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- PDB-1na1: The structure of HRV14 when complexed with Pleconaril -

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Basic information

Entry
Database: PDB / ID: 1na1
TitleThe structure of HRV14 when complexed with Pleconaril
Components(Coat protein ...) x 4
KeywordsVIRUS / HRV14 / human rhinovirus 14 / Pleconaril / Icosahedral virus
Function / homology
Function and homology information


lysis of host organelle involved in viral entry into host cell / 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 ...lysis of host organelle involved in viral entry into host cell / 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 / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / 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. / 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
Chem-W11 / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 14
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZhang, Y. / Simpson, A.A. / Bator, C.M. / Chakravarty, S. / Pevear, D.C. / Skochko, G.A. / Tull, T.M. / Diana, G. / Rossmann, M.G.
CitationJournal: J.Virol. / Year: 2004
Title: Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds
Authors: Zhang, Y. / Simpson, A.A. / Ledford, R.M. / Bator, C.M. / Chakravarty, S. / Skochko, G.A. / Demenczuk, T.M. / Watanyar, A. / Pevear, D.C. / Rossmann, M.G.
History
DepositionNov 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_ncs_oper / struct_sheet / 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[1][3] / _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_main_chain_plane.improper_torsion_angle / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_sheet.number_strands / _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 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999 AUTHORS STATE THAT RESIDUE 170 (CHAIN B) CAN BE ILE OR LEU, AS SEEN IN OTHER DATABASE REFERENCE SEQUENCES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coat protein VP1
B: Coat protein VP2
C: Coat protein VP3
D: Coat protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8645
Polymers94,4834
Non-polymers3811
Water4,360242
1
A: Coat protein VP1
B: Coat protein VP2
C: Coat protein VP3
D: Coat protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,691,833300
Polymers5,668,952240
Non-polymers22,88160
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
A: Coat protein VP1
B: Coat protein VP2
C: Coat protein VP3
D: Coat protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 474 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)474,31925
Polymers472,41320
Non-polymers1,9075
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein VP1
B: Coat protein VP2
C: Coat protein VP3
D: Coat protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 569 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)569,18330
Polymers566,89524
Non-polymers2,2886
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
A: Coat protein VP1
B: Coat protein VP2
C: Coat protein VP3
D: Coat protein VP4
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 1.9 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,897,278100
Polymers1,889,65180
Non-polymers7,62720
Water1,44180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)437.16, 437.16, 437.16
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number198
Space group name H-MP213
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.46508664, -0.82946752, 0.309344), (0.84362899, 0.30933191, -0.43887538), (0.26834289, 0.465061, 0.84361543)-0.16142, -0.04374, 0.08828
3generate(-0.400447, -0.49849121, 0.768872), (0.53555286, -0.80818043, -0.24502863), (0.74351984, 0.31360912, 0.59059344)-0.1729, -0.2322, 0.0991
4generate(-0.40046285, 0.53553092, 0.74353192), (-0.49847766, -0.80817296, 0.31365062), (0.76885245, -0.24505427, 0.59060182)-0.01857, -0.30493, 0.0175
5generate(0.465061, 0.84361543, 0.26834289), (-0.82946752, 0.309344, 0.46508664), (0.30933191, -0.43887538, 0.84362899)0.08828, -0.16142, -0.04374
6generate(-0.62765509, -0.70421141, 0.3318665), (-0.70421141, 0.3318665, -0.62765509), (0.3318665, -0.62765509, -0.70421141)-0.306, -0.306, -0.306
7generate(-0.79695314, 0.45712261, 0.39486742), (-0.2159739, 0.3948795, -0.89299113), (-0.56413148, -0.7969275, -0.21596034)-0.14458, -0.26226, -0.39428
8generate(0.12094949, 0.9860868, -0.11403629), (-0.00694261, -0.11400318, -0.99345422), (-0.99263258, 0.1209789, -0.00694631)-0.00107, -0.3235, -0.28743
9generate(0.85754257, 0.15167061, -0.49155698), (-0.36599167, -0.49152296, -0.79020777), (-0.36146284, 0.85754866, -0.36601961)-0.0738, -0.4051, -0.1331
10generate(0.3948795, -0.89299113, -0.2159739), (-0.7969275, -0.21596034, -0.56413148), (0.45712261, 0.39486742, -0.79695314)-0.26226, -0.39428, -0.14458
11generate(-0.49152296, -0.79020777, -0.36599167), (0.85754866, -0.36601961, -0.36146284), (0.15167061, -0.49155698, 0.85754257)-0.4051, -0.1331, -0.0738
12generate(-0.99345422, -0.00694261, -0.11400318), (-0.00694631, -0.99263258, 0.1209789), (-0.11403629, 0.12094949, 0.9860868)-0.3235, -0.28743, -0.00107
13generate(-0.49849121, 0.768872, -0.400447), (-0.80818043, -0.24502863, 0.53555286), (0.31360912, 0.59059344, 0.74351984)-0.1729, -0.2322, 0.0991
14generate(0.309344, 0.46508664, -0.82946752), (-0.43887538, 0.84362899, 0.30933191), (0.84361543, 0.26834289, 0.465061)-0.16142, -0.04374, 0.08828
15generate(0.31365062, -0.49847766, -0.80817296), (0.59060182, 0.76885245, -0.24505427), (0.74353192, -0.40046285, 0.53553092)-0.30493, 0.0175, -0.01857
16generate(-0.24505427, 0.59060182, 0.76885245), (0.53553092, 0.74353192, -0.40046285), (-0.80817296, 0.31365062, -0.49847766)0.0175, -0.01857, -0.30493
17generate(0.59059344, 0.74351984, 0.31360912), (0.768872, -0.400447, -0.49849121), (-0.24502863, 0.53555286, -0.80818043)0.0991, -0.1729, -0.2322
18generate(0.9860868, -0.11403629, 0.12094949), (-0.11400318, -0.99345422, -0.00694261), (0.1209789, -0.00694631, -0.99263258)-0.00107, -0.3235, -0.28743
19generate(0.39486742, -0.79695314, 0.45712261), (-0.89299113, -0.2159739, 0.3948795), (-0.21596034, -0.56413148, -0.7969275)-0.14458, -0.26226, -0.39428
20generate(-0.36601961, -0.36146284, 0.85754866), (-0.49155698, 0.85754257, 0.15167061), (-0.79020777, -0.36599167, -0.49152296)-0.1331, -0.0738, -0.4051

