUS
2: P1/MAHONEY POLIOVIRUS
3: P1/MAHONEY POLIOVIRUS
4: P1/MAHONEY POLIOVIRUS
hetero molecules
x 5


  • icosahedral pentamer
  • 493 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)493,43735
Polymers490,79825
Non-polymers2,63910
Water45025
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
0: P1/MAHONEY POLIOVIRUS
1: P1/MAHONEY POLIOVIRUS
2: P1/MAHONEY POLIOVIRUS
3: P1/MAHONEY POLIOVIRUS
4: P1/MAHONEY POLIOVIRUS
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 592 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)592,12542
Polymers588,95730
Non-polymers3,16712
Water54030
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: P1/MAHONEY POLIOVIRUS
1: P1/MAHONEY POLIOVIRUS
2: P1/MAHONEY POLIOVIRUS
3: P1/MAHONEY POLIOVIRUS
4: P1/MAHONEY POLIOVIRUS
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.96 MDa, 150 polymers
Theoretical massNumber of molelcules
Total (without water)2,960,623210
Polymers2,944,787150
Non-polymers15,83660
Water2,702150
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)323.040, 358.220, 380.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30953622, -0.81649274, 0.4875381), (0.80148857, 0.49948078, 0.32820499), (-0.51179769, 0.28949094, 0.80901699)46.27813, 31.1539, -18.1285
3generate(-0.8081178, -0.51941864, 0.27736031), (0.48044332, -0.30991617, 0.82021172), (-0.34044926, 0.79667735, 0.5)26.32761, 77.85619, -47.46104
4generate(-0.8084022, 0.480676, -0.3400748), (-0.51946213, -0.30963179, 0.7960836), (0.27724757, 0.82064484, 0.5)-32.2806, 75.5659, -47.46104
5generate(0.30907606, 0.80169437, -0.51149291), (-0.81639243, 0.49994093, 0.28916488), (0.48765679, 0.32827116, 0.80901699)-48.55197, 27.44813, -18.1285
6generate(-0.99697203, -0.07748528), (-0.07803763, 0.99697203), (-1)-189.84414
7generate(-0.37070252, 0.77531802, -0.51149291), (0.77490621, 0.56168552, 0.28916488), (0.51179769, -0.28949094, -0.80901699)-48.55197, 27.44813, -171.71564
8generate(0.76844356, 0.5418598, -0.3400748), (0.54205215, -0.26844356, 0.7960836), (0.34044926, -0.79667735, -0.5)-32.2806, 75.5659, -142.38311
9generate(0.84620505, -0.45522862, 0.27736031), (-0.45480343, -0.34620505, 0.82021172), (-0.27724757, -0.82064484, -0.5)26.32761, 77.85619, -142.38311
10generate(-0.24488179, -0.83800492, 0.4875381), (-0.83803998, 0.4358648, 0.32820499), (-0.48765679, -0.32827116, -0.80901699)46.27813, 31.1539, -171.71564
11generate(-0.03873855, -0.00150311, 0.99903101), (0.99838052, 0.03873855, 0.03904011), (-0.03906079, 0.99956009)94.83009, 3.70577, -94.92207
12generate(-0.52449747, 0.32008939, 0.78885322), (0.32010279, -0.78451952, 0.53104684), (0.78904526, 0.5311539, 0.30901699)74.87958, 50.40807, -65.58954
13generate(-0.30953622, 0.81649274, 0.4875381), (-0.80148857, -0.49948078, 0.32820499), (0.51179769, -0.28949094, 0.80901699)46.27813, 31.1539, -18.1285
14generate(0.30907606, 0.80169437, 0.51149291), (-0.81639243, 0.49994093, -0.28916488), (-0.48765679, -0.32827116, 0.80901699)48.55197, -27.44813, -18.1285
15generate(0.47643823, 0.29614513, 0.82761291), (0.29598783, 0.83257876, -0.46787861), (-0.82810605, 0.46840619, 0.30901699)78.55873, -44.41201, -65.58954
16generate(0.03873855, 0.00150311, 0.99903101), (-0.99838052, -0.03873855, 0.03904011), (0.03906079, -0.99956009)94.83009, 3.70577, -94.92207
17generate(-0.49810605, 0.25833146, 0.82761291), (-0.36006407, 0.80712304, -0.46787861), (-0.78904526, -0.5311539, -0.30901699)78.55873, -44.41201, -124.2546
18generate(-0.37070252, 0.77531802, 0.51149291), (0.77490621, 0.56168552, -0.28916488), (-0.51179769, 0.28949094, -0.80901699)48.55197, -27.44813, -171.71564
19generate(0.24488179, 0.83800492, 0.4875381), (0.83803998, -0.4358648, 0.32820499), (0.48765679, 0.32827116, -0.80901699)46.27813, 31.1539, -171.71564
20generate(0.49793029, 0.35976101, 0.78885322), (-0.25791148, -0.80694728, 0.53104684), (0.82810605, -0.46840619, -0.30901699)74.87958, 50.40807, -124.2546
21generate(-0.03902294, 0.99859153, -0.03875969), (-0.00152494, 0.03902294, 0.99892545), (0.99945448, 0.03878022)-3.67915, 94.82007, -94.92207
22generate(0.8081178, 0.51941864, 0.27736031), (-0.48044332, 0.30991617, 0.82021172), (0.34044926, -0.79667735, 0.5)26.32761, 77.85619, -47.46104
23generate(0.52449747, -0.32008939, 0.78885322), (-0.32010279, 0.78451952, 0.53104684), (-0.78904526, -0.5311539, 0.30901699)74.87958, 50.40807, -65.58954
24generate(-0.49793029, -0.35976101, 0.78885322), (0.25791148, 0.80694728, 0.53104684), (-0.82810605, 0.46840619, -0.30901699)74.87958, 50.40807, -124.2546
25generate(-0.84620505, 0.45522862, 0.27736031), (0.45480343, 0.34620505, 0.82021172), (0.27724757, 0.82064484, -0.5)26.32761, 77.85619, -142.38311
26generate(0.03902294, -0.99859153, -0.03875969), (0.00152494, -0.03902294, 0.99892545), (-0.99945448, -0.03878022)-3.67915, 94.82007, -94.92207
27generate(-0.76844356, -0.5418598, -0.3400748), (-0.54205215, 0.26844356, 0.7960836), (-0.34044926, 0.79667735, -0.5)-32.2806, 75.5659, -142.38311
28generate(-0.49810605, 0.25833146, -0.82761291), (-0.36006407, 0.80712304, 0.46787861), (0.78904526, 0.5311539, -0.30901699)-78.55873, 44.41201, -124.2546
29generate(0.47643823, 0.29614513, -0.82761291), (0.29598783, 0.83257876, 0.46787861), (0.82810605, -0.46840619, 0.30901699)-78.55873, 44.41201, -65.58954
30generate(0.8084022, -0.480676, -0.3400748), (0.51946213, 0.30963179, 0.7960836), (-0.27724757, -0.82064484, 0.5)-32.2806, 75.5659, -47.46104

