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- PDB-1k5m: Crystal Structure of a Human Rhinovirus Type 14:Human Immunodefic... -

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Basic information

Entry
Database: PDB / ID: 1k5m
TitleCrystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3 Loop Chimeric Virus MN-III-2
Components
  • (COAT PROTEIN ...) x 3
  • CHIMERA OF HRV14 COAT PROTEIN VP2 (P1B) AND the V3 loop of HIV-1 gp120
KeywordsVIRUS / engineered rhinovirus / HIV-1 V3 loop / beta turns / Icosahedral virus
Function / homology
Function and homology information


lysis of host organelle involved in viral entry into host cell / Dectin-2 family / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / 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 ...lysis of host organelle involved in viral entry into host cell / Dectin-2 family / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / 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 / clathrin-dependent endocytosis of virus by host cell / DNA replication / RNA helicase activity / viral protein processing / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / fusion of virus membrane with host plasma membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / identical protein binding / membrane
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Picornavirus coat protein VP4 superfamily / Jelly Rolls - #20 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 ...Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Picornavirus coat protein VP4 superfamily / Jelly Rolls - #20 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 / Few Secondary Structures / Irregular / 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
SPHINGOSINE / Genome polyprotein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman rhinovirus 14
Human immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDing, J. / Smith, A.D. / Geisler, S.C. / Ma, X. / Arnold, G.F. / Arnold, E.
Citation
Journal: Structure / Year: 2002
Title: Crystal Structure of a Human Rhinovirus that Displays Part of the HIV-1 V3 Loop and Induces Neutralizing Antibodies against HIV-1
Authors: Ding, J. / Smith, A.D. / Geisler, S.C. / Ma, X. / Arnold, G.F. / Arnold, E.
#1: Journal: J.Virol. / Year: 1998
Title: Human rhinovirus type 14:human immunodeficiency virus type 1 (HIV-1) V3 loop chimeras from a combinational library induce potent neutralizing antibody responses against HIV-1
Authors: Smith, A.D. / Geisler, S.C. / Chen, A.A. / Resnick, D.A. / Roy, B.M. / Lewi, P.J. / Arnold, E. / Arnold, G.F.
History
DepositionOct 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Aug 16, 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_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details / _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
A: COAT PROTEIN VP1 (P1D)
B: CHIMERA OF HRV14 COAT PROTEIN VP2 (P1B) AND the V3 loop of HIV-1 gp120
C: COAT PROTEIN VP3 (P1C)
D: COAT PROTEIN VP4 (P1A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3785
Polymers96,0784
Non-polymers2991
Water11,476637
1
A: COAT PROTEIN VP1 (P1D)
B: CHIMERA OF HRV14 COAT PROTEIN VP2 (P1B) AND the V3 loop of HIV-1 gp120
C: COAT PROTEIN VP3 (P1C)
D: COAT PROTEIN VP4 (P1A)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,782,666300
Polymers5,764,697240
Non-polymers17,97060
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 (P1D)
B: CHIMERA OF HRV14 COAT PROTEIN VP2 (P1B) AND the V3 loop of HIV-1 gp120
C: COAT PROTEIN VP3 (P1C)
D: COAT PROTEIN VP4 (P1A)
hetero molecules
x 5


  • icosahedral pentamer
  • 482 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)481,88925
Polymers480,39120
Non-polymers1,4975
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN VP1 (P1D)
B: CHIMERA OF HRV14 COAT PROTEIN VP2 (P1B) AND the V3 loop of HIV-1 gp120
C: COAT PROTEIN VP3 (P1C)
D: COAT PROTEIN VP4 (P1A)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 578 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)578,26730
Polymers576,47024
Non-polymers1,7976
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
A: COAT PROTEIN VP1 (P1D)
B: CHIMERA OF HRV14 COAT PROTEIN VP2 (P1B) AND the V3 loop of HIV-1 gp120
C: COAT PROTEIN VP3 (P1C)
D: COAT PROTEIN VP4 (P1A)
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 1.45 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,445,66775
Polymers1,441,17460
Non-polymers4,49215
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)318.9, 349.3, 368.4
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))
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(1), (1), (1)
7generate(-0.5, 0.30901699, 0.80901699), (0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699)
8generate(-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699)
9generate(0.30901699, 0.80901699, 0.5), (-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699)
10generate(0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699)
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 ... , 3 types, 3 molecules ACD

#1: Protein COAT PROTEIN VP1 (P1D)


Mass: 32560.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Plasmid: p3IIST-MN-III-2 / Cell line (production host): H1-HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303
#3: Protein COAT PROTEIN VP3 (P1C)


Mass: 26236.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Plasmid: p3IIST-MN-III-2 / Cell line (production host): H1-HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303
#4: Protein COAT PROTEIN VP4 (P1A)


Mass: 7183.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Plasmid: p3IIST-MN-III-2 / Cell line (production host): H1-HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303

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Protein , 1 types, 1 molecules B

#2: Protein CHIMERA OF HRV14 COAT PROTEIN VP2 (P1B) AND the V3 loop of HIV-1 gp120


Mass: 30097.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE CHIMERA CONSISTS OF THE HRV14 COAT PROTEIN VP2 (P1B) AND RESIDUES 314-325 OF HIV-1 gp120.
Source: (gene. exp.) Human rhinovirus 14, (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate MN)
Genus: Rhinovirus / Species: Human rhinovirus B / Plasmid: p3IIST-MN-III-2 / Gene: env / Cell line (production host): H1-HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303, UniProt: P05877

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Non-polymers , 2 types, 638 molecules

#5: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 Mammonium formate1reservoir
20.15 Msodium HEPES1reservoirpH7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11081
21081
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONCHESS F120.92
Detector
TypeIDDetectorDateDetails
NONIUS CAD41CCDFeb 1, 1998mirror
ADSC QUANTUM 42CCDNov 1, 1998mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GraphiteSINGLE WAVELENGTHMx-ray1
2GraphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.921
ReflectionResolution: 2.7→50 Å / Num. all: 513239 / Num. obs: 513239 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 10
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4 / Num. unique all: 46826 / % possible all: 82.7
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 92.4 % / Num. measured all: 7100958
Reflection shell
*PLUS
% possible obs: 81.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Wild-type HRV14 structure coordinates (PDB entry 4RHV)

4rhv


Resolution: 2.7→50 Å / Isotropic thermal model: isotropic
Cross valid method: The free R-factor was calculated in early stages of model building and refinement to monitor the progress. Due to the strong interdependency of structure factors in the presence ...Cross valid method: The free R-factor was calculated in early stages of model building and refinement to monitor the progress. Due to the strong interdependency of structure factors in the presence of high NCS, the free R-factor did not provide any useful information. Therefore, in the later stages of structure refinement, all data were included and no free R factor was calculated.
σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.216 --
all0.216 513239 -
obs-494360 89 %
Displacement parametersBiso mean: 18.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6459 0 21 637 7117
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_improper_angle_d1.7
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Num. reflection Rfree: _ / Total num. of bins used: 10

Resolution (Å)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.7-2.80.274403744037473.1
2.8-2.910.26294469681
2.91-3.20.23629569386.6
3.2-3.660.21410147191.5
3.66-4.620.189310545795
4.62-500.203910666994.9
Xplor fileSerial no: 1 / Param file: parhcsdx.pro / Topol file: tophcsdx.pro
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 2 / Rfactor all: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / Rfactor all: 0.287

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