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- PDB-1v9u: Human Rhinovirus 2 bound to a fragment of its cellular receptor p... -

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Basic information

Entry
Database: PDB / ID: 1v9u
TitleHuman Rhinovirus 2 bound to a fragment of its cellular receptor protein
Components
  • (Coat protein ...) x 4
  • LDL-receptor class A 3
KeywordsVirus/Receptor / human rhinovirus / VLDL-receptor / virus-protein complex / Icosahedral virus / Virus-Receptor COMPLEX
Function / homology
Function and homology information


reelin receptor activity / glycoprotein transport / VLDL clearance / very-low-density lipoprotein particle receptor activity / ventral spinal cord development / Reelin signalling pathway / very-low-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / reelin-mediated signaling pathway ...reelin receptor activity / glycoprotein transport / VLDL clearance / very-low-density lipoprotein particle receptor activity / ventral spinal cord development / Reelin signalling pathway / very-low-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / reelin-mediated signaling pathway / very-low-density lipoprotein particle / cargo receptor activity / positive regulation of dendrite development / dendrite morphogenesis / lipid transport / regulation of synapse assembly / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / apolipoprotein binding / clathrin-coated pit / receptor-mediated endocytosis / cholesterol metabolic process / VLDLR internalisation and degradation / ribonucleoside triphosphate phosphatase 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 / memory / calcium-dependent protein binding / nervous system development / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / receptor complex / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / lysosomal membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / calcium ion binding / virion attachment to host cell / host cell nucleus / glutamatergic synapse / structural molecule activity / signal transduction / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / plasma membrane
Similarity search - Function
: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / : / Calcium-binding EGF domain ...: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / : / Calcium-binding EGF domain / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / Jelly Rolls - #20 / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / 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. / 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 / Very low-density lipoprotein receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Human rhinovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsVerdaguer, N. / Fita, I. / Reithmayer, M. / Moser, R. / Blaas, D.
CitationJournal: NAT.STRUCT.MOL.BIOL. / Year: 2004
Title: X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein
Authors: Verdaguer, N. / Fita, I. / Reithmayer, M. / Moser, R. / Blaas, D.
History
DepositionFeb 3, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Coat protein VP1
2: Coat protein VP2
3: Coat protein VP3
4: Coat protein VP4
5: LDL-receptor class A 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1727
Polymers99,9325
Non-polymers2402
Water00
1
1: Coat protein VP1
2: Coat protein VP2
3: Coat protein VP3
4: Coat protein VP4
5: LDL-receptor class A 3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,010,343420
Polymers5,995,919300
Non-polymers14,424120
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: Coat protein VP1
2: Coat protein VP2
3: Coat protein VP3
4: Coat protein VP4
5: LDL-receptor class A 3
hetero molecules
x 5


