[English] 日本語
Yorodumi
- PDB-1eah: PV2L COMPLEXED WITH ANTIVIRAL AGENT SCH48973 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eah
TitlePV2L COMPLEXED WITH ANTIVIRAL AGENT SCH48973
Components(POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO ...) x 4
KeywordsVIRUS / TYPE 2 / LANSING / ANTIVIRAL / PICORNAVIRUS / MOUSE NEUROVIRULENCE / COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


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 / receptor-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...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 / receptor-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / Few Secondary Structures / Irregular / Viral coat protein subunit / 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 / Chem-SC4 / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsLentz, K. / Arnold, E.
Citation
Journal: Structure / Year: 1997
Title: Structure of poliovirus type 2 Lansing complexed with antiviral agent SCH48973: comparison of the structural and biological properties of three poliovirus serotypes.
Authors: Lentz, K.N. / Smith, A.D. / Geisler, S.C. / Cox, S. / Buontempo, P. / Skelton, A. / DeMartino, J. / Rozhon, E. / Schwartz, J. / Girijavallabhan, V. / O'Connell, J. / Arnold, E.
#1: Journal: Curr.Biol. / Year: 1994
Title: Structures of Poliovirus Complexes with Anti-Viral Drugs: Implications for Viral Stability and Drug Design
Authors: Grant, R.A. / Hiremath, C.N. / Filman, D.J. / Syed, R. / Andries, K. / Hogle, J.M.
#2: Journal: Semin.Virol. / Year: 1992
Title: Three Dimensional Structure-Activity Relationships for Antiviral Agents that Interact with Picornavirus Capsids
Authors: Zhang, A. / Nanni, R. / Oren, D.A. / Rozhon, E.J. / Arnold, E.
#3: Journal: Embo J. / Year: 1991
Title: Three-Dimensional Structure of a Mouse-Adapted Type 2/Type 1 Poliovirus Chimera
Authors: Yeates, T.O. / Jacobson, D.H. / Martin, A. / Wychowski, C. / Girard, M. / 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 2.9 A Resolution
Authors: Hogle, J.M. / Chow, M. / Filman, D.J.
History
DepositionJul 22, 1997Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact / 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][3] / _database_PDB_matrix.origx[3][1] / _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_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.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_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
Revision 2.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
2: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
3: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
4: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4916
Polymers96,8394
Non-polymers6522
Water4,882271
1
1: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
2: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
3: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
4: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,849,478360
Polymers5,810,353240
Non-polymers39,125120
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: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
2: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
3: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
4: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 487 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)487,45730
Polymers484,19620
Non-polymers3,26010
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
2: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
3: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
4: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 585 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)584,94836
Polymers581,03524
Non-polymers3,91312
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: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
2: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
3: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
4: POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.92 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,924,739180
Polymers2,905,177120
Non-polymers19,56360
Water2,162120
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)345.700, 497.200, 485.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.64288003, -0.71885497, 0.26448569), (0.21383163, 0.5, 0.83921163), (-0.73551431, -0.48295691, 0.47515394)36.13781, -54.46063, 109.61977
3generate(0.0650478, -0.94930019, -0.30756748), (-0.37286826, -0.30901699, 0.87491595), (-0.92560145, 0.05777078, -0.37406479)127.51224, 18.03064, 161.42831
4generate(0.0650478, -0.37286819, -0.92560145), (-0.94930037, -0.30901699, 0.05777079), (-0.30756747, 0.87491578, -0.37406479)147.84694, 117.29335, 83.82797
5generate(0.64288003, 0.21383159, -0.73551431), (-0.71885511, 0.5, -0.482957), (0.26448569, 0.83921147, 0.47515395)69.04004, 106.1498, -15.94021
6generate(-0.72193856, -0.23044522, -0.65245666), (-0.23044526, -0.80901699, 0.54072779), (-0.65245666, 0.54072769, 0.53095555)101.14145, 106.10875, 5.62686
7generate(-0.03350516, 0.71885497, -0.69435208), (-0.71885511, -0.5, -0.482957), (-0.69435208, 0.48295691, 0.53350516)16.08021, 201.115, 10.80336
8generate(0.64288003, 0.71885497, 0.26448569), (-0.21383163, 0.5, -0.83921163), (-0.73551431, 0.48295691, 0.47515394)-100.39461, 149.42583, 17.89157
9generate(0.37247566, -0.23044522, 0.89897545), (0.5866999, 0.80901699, -0.03570432), (-0.71905852, 0.54072769, 0.43654132)-87.31877, 22.47392, 17.09583
10generate(-0.47102862, -0.817145, 0.33227391), (0.57643211, 0.81714516), (-0.66772608, 0.576432, 0.47102862)37.23736, -4.29751, 9.51582
11generate(-0.31156659, 0.94930019, -0.04189543), (0.94930037, 0.30901699, -0.05777079), (-0.04189542, -0.05777078, -0.99745039)-85.06124, 72.63705, 248.1265
12generate(0.03350516, 0.71885497, 0.69435208), (0.71885511, -0.5, 0.482957), (0.69435208, 0.48295691, -0.53350516)-152.61263, 83.7806, 140.41844
13generate(-0.33545217, 0.94205724), (-1), (0.94205724, 0.33545217)-114.4364, 189.9304, 80.72595
14generate(-0.90855208, -0.21383159, 0.35889992), (-0.21383163, -0.5, -0.83921163), (0.35889992, -0.83921147, 0.40855208)-23.29081, 244.39103, 151.54202
15generate(-0.89378997, 0.37286819, -0.24921627), (0.37286826, 0.30901699, -0.87491595), (-0.24921626, -0.87491578, -0.41522701)-5.13596, 171.89976, 255.00125
16generate(-0.37247566, -0.58669978, 0.71905852), (-0.23044526, 0.80901699, 0.54072779), (-0.89897545, 0.03570431, -0.43654133)-31.63157, -47.54817, 171.11319
17generate(-0.89378997, -0.37286819, -0.24921627), (-0.37286826, 0.30901699, 0.87491595), (-0.24921626, 0.87491578, -0.41522701)65.68305, -40.66108, 88.82815
18generate(-0.47102862, 0.576432, -0.66772608), (-0.81714516, 0.57643211), (0.33227391, 0.817145, 0.47102862)26.37105, 24.94311, -13.34354
19generate(0.31156659, 0.94930019, 0.04189543), (-0.94930037, 0.30901699, 0.05777079), (0.04189542, -0.05777078, 0.99745039)-95.23973, 58.60163, 5.79593
20generate(0.37247566, 0.23044522, 0.89897545), (-0.5866999, 0.80901699, 0.03570432), (-0.71905852, -0.54072769, 0.43654132)-131.08732, 13.79956, 119.79646
21generate(-0.47102862, -0.576432, -0.66772608), (0.81714516, -0.57643211), (0.33227391, -0.817145, 0.47102862)135.85301, 164.98729, 141.85714
22generate(0.0650478, 0.37286819, -0.92560145), (0.94930037, -0.30901699, -0.05777079), (-0.30756747, -0.87491578, -0.37406479)77.02793, 131.32877, 250.00107
23generate(0.80234206, 0.58669978, -0.10968365), (0.5866999, -0.80901699, -0.03570432), (-0.10968365, -0.03570431, -0.99332507)-42.39224, 176.13084, 245.52983
24generate(0.72193856, -0.23044522, 0.65245666), (0.23044526, -0.80901699, -0.54072779), (0.65245666, 0.54072769, -0.53095555)-57.3729, 237.47857, 134.62251
25generate(-0.0650478, -0.94930019, 0.30756748), (0.37286826, -0.30901699, -0.87491595), (0.92560145, 0.05777078, 0.37406479)52.78872, 230.59148, 70.54927
26generate(0.90855208, -0.21383159, -0.35889992), (0.21383163, -0.5, 0.83921163), (-0.35889992, -0.83921147, -0.40855208)63.90393, 40.50457, 250.79975
27generate(0.80234206, -0.58669978, -0.10968365), (-0.5866999, -0.80901699, 0.03570432), (-0.10968365, 0.03570431, -0.99332507)69.03988, 167.45648, 238.7485
28generate(0.47102862, -0.817145, -0.33227391), (-0.57643211, -0.81714516), (0.66772608, 0.576432, -0.47102862)117.96331, 194.22791, 123.95222
29generate(0.37247566, -0.58669978, -0.71905852), (0.23044526, 0.80901699, -0.54072779), (0.89897545, 0.03570431, 0.43654133)143.0637, 83.82165, 65.05548
30generate(0.64288003, -0.21383159, -0.73551431), (0.71885511, 0.5, 0.482957), (0.26448569, -0.83921147, 0.47515395)109.65316, -11.1846, 143.45156

