[English] 日本語
Yorodumi
- PDB-1rhi: HUMAN RHINOVIRUS 3 COAT PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rhi
TitleHUMAN RHINOVIRUS 3 COAT PROTEIN
Components(HUMAN RHINOVIRUS 3 COAT PROTEIN) x 4
KeywordsVIRUS / HUMAN RHINOVIRUS 3 / COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / 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 genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / 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 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 / DNA replication / 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 / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / 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 coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / 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
Biological speciesHuman rhinovirus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhao, R. / Rossmann, M.G.
Citation
#1: Journal: Protein Sci. / Year: 1994
Title: Viral Cell Recognition and Entry
Authors: Rossmann, M.G.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: A Comparison of the Anti-Rhinoviral Drug Binding Pocket in Hrv14 and Hrv1A
Authors: Kim, K.H. / Willingmann, P. / Gong, Z.X. / Kremer, M.J. / Chapman, M.S. / Minor, I. / Oliveira, M.A. / Rossmann, M.G. / Andries, K. / Diana, G.D. / al., et
#4: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of Human Rhinovirus Serotype 1A (Hrv1A)
Authors: Kim, S.S. / Smith, T.J. / Chapman, M.S. / Rossmann, M.C. / Pevear, D.C. / Dutko, F.J. / Felock, P.J. / Diana, G.D. / Mckinlay, M.A.
#5: Journal: Nature / Year: 1985
Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G. / al., et
History
DepositionJun 17, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 16, 2012Group: Advisory
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_assembly / pdbx_struct_assembly_gen / 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][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[2] / _pdbx_database_status.process_site / _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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 2.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: HUMAN RHINOVIRUS 3 COAT PROTEIN
2: HUMAN RHINOVIRUS 3 COAT PROTEIN
3: HUMAN RHINOVIRUS 3 COAT PROTEIN
4: HUMAN RHINOVIRUS 3 COAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3475
Polymers94,3074
Non-polymers401
Water0
1
1: HUMAN RHINOVIRUS 3 COAT PROTEIN
2: HUMAN RHINOVIRUS 3 COAT PROTEIN
3: HUMAN RHINOVIRUS 3 COAT PROTEIN
4: HUMAN RHINOVIRUS 3 COAT PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,660,834300
Polymers5,658,430240
Non-polymers2,40560
Water0
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: HUMAN RHINOVIRUS 3 COAT PROTEIN
2: HUMAN RHINOVIRUS 3 COAT PROTEIN
3: HUMAN RHINOVIRUS 3 COAT PROTEIN
4: HUMAN RHINOVIRUS 3 COAT PROTEIN
hetero molecules
x 5