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Components

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Coat protein ... , 4 types, 4 molecules ABCD

#1: Protein Coat protein VP1


Mass: 32560.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: HELA CELLS / Species: Human rhinovirus B / References: UniProt: P03303
#2: Protein Coat protein VP2


Mass: 28501.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: HELA CELLS / Species: Human rhinovirus B / References: UniProt: P03303
#3: Protein Coat protein VP3


Mass: 26236.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: HELA CELLS / Species: Human rhinovirus B / References: UniProt: P03303
#4: Protein Coat protein VP4


Mass: 7183.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: HELA CELLS / Species: Human rhinovirus B / References: UniProt: P03303

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Non-polymers , 2 types, 243 molecules

#5: Chemical ChemComp-W11 / 3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE / WIN63843


Mass: 381.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18F3N3O3 / Comment: antivirus*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, NaCl, CaCl2, PEG8K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.25 MHEPES1reservoir
20.25 M1reservoirNaCl
30.1 M1reservoirCaCl2
40.3 %PEG80001reservoir
520000 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Sep 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. all: 320952 / Num. obs: 320952 / % possible obs: 77.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.164
Reflection shellHighest resolution: 3.3 Å / % possible all: 77.8
Reflection
*PLUS
Num. measured all: 545390 / Rmerge(I) obs: 0.164
Reflection shell
*PLUS
% possible obs: 68.2 % / Rmerge(I) obs: 0.477

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
ENVELOPEmodel building
CNS1refinement
CCP4(TRUNCATE)data scaling
ENVELOPEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.228 16048 RANDOM
Rwork0.222 --
all0.223 --
obs0.223 319981 -
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6268 0 27 242 6537
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0096
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.54

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