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- PDB-1fpn: HUMAN RHINOVIRUS SEROTYPE 2 (HRV2) -

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Basic information

Entry
Database: PDB / ID: 1fpn
TitleHUMAN RHINOVIRUS SEROTYPE 2 (HRV2)
Components(COAT PROTEIN ...) x 4
KeywordsVIRUS / human rhinovirus / pocket factor / 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 / 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 ...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 / 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 / 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 / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
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) / 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 / 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
LAURIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsVerdaguer, N. / Blaas, D. / Fita, I.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structure of human rhinovirus serotype 2 (HRV2).
Authors: Verdaguer, N. / Blaas, D. / Fita, I.
History
DepositionAug 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: COAT PROTEIN VP1
2: COAT PROTEIN VP2
3: COAT PROTEIN VP3
4: COAT PROTEIN VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5995
Polymers95,3994
Non-polymers2001
Water2,864159
1
1: COAT PROTEIN VP1
2: COAT PROTEIN VP2
3: COAT PROTEIN VP3
4: COAT PROTEIN VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,735,968300
Polymers5,723,949240
Non-polymers12,01960
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: COAT PROTEIN VP1
2: COAT PROTEIN VP2
3: COAT PROTEIN VP3
4: COAT PROTEIN VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 478 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)477,99725
Polymers476,99620
Non-polymers1,0025
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: COAT PROTEIN VP1
2: COAT PROTEIN VP2
3: COAT PROTEIN VP3
4: COAT PROTEIN VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 574 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)573,59730
Polymers572,39524
Non-polymers1,2026
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: COAT PROTEIN VP1
2: COAT PROTEIN VP2
3: COAT PROTEIN VP3
4: COAT PROTEIN VP4
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 1.43 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,433,99275
Polymers1,430,98760
Non-polymers3,00515
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)308.680, 352.980, 380.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Components on special symmetry positions
IDModelComponents
112-5023-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.80901699, -0.5), (0.80901699, 0.5, -0.30901699), (0.5, -0.30901699, 0.80901699)
3generate(-0.80901699, -0.5, -0.30901699), (0.5, -0.30901699, -0.80901699), (0.30901699, -0.80901699, 0.5)
4generate(-0.80901699, 0.5, 0.30901699), (-0.5, -0.30901699, -0.80901699), (-0.30901699, -0.80901699, 0.5)
5generate(0.30901699, 0.80901699, 0.5), (-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699)
6generate(-0.5, -0.30901699, 0.80901699), (-0.30901699, -0.80901699, -0.5), (0.80901699, -0.5, 0.30901699)
7generate(1), (-1), (-1)
8generate(0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699)
9generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
10generate(-0.30901699, -0.80901699, 0.5), (0.80901699, -0.5, -0.30901699), (0.5, 0.30901699, 0.80901699)
11generate(1), (1), (1)
12generate(0.80901699, 0.5, -0.30901699), (0.5, -0.30901699, 0.80901699), (0.30901699, -0.80901699, -0.5)
13generate(0.5, -0.30901699, -0.80901699), (0.30901699, -0.80901699, 0.5), (-0.80901699, -0.5, -0.30901699)
14generate(-0.5, -0.30901699, -0.80901699), (-0.30901699, -0.80901699, 0.5), (-0.80901699, 0.5, 0.30901699)
15generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)

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Components

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COAT PROTEIN ... , 4 types, 4 molecules 1234

#1: Protein COAT PROTEIN VP1


Mass: 32924.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CELL_LINE: HELA CELLS / Source: (natural) Human rhinovirus 2 / Genus: Rhinovirus / Species: Human rhinovirus A / References: UniProt: P04936
#2: Protein COAT PROTEIN VP2


Mass: 29009.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CELL_LINE: HELA CELLS / Source: (natural) Human rhinovirus 2 / Genus: Rhinovirus / Species: Human rhinovirus A / References: UniProt: P04936
#3: Protein COAT PROTEIN VP3


Mass: 26107.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CELL_LINE: HELA CELLS / Source: (natural) Human rhinovirus 2 / Genus: Rhinovirus / Species: Human rhinovirus A / References: UniProt: P04936
#4: Protein COAT PROTEIN VP4


Mass: 7356.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CELL_LINE: HELA CELLS / Source: (natural) Human rhinovirus 2 / Genus: Rhinovirus / Species: Human rhinovirus A / References: UniProt: P04936

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Non-polymers , 2 types, 160 molecules

#5: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 65

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulphate, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlvirus1drop
250 mMTris-HCl1drop
30.4 Mammonium sulfate1reservoir
40.1 Msodium/potassium phosphate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG X1110.96
SYNCHROTRONESRF ID14-220.9315
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJul 15, 1998
MARRESEARCH2CCDMar 2, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961
20.93151
ReflectionResolution: 2.5→30 Å / Num. all: 504407 / Num. obs: 392077 / % possible obs: 58.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.3 % / Biso Wilson estimate: 34.88 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 7.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.23 / Num. unique all: 33646 / % possible all: 55.8
Reflection shell
*PLUS
% possible obs: 55.8 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementResolution: 2.6→20 Å / σ(F): 2 /
RfactorNum. reflection
obs0.18 355153
all-377428
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6143 0 14 159 6316
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_dihedral_angle_d1.9
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d

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