1k5m

Crystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3 Loop Chimeric Virus MN-III-2

Method: X-RAY DIFFRACTION Dmax: 95.7 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

COAT PROTEIN VP1 (P1D)

Human rhinovirus 14

UniProt P03303

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 240 PDB declaration: 240-MERIC(240) Consistent with protein copy count Chain A; UniProt 568–856 Chain B; UniProt 70–228 Chain B; UniProt 229–331 Chain C; UniProt 332–567 Chain D; UniProt 2–69 Not recorded SPH SPHINGOSINE × 60 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å
2 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 568–856 Chain B; UniProt 70–228 Chain B; UniProt 229–331 Chain C; UniProt 332–567 Chain D; UniProt 2–69 Not recorded SPH SPHINGOSINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å
3 Insufficient information Heteromer Protein × 20 PDB declaration: eicosameric(20) Consistent with protein copy count Chain A; UniProt 568–856 Chain B; UniProt 70–228 Chain B; UniProt 229–331 Chain C; UniProt 332–567 Chain D; UniProt 2–69 Not recorded SPH SPHINGOSINE × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å
4 Insufficient information Heteromer Protein × 24 PDB declaration: 24-meric(24) Consistent with protein copy count Chain A; UniProt 568–856 Chain B; UniProt 70–228 Chain B; UniProt 229–331 Chain C; UniProt 332–567 Chain D; UniProt 2–69 Not recorded SPH SPHINGOSINE × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å
5 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 568–856 Chain B; UniProt 70–228 Chain B; UniProt 229–331 Chain C; UniProt 332–567 Chain D; UniProt 2–69 Not recorded SPH SPHINGOSINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å
6 Insufficient information Heteromer Protein × 60 PDB declaration: 60-meric(60) Consistent with protein copy count Chain A; UniProt 568–856 Chain B; UniProt 70–228 Chain B; UniProt 229–331 Chain C; UniProt 332–567 Chain D; UniProt 2–69 Not recorded SPH SPHINGOSINE × 15 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

58 other PDB entries and 235 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_HRV14
Isoform
PDB entities 1, 2, 3, 4
Chains and sequence ranges Author chain A; PDBConstruct 1–289; UniProt 568–856 Author chain B; PDBConstruct 1–159; UniProt 70–228 Author chain B; PDBConstruct 175–277; UniProt 229–331 Author chain C; PDBConstruct 1–236; UniProt 332–567 Author chain D; PDBConstruct 1–68; UniProt 2–69

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

Human immunodeficiency virus type 1 group M subtype B (isolate MN)

UniProt P05877

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 240 PDB declaration: 240-MERIC(240) Consistent with protein copy count Chain B; UniProt 314–325 Not recorded COAT PROTEIN VP1 (P1D) × 60 (P03303) COAT PROTEIN VP3 (P1C) × 60 (P03303) COAT PROTEIN VP4 (P1A) × 60 (P03303) SPH SPHINGOSINE × 60 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å
2 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 314–325 Not recorded COAT PROTEIN VP1 (P1D) × 1 (P03303) COAT PROTEIN VP3 (P1C) × 1 (P03303) COAT PROTEIN VP4 (P1A) × 1 (P03303) SPH SPHINGOSINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å
3 Insufficient information Heteromer Protein × 20 PDB declaration: eicosameric(20) Consistent with protein copy count Chain B; UniProt 314–325 Not recorded COAT PROTEIN VP1 (P1D) × 5 (P03303) COAT PROTEIN VP3 (P1C) × 5 (P03303) COAT PROTEIN VP4 (P1A) × 5 (P03303) SPH SPHINGOSINE × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å
4 Insufficient information Heteromer Protein × 24 PDB declaration: 24-meric(24) Consistent with protein copy count Chain B; UniProt 314–325 Not recorded COAT PROTEIN VP1 (P1D) × 6 (P03303) COAT PROTEIN VP3 (P1C) × 6 (P03303) COAT PROTEIN VP4 (P1A) × 6 (P03303) SPH SPHINGOSINE × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å
5 Insufficient information Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 314–325 Not recorded COAT PROTEIN VP1 (P1D) × 1 (P03303) COAT PROTEIN VP3 (P1C) × 1 (P03303) COAT PROTEIN VP4 (P1A) × 1 (P03303) SPH SPHINGOSINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å
6 Insufficient information Heteromer Protein × 60 PDB declaration: 60-meric(60) Consistent with protein copy count Chain B; UniProt 314–325 Not recorded COAT PROTEIN VP1 (P1D) × 15 (P03303) COAT PROTEIN VP3 (P1C) × 15 (P03303) COAT PROTEIN VP4 (P1A) × 15 (P03303) SPH SPHINGOSINE × 15 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

13 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ENV_HV1MN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 163–174; UniProt 314–325

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1k5m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1k5m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1k5m
Deposition date deposition_date2001-10-11
Structure title titleCrystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3 Loop Chimeric Virus MN-III-2
Keywords keywordsengineered rhinovirus, HIV-1 V3 loop, beta turns, Icosahedral virus, Virus; VIRUS
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.66
Radius of gyration Rg (electron density) rg_electron28.56
Forward intensity I(0) i0133066000.00
Molecular weight molecular_weight91991.0 kDa
Excluded volume excluded_volume115390 ų
Envelope volume envelope_volume143330 ų
Hydration-shell volume shell_volume40725 ų
Envelope diameter envelope_diameter101.1
Shell Rg shell_rg36.67
Envelope Rg envelope_rg29.24
Shape Rg shape_rg28.57
Total Rg total_rg29.27
Total atoms total_atoms6480
Residues n_residues829
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax95.7
Rg (real space) rg_real29.61
Rg uncertainty (real space) rg_real_error0.59
I(0) (real space) i0_real1.3310e+08
I(0) uncertainty (real space) i0_real_error2.0080e+06
Rg (reciprocal space) rg_reciprocal29.63
I(0) (reciprocal space) i0_reciprocal133100000.0000
Solution quality estimate total_estimate0.8895
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.3
Skewness Skewness skewness0.336
Kurtosis Kurtosis kurtosis-0.282
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27290000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.923

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1k5m.1
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
Domain ID domain_idd1k5ma_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
Domain ID domain_idd1k5mc_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

CATH v4.4 (4 domains)

Domain ID domain_id1k5mA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id1k5mB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id1k5mC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id1k5mD00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily10 — Picornavirus coat protein VP4

8. Citations (2)

9. Files and Curves (10)