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- PDB-1hxs: CRYSTAL STRUCTURE OF MAHONEY STRAIN OF POLIOVIRUS AT 2.2A RESOLUTION -

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Entry
Database: PDB / ID: 1hxs
TitleCRYSTAL STRUCTURE OF MAHONEY STRAIN OF POLIOVIRUS AT 2.2A RESOLUTION
Components(GENOME POLYPROTEIN, COAT PROTEIN ...) x 4
KeywordsVIRUS / Picornavirus / Poliovirus / Coat Protein / ab initio phase determinaion / 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 / PALMITIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMiller, S.T. / Hogle, J.M. / Filman, D.J.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Ab initio phasing of high-symmetry macromolecular complexes: successful phasing of authentic poliovirus data to 3.0 A resolution.
Authors: Miller, S.T. / Hogle, J.M. / Filman, D.J.
#1: Journal: To be Published
Title: Ab initio Phasing of High-Symmetry Macromolecular Complexes: Successful Phasing of Authentic Poliovirus Data to 3.0A Resolution
Authors: Miller, S.T. / Hogle, J.M. / Filman, D.J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: A Genetic Algorithm for the ab initio phasing of Icosahedral Viruses
Authors: Miller, S.T. / Hogle, J.M. / Filman, D.J.
#3: 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.
#4: 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.
#5: Journal: Science / Year: 1985
Title: Three-dimensional structure of poliovirus at 2.9A resolution
Authors: Hogle, J.M. / Chow, M. / Filman, D.J.
#6: Journal: J.APPL.CRYSTALLOGR. / Year: 1999
Title: Collection of very low resolution protein data
Authors: Miller, S.T. / Genova, J.G. / Hogle, J.M.
History
DepositionJan 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 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_oper_list / 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[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 / _struct_conn.pdbx_leaving_atom_flag / _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 2.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: GENOME POLYPROTEIN, COAT PROTEIN VP1
2: GENOME POLYPROTEIN, COAT PROTEIN VP2
3: GENOME POLYPROTEIN, COAT PROTEIN VP3
4: GENOME POLYPROTEIN, COAT PROTEIN VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7076
Polymers97,2224
Non-polymers4852
Water9,818545
1
1: GENOME POLYPROTEIN, COAT PROTEIN VP1
2: GENOME POLYPROTEIN, COAT PROTEIN VP2
3: GENOME POLYPROTEIN, COAT PROTEIN VP3
4: GENOME POLYPROTEIN, COAT PROTEIN VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,862,437360
Polymers5,833,349240
Non-polymers29,088120
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: GENOME POLYPROTEIN, COAT PROTEIN VP1
2: GENOME POLYPROTEIN, COAT PROTEIN VP2
3: GENOME POLYPROTEIN, COAT PROTEIN VP3
4: GENOME POLYPROTEIN, COAT PROTEIN VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 489 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)488,53630
Polymers486,11220
Non-polymers2,42410
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: GENOME POLYPROTEIN, COAT PROTEIN VP1
2: GENOME POLYPROTEIN, COAT PROTEIN VP2
3: GENOME POLYPROTEIN, COAT PROTEIN VP3
4: GENOME POLYPROTEIN, COAT PROTEIN VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 586 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)586,24436
Polymers583,33524
Non-polymers2,90912
Water43224
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
1: GENOME POLYPROTEIN, COAT PROTEIN VP1
2: GENOME POLYPROTEIN, COAT PROTEIN VP2
3: GENOME POLYPROTEIN, COAT PROTEIN VP3
4: GENOME POLYPROTEIN, COAT PROTEIN VP4
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.93 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,931,218180
Polymers2,916,675120
Non-polymers14,54460
Water2,162120
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)320.50, 355.25, 377.25
Angle α, β, γ (deg.)90.0, 90.0, 90.0
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(0.30928879, -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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GENOME POLYPROTEIN, COAT PROTEIN ... , 4 types, 4 molecules 1234

#1: Protein GENOME POLYPROTEIN, COAT PROTEIN VP1


Mass: 33334.301 Da / Num. of mol.: 1 / Fragment: RESIDUES 579-880 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#2: Protein GENOME POLYPROTEIN, COAT PROTEIN VP2


Mass: 30075.783 Da / Num. of mol.: 1 / Fragment: RESIDUES 69-340 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#3: Protein GENOME POLYPROTEIN, COAT PROTEIN VP3


Mass: 26419.352 Da / Num. of mol.: 1 / Fragment: RESIDUES 341-577 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#4: Protein GENOME POLYPROTEIN, COAT PROTEIN VP4


Mass: 7393.050 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-68 / 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, 547 molecules

#5: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#6: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


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


Mass: 18.015 Da / Num. of mol.: 545 / 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: 1

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Sample preparation

Crystal growTemperature: 277 K / Method: microdialysis / pH: 7
Details: 10mM Pipes, 50-70 mM NaCl, 5 mM MgCl2, 1mM CaCl2, pH 7.0, MICRODIALYSIS, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 mg/mlprotein11
250-70 mM11NaCl
310 mMPIPES Na11pH7.0
45 mM11MgCl2
51 mM11CaCl2

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1998 / Details: Supper 65 mm double reflective mirrors
RadiationMonochromator: SUPPER MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→300 Å / Num. all: 1770661 / Num. obs: 2851578 / % possible obs: 77.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.61 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 5.1
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 1.47 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 1.13 / Num. unique all: 84380 / % possible all: 77.2
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 1770661 / Num. measured all: 1778215

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Processing

Software
NameVersionClassification
DJFmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
DJFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1ASJ

1asj


Resolution: 2.2→10 Å / Isotropic thermal model: Resolution dependant bin scales / σ(F): 0 / σ(I): 0 / Stereochemistry target values: param19x
Details: Bin scaling using 16 bins; The refinement used pseudeo-Fs based on a 'protomer box' construction which is covered in the Jacobson et al, 1996, Acata Cryst D52, 693-711.
RfactorNum. reflection
Rwork0.268 -
all0.268 1660491
obs0.268 1660491
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6678 0 33 545 7256
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg2.325
X-RAY DIFFRACTIONx_dihedral_angle_deg25.299
X-RAY DIFFRACTIONx_improper_angle_deg1.14
Refine LS restraints NCSNCS model details: EXACT ICOSAHEDRAL SYMMETRY
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Num. reflection Rfree: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeRfactor RworkNum. reflection obsRfactor Rfree error
2.2-2.270.4525150811
2.27-2.3500.42311487330
2.35-2.4400.39041435540
2.44-2.5400.35711375070
Xplor fileSerial no: 1 / Param file: PARAM19X.PARAM / Topol file: PARAM19X.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.2 Å

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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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