[English] 日本語
Yorodumi
- PDB-1ar9: P1/MAHONEY POLIOVIRUS, SINGLE SITE MUTANT H2142Y -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ar9
TitleP1/MAHONEY POLIOVIRUS, SINGLE SITE MUTANT H2142Y
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 / 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 / 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: 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_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / 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_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)98,4957
Polymers97,9675
Non-polymers5282
Water9,638535
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)5,909,713420
Polymers5,878,042300
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
  • 492 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)492,47635
Polymers489,83725
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
  • 591 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)590,97142
Polymers587,80430
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
  • 2.95 MDa, 150 polymers
Theoretical massNumber of molelcules
Total (without water)2,954,857210
Polymers2,939,021150
Non-polymers15,83660
Water2,702150
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)319.950, 355.150, 377.050
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(0.30923344, -0.81767247, 0.48623159), (0.80040263, 0.49978355, 0.33034972), (-0.51276242, 0.28700732, 0.80901699)45.77764, 31.10171, -17.98063
3generate(-0.80816317, -0.5219589, 0.27361081), (0.47814841, -0.30987081, 0.82154294), (-0.34367538, 0.79490706, 0.5)25.75986, 77.34648, -47.07391
4generate(-0.8079857, 0.47847462, -0.34402764), (-0.52141829, -0.31004828, 0.79476733), (0.27358857, 0.82179903, 0.5)-32.38945, 74.82561, -47.07391
5generate(0.30952059, 0.80106295, -0.51312843), (-0.81693026, 0.4994964, 0.28702586), (0.48599165, 0.33051945, 0.80901699)-48.30992, 27.02286, -17.98063
6generate(-0.99622977, -0.08696857), (-0.08653977, 0.99622977), (-1)-188.29564
7generate(-0.37767743, 0.7711242, -0.51312843), (0.77062394, 0.56866044, 0.28702586), (0.51276242, -0.28700732, -0.80901699)-48.30992, 27.02286, -170.31501
8generate(0.76353233, 0.54694002, -0.34402764), (0.54628393, -0.26353233, 0.79476733), (0.34367538, -0.79490706, -0.5)-32.38945, 74.82561, -141.22173
9generate(0.85028641, -0.4497062, 0.27361081), (-0.44952954, -0.35028641, 0.82154294), (-0.27358857, -0.82179903, -0.5)25.75986, 77.34648, -141.22173
10generate(-0.23730637, -0.84148325, 0.48623159), (-0.84063609, 0.42828938, 0.33034972), (-0.48599165, -0.33051945, -0.80901699)45.77764, 31.10171, -170.31501
11generate(-0.04346578, -0.00189365, 0.99936002), (0.99769009, 0.04346578, 0.04332386), (-0.04331603, 0.99917932)94.08757, 4.07885, -94.14782
12generate(-0.52739102, 0.321418, 0.78673924), (0.32109441, -0.78162597, 0.53451708), (0.786351, 0.53479171, 0.30901699)74.06978, 50.32362, -65.05454
13generate(-0.30923344, 0.81767247, 0.48623159), (-0.80040263, -0.49978355, 0.33034972), (0.51276242, -0.28700732, 0.80901699)45.77764, 31.10171, -17.98063
14generate(0.30952059, 0.80106295, 0.51312843), (-0.81693026, 0.4994964, -0.28702586), (-0.48599165, -0.33051945, 0.80901699)48.30992, -27.02286, -17.98063
15generate(0.47377405, 0.29454323, 0.83025924), (0.29435215, 0.83524294, -0.46441761), (-0.82966703, 0.46438761, 0.30901699)78.1671, -43.72391, -65.05454
16generate(0.04346578, 0.00189365, 0.99936002), (-0.99769009, -0.04346578, 0.04332386), (0.04331603, -0.99917932)94.08757, 4.07885, -94.14782
17generate(-0.49747751, 0.25222929, 0.83025924), (-0.36552411, 0.8064945, -0.46441761), (-0.786351, -0.53479171, -0.30901699)78.1671, -43.72391, -123.2411
18generate(-0.37767743, 0.7711242, 0.51312843), (0.77062394, 0.56866044, -0.28702586), (-0.51276242, 0.28700732, -0.80901699)48.30992, -27.02286, -170.31501
19generate(0.23730637, 0.84148325, 0.48623159), (0.84063609, -0.42828938, 0.33034972), (0.48599165, 0.33051945, -0.80901699)45.77764, 31.10171, -170.31501
20generate(0.4975872, 0.36607262, 0.78673924), (-0.25224208, -0.80660418, 0.53451708), (0.82966703, -0.46438761, -0.30901699)74.06978, 50.32362, -123.2411
21generate(-0.04328831, 0.99853987, -0.04352), (-0.00187662, 0.0432883, 0.99893469), (0.99875407, 0.04351213)-4.09731, 94.04752, -94.14782
22generate(0.80816317, 0.5219589, 0.27361081), (-0.47814841, 0.30987081, 0.82154294), (0.34367538, -0.79490706, 0.5)25.75986, 77.34648, -47.07391
23generate(0.52739102, -0.321418, 0.78673924), (-0.32109441, 0.78162597, 0.53451708), (-0.786351, -0.53479171, 0.30901699)74.06978, 50.32362, -65.05454
24generate(-0.4975872, -0.36607262, 0.78673924), (0.25224208, 0.80660418, 0.53451708), (-0.82966703, 0.46438761, -0.30901699)74.06978, 50.32362, -123.2411
25generate(-0.85028641, 0.4497062, 0.27361081), (0.44952954, 0.35028641, 0.82154294), (0.27358857, 0.82179903, -0.5)25.75986, 77.34648, -141.22173
26generate(0.04328831, -0.99853987, -0.04352), (0.00187662, -0.0432883, 0.99893469), (-0.99875407, -0.04351213)-4.09731, 94.04752, -94.14782
27generate(-0.76353233, -0.54694002, -0.34402764), (-0.54628393, 0.26353233, 0.79476733), (-0.34367538, 0.79490706, -0.5)-32.38945, 74.82561, -141.22173
28generate(-0.49747751, 0.25222929, -0.83025924), (-0.36552411, 0.8064945, 0.46441761), (0.786351, 0.53479171, -0.30901699)-78.1671, 43.72391, -123.2411
29generate(0.47377405, 0.29454323, -0.83025924), (0.29435215, 0.83524294, 0.46441761), (0.82966703, -0.46438761, 0.30901699)-78.1671, 43.72391, -65.05454
30generate(0.8079857, -0.47847462, -0.34402764), (0.52141829, 0.31004828, 0.79476733), (-0.27358857, -0.82179903, 0.5)-32.38945, 74.82561, -47.07391