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Components

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Protein/peptide , 1 types, 1 molecules 0

#1: Protein/peptide P1/MAHONEY POLIOVIRUS


Mass: 664.664 Da / Num. of mol.: 1 / Fragment: VIRUS PROTOMER / Mutation: CHAIN 1, P95S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney

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Protein , 4 types, 4 molecules 1234

#2: Protein P1/MAHONEY POLIOVIRUS


Mass: 33478.578 Da / Num. of mol.: 1 / Fragment: VIRUS PROTOMER / Mutation: CHAIN 1, P95S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#3: Protein P1/MAHONEY POLIOVIRUS


Mass: 30075.783 Da / Num. of mol.: 1 / Fragment: VIRUS PROTOMER / Mutation: CHAIN 1, P95S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#4: Protein P1/MAHONEY POLIOVIRUS


Mass: 26547.482 Da / Num. of mol.: 1 / Fragment: VIRUS PROTOMER / Mutation: CHAIN 1, P95S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#5: Protein P1/MAHONEY POLIOVIRUS


Mass: 7393.050 Da / Num. of mol.: 1 / Fragment: VIRUS PROTOMER / Mutation: CHAIN 1, P95S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03299, UniProt: P03300*PLUS

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Non-polymers , 3 types, 505 molecules 1

#6: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#7: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 7

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 30 %
Crystal growMethod: microdiaylsis / pH: 7.5
Details: VIRUS WAS CRYSTALLIZED BY MICRODIALYSIS AGAINST 10MM PIPES, 0-70 MM NACL, PH 7.5, 2% PEG 400, microdiaylsis
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
170 mM11NaCl
22 %PEG40011

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Data collection

DiffractionMean temperature: 258 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorDetector: FILM / Date: Dec 1, 1995 / Details: SUPPER LONG MIRRORS
RadiationMonochromator: SUPPER LONG MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 333627 / % possible obs: 34 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.151
Reflection
*PLUS
Num. measured all: 811288

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
CIRCLESdata reduction
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PLV

2plv


Resolution: 2.9→11 Å
Details: OTHER PROGRAMS USED PROGRAM : X-PLOR 3.0 AUTHORS : BRUNGER
RfactorNum. reflection% reflection
Rwork0.27 --
obs-333627 34 %
Refinement stepCycle: LAST / Resolution: 2.9→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6645 0 36 503 7184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
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_deg2.46
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d26.2
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d1.32
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 2.9→2.99 Å / Total num. of bins used: 16 /
RfactorNum. reflection
Rwork0.44 54758
Software
*PLUS
Name: 'PROTOMER-BOX-BASED PSEUDO-REAL-SPACE' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32
LS refinement shell
*PLUS
Rfactor obs: 0.44

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • 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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