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- PDB-1r1a: CRYSTAL STRUCTURE OF HUMAN RHINOVIRUS SEROTYPE 1A (HRV1A) -

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Basic information

Entry
Database: PDB / ID: 1r1a
TitleCRYSTAL STRUCTURE OF HUMAN RHINOVIRUS SEROTYPE 1A (HRV1A)
Components
  • HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)
  • HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
  • HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
  • HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
KeywordsVIRUS / RHINOVIRUS 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 / 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 ...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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / 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 / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
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) ...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 / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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
sucrose / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 1A
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsKim, S. / Rossmann, M.G.
Citation
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.G. / Pevear, D.C. / Dutko, F.J. / Felock, P.J. / Diana, G.D. / McKinlay, M.A.
#1: 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. / Rueckert, R.R. / Sherry, B. / Vriend, G.
History
DepositionMar 15, 1989Processing site: BNL
Revision 1.0Jul 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 7, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.process_site / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Feb 8, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / cell ...atom_site / cell / chem_comp / database_2 / database_PDB_matrix / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / 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 / _chem_comp.pdbx_synonyms / _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[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _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_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_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_angle.linker_flag / _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 3.1Mar 15, 2023Group: Advisory / Category: pdbx_database_remark
Revision 3.2Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_mon_prot_cis
Item: _struct_mon_prot_cis.pdbx_omega_angle

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8295
Polymers92,4864
Non-polymers3421
Water00
1
1: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,569,714300
Polymers5,549,176240
Non-polymers20,53860
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 1A COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 5


  • icosahedral pentamer
  • 464 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)464,14325
Polymers462,43120
Non-polymers1,7115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 557 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)556,97130
Polymers554,91824
Non-polymers2,0546
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 1A COAT PROTEIN (SUBUNIT VP1)
2: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
3: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
4: HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
hetero molecules
x 10


  • crystal asymmetric unit, crystal frame
  • 928 kDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)928,28650
Polymers924,86340
Non-polymers3,42310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)341.300, 341.300, 465.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.56363135, -0.75576154, 0.33338397), (0.75581305, 0.30901668, -0.57728236), (0.33326614, 0.57735015, 0.74538593)110.09668, 6.33845, -84.09901
3generate(-0.14242854, -0.46703455, 0.87269318), (0.46717012, -0.80901718, -0.35671208), (0.87261991, 0.35688978, 0.33341172)139.323, 140.05852, -106.43423
4generate(-0.14242891, 0.46717008, 0.87262064), (-0.46703407, -0.80901679, 0.3568902), (0.87269274, -0.35671236, 0.33341172)47.28918, 216.36362, -36.13915
5generate(0.56363075, 0.7558133, 0.33326659), (-0.75576107, 0.30901731, 0.57735039), (0.33338398, -0.57728238, 0.74538593)-38.81717, 129.8027, 29.64083
6generate(0.16673337, 0.64541332, -0.74541405), (-0.64552899, -0.49999974, -0.57731465), (-0.74531312, 0.57744419, 0.33326637)165.42984, 325.18945, 147.95292
7generate(0.3333667, -0.35693209, -0.87262064), (-0.93414613, 4.502E-5, -0.3568902), (0.1274244, 0.93413027, -0.33341172)250.56614, 299.50122, 41.52915
8generate(-0.37269292, -0.86605136, -0.33324944), (-0.64541945, 0.49995502, -0.57747627), (0.6667334, -0.00013592, -0.74529608)358.39285, 226.66923, 89.51868
9generate(-0.97569509, -0.17835896, 0.12730688), (-0.1783594, 0.30887163, -0.93423039), (0.12730717, -0.93423027, -0.33317653)339.89712, 207.34481, 225.60162
10generate(-0.64231131, 0.75577758, -0.12742485), (-0.1784271, -0.30913439, -0.9341305), (-0.74538556, -0.57726613, 0.33341172)220.63943, 268.23366, 261.71597

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Components

#1: Protein HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)


Mass: 32610.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 1A / Genus: Rhinovirus / Species: Human rhinovirus A / Plasmid: CLASSIFIED / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P23008
#2: Protein HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)


Mass: 29114.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 1A / Genus: Rhinovirus / Species: Human rhinovirus A / Plasmid: CLASSIFIED / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P23008
#3: Protein HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)


Mass: 26176.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 1A / Genus: Rhinovirus / Species: Human rhinovirus A / Plasmid: CLASSIFIED / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P23008
#4: Protein/peptide HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)


Mass: 4583.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 1A / Genus: Rhinovirus / Species: Human rhinovirus A / Plasmid: CLASSIFIED / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P23008
#5: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Temperature: 6 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.15 Mammonium formate11
23-5 mg/mlvirus12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 3.2→10 Å /
RfactorNum. reflection
obs0.293 121431
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6223 0 23 0 6246
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.293
Solvent computation
*PLUS
Displacement parameters
*PLUS

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