  • icosahedral pentamer
  • 472 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)471,73625
Polymers471,53620
Non-polymers2005
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: HUMAN RHINOVIRUS 3 COAT PROTEIN
2: HUMAN RHINOVIRUS 3 COAT PROTEIN
3: HUMAN RHINOVIRUS 3 COAT PROTEIN
4: HUMAN RHINOVIRUS 3 COAT PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 566 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)566,08330
Polymers565,84324
Non-polymers2406
Water0
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: HUMAN RHINOVIRUS 3 COAT PROTEIN
2: HUMAN RHINOVIRUS 3 COAT PROTEIN
3: HUMAN RHINOVIRUS 3 COAT PROTEIN
4: HUMAN RHINOVIRUS 3 COAT PROTEIN
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 120-MERIC
  • 2.83 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,830,417150
Polymers2,829,215120
Non-polymers1,20230
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation29
Unit cell
Length a, b, c (Å)397.900, 341.800, 301.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.81609459, 0.49064786, -0.30537569), (-0.49064782, 0.30901699, -0.81472273), (-0.30537569, 0.8147228, 0.4929224)-41.99294, 59.13897, -69.72945
3generate(0.51852939, 0.30323705, -0.79948393), (-0.30323702, -0.80901699, -0.50352634), (-0.79948393, 0.50352639, -0.32754638)-25.95306, 154.82783, -43.09517
4generate(0.51852939, -0.30323705, -0.79948393), (0.30323702, -0.80901699, 0.50352634), (-0.79948393, -0.50352639, -0.32754638)25.95306, 154.82783, 43.09517
5generate(0.81609459, -0.49064786, -0.30537569), (0.49064782, 0.30901699, 0.81472273), (-0.30537569, -0.8147228, 0.4929224)41.99294, 59.13897, 69.72945
6generate(0.32038678, 0.81252289, -0.48698965), (0.81252282, -0.5, -0.29967749), (-0.48698965, -0.29967752, -0.82038678)-69.54117, 128.38008, 25.64842
7generate(0.01151814, 0.0115189, -0.99986731), (0.99993361, 0.0115189), (0.00013269, -0.9999337, -0.01151814)-0.98586, 85.58672, 85.58105
8generate(0.30908333, -0.80540382, -0.50575907), (0.81252282, 0.5, -0.29967749), (0.49424093, -0.31831549, 0.80895065)68.93187, 42.79336, 27.24358
9generate(0.80185739, -0.50928584, 0.31249429), (0.50928579, 0.30901699, -0.80320383), (0.31249428, 0.8032039, 0.5071596)43.5881, 59.13897, -68.74359
10generate(0.8088433, 0.49064786, 0.32409443), (0.50928579, -0.30901699, -0.80320383), (-0.29393955, 0.8147228, -0.49982631)-41.99294, 112.03447, -69.72945
11generate(-0.80185739, -0.50928584, -0.31249429), (-0.50928579, 0.30901699, 0.80320383), (-0.31249428, 0.8032039, -0.5071596)43.5881, 59.13897, -68.74359
12generate(-0.30908333, -0.80540382, 0.50575907), (-0.81252282, 0.5, 0.29967749), (-0.49424093, -0.31831549, -0.80895065)68.93187, 42.79336, 27.24358
13generate(-0.01151814, 0.0115189, 0.99986731), (-0.99993361, -0.0115189), (-0.00013269, -0.9999337, 0.01151814)-0.98586, 85.58672, 85.58105
14generate(-0.32038678, 0.81252289, 0.48698965), (-0.81252282, -0.5, 0.29967749), (0.48698965, -0.29967752, 0.82038678)-69.54117, 128.38008, 25.64842
15generate(-0.8088433, 0.49064786, -0.32409443), (-0.50928579, -0.30901699, 0.80320383), (0.29393955, 0.8147228, 0.49982631)-41.99294, 112.03447, -69.72945
16generate(0.8088433, -0.50928584, -0.29393955), (-0.49064782, -0.30901699, -0.81472273), (0.32409443, 0.8032039, -0.49982631)43.5881, 112.03447, -68.74359
17generate(0.99973463, 0.02303627), (-1), (0.02303627, -0.99973463)171.17344
18generate(0.8088433, 0.50928584, -0.29393955), (0.49064782, -0.30901699, 0.81472273), (0.32409443, -0.8032039, -0.49982631)-43.5881, 112.03447, 68.74359
19generate(0.49997466, 0.31475595, -0.80681722), (0.30323702, 0.80901699, 0.50352634), (0.81121676, -0.49640731, 0.30904233)-26.93893, 16.34561, 42.48587
20generate(0.49997466, -0.31475595, -0.80681722), (-0.30323702, 0.80901699, -0.50352634), (0.81121676, 0.49640731, 0.30904233)26.93893, 16.34561, -42.48587
21generate(-0.01151814, 0.9999337, -0.00013269), (-0.0115189, 0.99993361), (0.99986731, 0.0115189, 0.01151814)-85.58105, 85.58672, -0.98586
22generate(-0.49997466, 0.30323705, -0.81121676), (-0.31475592, 0.80901699, 0.49640727), (0.80681722, 0.50352639, -0.30904233)-25.95306, 16.34561, -43.09517
23generate(-0.30908333, -0.81252289, -0.49424093), (-0.80540374, 0.5, -0.31831546), (0.50575907, 0.29967752, -0.80895065)69.54117, 42.79336, -25.64842
24generate(0.29735051, -0.80540382, 0.51274498), (-0.80540374, -0.5, -0.31831546), (0.51274498, -0.31831549, -0.79735051)68.93187, 128.38008, 27.24358
25generate(0.48125592, 0.31475595, 0.81812067), (-0.31475592, -0.80901699, 0.49640727), (0.81812067, -0.49640731, -0.29027291)-26.93893, 154.82783, 42.48587
26generate(-0.29735051, -0.80540382, -0.51274498), (0.80540374, -0.5, 0.31831546), (-0.51274498, -0.31831549, 0.79735051)68.93187, 128.38008, 27.24358
27generate(0.30908333, -0.81252289, 0.49424093), (0.80540374, 0.5, 0.31831546), (-0.50575907, 0.29967752, 0.80895065)69.54117, 42.79336, -25.64842
28generate(0.49997466, 0.30323705, 0.81121676), (0.31475592, 0.80901699, -0.49640727), (-0.80681722, 0.50352639, 0.30904233)-25.95306, 16.34561, -43.09517
29generate(0.01151814, 0.9999337, 0.00013269), (0.0115189, -0.99993361), (-0.99986731, 0.0115189, -0.01151814)-85.58105, 85.58672, -0.98586
30generate(-0.48125592, 0.31475595, -0.81812067), (0.31475592, -0.80901699, -0.49640727), (-0.81812067, -0.49640731, 0.29027291)-26.93893, 154.82783, 42.48587