-
Components

-
POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO ... , 4 types, 4 molecules 1234

#1: Protein POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4


Mass: 33039.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 2 / Genus: Enterovirus / Species: Poliovirus / Strain: LANSING / Cell line: HELA CELLS / Cell line (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: P06210
#2: Protein POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4


Mass: 29980.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 2 / Genus: Enterovirus / Species: Poliovirus / Strain: LANSING / Cell line: HELA CELLS / Cell line (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: P06210
#3: Protein POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4


Mass: 26472.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 2 / Genus: Enterovirus / Species: Poliovirus / Strain: LANSING / Cell line: HELA CELLS / Cell line (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: P06210
#4: Protein POLIOVIRUS TYPE 2 COAT PROTEINS VP1 TO VP4


Mass: 7346.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 2 / Genus: Enterovirus / Species: Poliovirus / Strain: LANSING / Cell line: HELA CELLS / Cell line (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: P06210

-
Non-polymers , 3 types, 273 molecules

#5: Chemical ChemComp-SC4 / 1[2-CHLORO-4-METHOXY-PHENYL-OXYMETHYL]-4-[2,6-DICHLORO-PHENYL-OXYMETHYL]-BENZENE


Mass: 423.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17Cl3O3
#6: Chemical ChemComp-MYR / MYRISTIC ACID


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


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity % sol: 50 %
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.9-1.4 %PEG80001reservoir
2100-250 mM1reservoirLi2SO4
35 mg/mlvirus1drop

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Mar 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionRedundancy: 2.79 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.11
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 30 Å / Num. obs: 444639 / % possible obs: 48.9 % / Num. measured all: 1242301 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 34.9 % / Rmerge(I) obs: 0.227

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementHighest resolution: 2.9 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED
RfactorNum. reflection% reflection
Rwork0.185 --
obs0.185 402860 45.4 %
Displacement parametersBiso mean: 14.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 38 271 6825
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.35
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSNCS model details: STRICT (THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS 30 PROTOMERS RELATED BY ICOSAHEDRAL SYMMETRY)
LS refinement shellResolution: 2.9→3.03 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.231 32694 -
obs--29.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2ADDITIONAL.PARADDITIONAL.TOP
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.35

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more