  • icosahedral pentamer
  • 501 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)500,86235
Polymers499,66025
Non-polymers1,20210
Water0
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
5: LDL-receptor class A 3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 601 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)601,03442
Polymers599,59230
Non-polymers1,44212
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: Coat protein VP1
2: Coat protein VP2
3: Coat protein VP3
4: Coat protein VP4
5: LDL-receptor class A 3
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 3.01 MDa, 150 polymers
Theoretical massNumber of molelcules
Total (without water)3,005,171210
Polymers2,997,960150
Non-polymers7,21260
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)313.100, 348.790, 380.890
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(0.30940681, -0.80007327, -0.51395544), (0.81732987, 0.5, -0.28630733), (0.48604456, -0.3314857, 0.80862718)-69.43036, -43.39, -28.76633
3generate(-0.80799645, -0.47721587, -0.34555281), (0.52239424, -0.30901699, -0.79474068), (0.27248118, -0.82266245, 0.49897946)-41.41279, -113.59649, -71.39065
4generate(-0.80799645, 0.52239424, 0.27248118), (-0.47721587, -0.30901699, -0.82266245), (-0.34555281, -0.79474068, 0.49897946)45.33337, -113.59649, -68.9676
5generate(0.30940681, 0.81732987, 0.48604456), (-0.80007327, 0.5, -0.3314857), (-0.51395544, -0.28630733, 0.80862718)70.92789, -43.39, -24.84575
6generate(-0.54453002, -0.29493563, 0.78517516), (-0.29493563, -0.80901699, -0.50843336), (0.78517516, -0.50843336, 0.35354702)-25.59451, -156.98649, -44.12185
7generate(-0.02791088, 0.02792177, 0.99922038), (-0.99961011, -0.02792177), (-0.00077963, -0.99961011, 0.02791088)2.42305, -86.78, -86.74617
8generate(0.4998511, -0.29493563, 0.8143475), (-0.3228574, 0.80901699, 0.49117676), (-0.80368649, -0.50843336, 0.30916589)-25.59451, -16.57351, -44.12185
9generate(0.30940681, -0.81732987, 0.48604456), (0.80007327, 0.5, 0.3314857), (-0.51395544, 0.28630733, 0.80862718)-70.92789, -43.39, 24.84575
10generate(-0.33605623, -0.81732987, 0.46801506), (0.81732987, -0.5, -0.28630733), (0.46801506, 0.28630733, 0.83605623)-70.92789, -130.17, 24.84575
11generate(-0.7915262, -0.52239424, -0.3171601), (-0.52239424, 0.30901699, 0.79474068), (-0.3171601, 0.79474068, -0.51749079)-45.33337, -59.96351, 68.9676
12generate(-0.82602595, 0.47721587, 0.29991022), (0.47721587, 0.30901699, 0.82266245), (0.29991022, 0.82266245, -0.48299104)41.41279, -59.96351, 71.39065
13generate(0.28023447, 0.80007327, 0.53042569), (0.80007327, -0.5, 0.3314857), (0.53042569, 0.3314857, -0.78023447)69.43036, -130.17, 28.76633
14generate(0.99844075, 0.05582176), (-1), (0.05582176, -0.99844075)-173.56
15generate(0.33605623, -0.81732987, -0.46801506), (-0.81732987, -0.5, 0.28630733), (-0.46801506, 0.28630733, -0.83605623)-70.92789, -130.17, 24.84575
16generate(-0.02791088, 0.99961011, -0.00077962), (-0.02792177, 0.99961011), (0.99922037, 0.02792177, 0.02791088)86.74617, -86.78, 2.42305
17generate(0.80799645, 0.52239424, -0.27248118), (0.47721587, -0.30901699, 0.82266245), (0.34555281, -0.79474068, -0.49897946)45.33337, -113.59649, -68.9676
18generate(0.54453002, -0.29493563, -0.78517516), (0.29493563, -0.80901699, 0.50843336), (-0.78517516, -0.50843336, -0.35354702)-25.59451, -156.98649, -44.12185
19generate(-0.45420852, -0.3228574, -0.83033591), (-0.3228574, -0.80901699, 0.49117676), (-0.83033591, 0.49117676, 0.26322551)-28.01756, -156.98649, 42.62432
20generate(-0.80799645, 0.47721587, -0.34555281), (-0.52239424, -0.30901699, 0.79474068), (0.27248118, 0.82266245, 0.49897946)41.41279, -113.59649, 71.39065
21generate(-0.4998511, 0.3228574, 0.80368649), (-0.29493563, 0.80901699, -0.50843336), (-0.8143475, -0.49117676, -0.30916589)28.01756, -16.57351, -42.62432
22generate(0.4998511, 0.29493563, 0.8143475), (0.3228574, 0.80901699, -0.49117676), (-0.80368649, 0.50843336, 0.30916589)25.59451, -16.57351, 44.12185
23generate(0.7915262, -0.52239424, 0.3171601), (0.52239424, 0.30901699, -0.79474068), (0.3171601, 0.79474068, 0.51749079)-45.33337, -59.96351, 68.9676
24generate(-0.02791088, -0.99961011, -0.00077963), (0.02792177, -0.99961011), (0.99922037, -0.02792177, 0.02791088)-86.74617, -86.78, -2.42305
25generate(-0.82602595, -0.47721587, 0.29991022), (-0.47721587, 0.30901699, -0.82266245), (0.29991022, -0.82266245, -0.48299104)-41.41279, -59.96351, -71.39065
26generate(-0.28023447, 0.80007327, -0.53042569), (-0.80007327, -0.5, -0.3314857), (-0.53042569, 0.3314857, 0.78023447)69.43036, -130.17, 28.76633
27generate(0.30940681, 0.80007327, -0.51395544), (-0.81732987, 0.5, 0.28630733), (0.48604456, 0.3314857, 0.80862718)69.43036, -43.39, 28.76633
28generate(0.4998511, 0.3228574, -0.80368649), (0.29493563, 0.80901699, 0.50843336), (0.8143475, -0.49117676, 0.30916589)28.01756, -16.57351, -42.62432
29generate(0.02791088, 0.02792177, -0.99922038), (0.99961011, 0.02792177), (0.00077963, -0.99961011, -0.02791088)2.42305, -86.78, -86.74617
30generate(-0.45420852, 0.3228574, -0.83033591), (0.3228574, -0.80901699, -0.49117676), (-0.83033591, -0.49117676, 0.26322551)28.01756, -156.98649, -42.62432

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Components

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Coat protein ... , 4 types, 4 molecules 1234

#1: Protein Coat protein VP1 / P1D


Mass: 32924.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 2 / Genus: Rhinovirus / Species: Human rhinovirus A / Strain: serotype 2 / References: UniProt: P04936
#2: Protein Coat protein VP2 / P1B


Mass: 29009.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 2 / Genus: Rhinovirus / Species: Human rhinovirus A / Strain: serotype 2 / References: UniProt: P04936
#3: Protein Coat protein VP3 / P1C


Mass: 26107.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 2 / Genus: Rhinovirus / Species: Human rhinovirus A / Strain: serotype 2 / References: UniProt: P04936
#4: Protein Coat protein VP4 / P1A


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

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Protein/peptide , 1 types, 1 molecules 5

#5: Protein/peptide LDL-receptor class A 3 / VLDL-receptor module V3


Mass: 4532.837 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMAL-c2x / Production host: Escherichia coli (E. coli) / References: UniProt: P98155

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#7: Chemical ChemComp-CA / CALCIUM ION


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

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonim sulfate, sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 9, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. all: 379575 / Num. obs: 362883 / % possible obs: 71.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FPN

1fpn


Resolution: 3.6→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.295 17241 random
Rwork0.285 --
all-360201 -
obs-347418 -
Refinement stepCycle: LAST / Resolution: 3.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6436 0 15 0 6451
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0128
X-RAY DIFFRACTIONc_angle_deg1.63

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