-
Components

#1: Protein HUMAN RHINOVIRUS 3 COAT PROTEIN


Mass: 32328.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 3 / Genus: Rhinovirus / Cell line: HELA CELL / Species: Human rhinovirus B / References: UniProt: Q82081
#2: Protein HUMAN RHINOVIRUS 3 COAT PROTEIN


Mass: 28700.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 3 / Genus: Rhinovirus / Cell line: HELA CELL / Species: Human rhinovirus B / References: UniProt: Q82081
#3: Protein HUMAN RHINOVIRUS 3 COAT PROTEIN


Mass: 26058.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 3 / Genus: Rhinovirus / Cell line: HELA CELL / Species: Human rhinovirus B / References: UniProt: Q82081
#4: Protein HUMAN RHINOVIRUS 3 COAT PROTEIN


Mass: 7219.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 3 / Genus: Rhinovirus / Cell line: HELA CELL / Species: Human rhinovirus B / References: UniProt: Q82081
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 45

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 49 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.2
Details: RESERVOIR SOLUTION: 10MM CACL2 AND 0.75% PEG8000 IN A 0.25M HEPES/0.75M NACL/PH7.2 BUFFER HANGING DROP: 5UL OF 10MG/ML VIRUS + 5UL OF RESERVOIR SOLUTION, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlvirus1drop
25 mM1dropCaCl2
30.375 %PEG80001drop
40.125 MHEPES1drop
50.375 M1dropNaCl
610 mM1reservoirCaCl2
70.75 %PEG80001reservoir
80.25 MHEPES1reservoir
90.75 M1reservoirNaCl

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Sep 16, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 730925 / % possible obs: 73.1 % / Observed criterion σ(I): 3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 3
Reflection shellResolution: 2.8→3.12 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 3 / % possible all: 47
Reflection shell
*PLUS
% possible obs: 47 % / Num. unique obs: 139901

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MGROSCdata reduction
MGRSCLdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN RHINOVIRUS 14

Resolution: 3→5 Å / σ(F): 3
Details: REFINEMENT WAS CARRIED OUT PRIMARILY TO OBTAIN REASONABLE GEOMETRY AND TO AVOID UNACCEPTABLE NON-BONDED ATOMIC CONTACTS. ICOSAHEDRAL SYMMETRY WAS RETAINED BY CONSTRAINING THE NON- ...Details: REFINEMENT WAS CARRIED OUT PRIMARILY TO OBTAIN REASONABLE GEOMETRY AND TO AVOID UNACCEPTABLE NON-BONDED ATOMIC CONTACTS. ICOSAHEDRAL SYMMETRY WAS RETAINED BY CONSTRAINING THE NON-CRYSTALLOGRAPHICALLY RELATED SUBUNITS DURING CONJUGATE GRADIENT ENERGY MINIMIZATION. THE PUTATIVE CALCIUM ION WAS NOT INCLUDED IN THE REFINEMENTS.
RfactorNum. reflection% reflection
Rfree0.288 -20 %
Rwork0.284 --
obs0.284 397586 64 %
Displacement parametersBiso mean: 15 Å2
Refinement stepCycle: LAST / Resolution: 3→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6287 0 1 0 6288
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.769
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.08
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.211
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: ICOSAHEDRON
LS refinement shellResolution: 3→3.1 Å
RfactorNum. reflection% reflection
Rfree0.349 -20 %
Rwork0.345 41869 -
obs--56 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION2TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.281
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.08
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.211

+
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