-
Components

-
Protein/peptide , 1 types, 1 molecules 0

#1: Protein/peptide P1/MAHONEY POLIOVIRUS


Mass: 437.404 Da / Num. of mol.: 1 / Fragment: VIRUS PROTOMER / Mutation: CHAIN 2, H142Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney

-
Protein , 4 types, 4 molecules 1234

#2: Protein P1/MAHONEY POLIOVIRUS


Mass: 33488.613 Da / Num. of mol.: 1 / Fragment: VIRUS PROTOMER / Mutation: CHAIN 2, H142Y
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: 30100.811 Da / Num. of mol.: 1 / Fragment: VIRUS PROTOMER / Mutation: CHAIN 2, H142Y
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 2, H142Y
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 2, H142Y
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

-
Non-polymers , 3 types, 537 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.: 535 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / 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: 777630 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.15
Reflection
*PLUS
Num. measured all: 2807335

-
Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
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
Rwork0.244 --
obs-777630 81 %
Refinement stepCycle: LAST / Resolution: 2.9→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6634 0 36 535 7205
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.013
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_deg2.54
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d25.8
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d1.29
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
Rwork0.347 67285
Software
*PLUS
Name: 'PROTOMER-BOX-BASED PSEUDO-REAL-SPACE' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29
LS refinement shell
*PLUS
Rfactor obs: 0.347

+
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