1d3i

CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 14 (HRV14) COMPLEXED WITH A TWO-DOMAIN FRAGMENT OF ITS CELLULAR RECEPTOR, INTERCELLULAR ADHESION MOLECULE-1 (D1D2-ICAM-1). IMPLICATIONS FOR VIRUS-RECEPTOR INTERACTIONS. ALPHA CARBONS ONLY

Method: ELECTRON MICROSCOPY Dmax: 114.1 Å Quality: GOOD

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

PROTEIN (INTERCELLULAR ADHESION MOLECULE-1)

OrganismNot specified

UniProt P05362

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 300 PDB declaration: 300-MERIC(300) Consistent with protein copy count Chain I; UniProt 28–212 Fragment:FIRST TWO DOMAINS, RESIDUES 1-185 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1) × 60 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2) × 60 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3) × 60 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4) × 60 (P03303) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. Resolution 26.00 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain I; UniProt 28–212 Fragment:FIRST TWO DOMAINS, RESIDUES 1-185 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1) × 1 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2) × 1 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3) × 1 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4) × 1 (P03303) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. Resolution 26.00 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain I; UniProt 28–212 Fragment:FIRST TWO DOMAINS, RESIDUES 1-185 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1) × 5 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2) × 5 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3) × 5 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4) × 5 (P03303) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. Resolution 26.00 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain I; UniProt 28–212 Fragment:FIRST TWO DOMAINS, RESIDUES 1-185 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1) × 6 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2) × 6 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3) × 6 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4) × 6 (P03303) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. Resolution 26.00 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain I; UniProt 28–212 Fragment:FIRST TWO DOMAINS, RESIDUES 1-185 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1) × 1 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2) × 1 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3) × 1 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4) × 1 (P03303) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. Resolution 26.00 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.

12 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ICAM1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain I; PDBConstruct 1–185; UniProt 28–212

PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1)

OrganismNot specified

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 Protein heterocomplex Heteromer Protein × 300 PDB declaration: 300-MERIC(300) Consistent with protein copy count Chain 1; UniProt 567–855 Chain 2; UniProt 69–330 Chain 3; UniProt 331–566 Chain 4; UniProt 1–68 Not recorded PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 60 (P05362) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. Resolution 26.00 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain 1; UniProt 567–855 Chain 2; UniProt 69–330 Chain 3; UniProt 331–566 Chain 4; UniProt 1–68 Not recorded PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 1 (P05362) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. Resolution 26.00 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain 1; UniProt 567–855 Chain 2; UniProt 69–330 Chain 3; UniProt 331–566 Chain 4; UniProt 1–68 Not recorded PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 5 (P05362) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. Resolution 26.00 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain 1; UniProt 567–855 Chain 2; UniProt 69–330 Chain 3; UniProt 331–566 Chain 4; UniProt 1–68 Not recorded PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 6 (P05362) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. Resolution 26.00 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain 1; UniProt 567–855 Chain 2; UniProt 69–330 Chain 3; UniProt 331–566 Chain 4; UniProt 1–68 Not recorded PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 1 (P05362) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. Resolution 26.00 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 236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_HRV14
Isoform
PDB entities 2, 3, 4, 5
Chains and sequence ranges Author chain 1; PDBConstruct 1–289; UniProt 567–855 Author chain 2; PDBConstruct 1–262; UniProt 69–330 Author chain 3; PDBConstruct 1–236; UniProt 331–566 Author chain 4; PDBConstruct 1–68; UniProt 1–68

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 1d3i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d3i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d3i
Deposition date deposition_date1999-09-29
Structure title titleCRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 14 (HRV14) COMPLEXED WITH A TWO-DOMAIN FRAGMENT OF ITS CELLULAR RECEPTOR, INTERCELLULAR ADHESION MOLECULE-1 (D1D2-ICAM-1). IMPLICATIONS FOR VIRUS-RECEPTOR INTERACTIONS. ALPHA CARBONS ONLY
Keywords keywords;HUMAN RHINOVIRUS, HRV14, ICAM-1, FITTING OF X-RAY STRUCTURES INTO CRYO-EM RECONSTRUCTIONS, COMMON COLD, VIRUS UNCOATING, VIRUS/ VIRAL PROTEIN, RHINOVIRUS-RECEPTOR COMPLEX, Icosahedral virus, Virus-Receptor COMPLEX ;; Virus/Receptor
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier33.90
Radius of gyration Rg (electron density) rg_electron33.49
Forward intensity I(0) i0182260000.00
Molecular weight molecular_weight109410.0 kDa
Excluded volume excluded_volume133650 ų
Envelope volume envelope_volume118210 ų
Hydration-shell volume shell_volume33103 ų
Envelope diameter envelope_diameter123.2
Shell Rg shell_rg35.89
Envelope Rg envelope_rg31.88
Shape Rg shape_rg33.47
Total Rg total_rg33.64
Total atoms total_atoms
Residues n_residues
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 dmax114.1
Rg (real space) rg_real33.94
Rg uncertainty (real space) rg_real_error0.87
I(0) (real space) i0_real1.8230e+08
I(0) uncertainty (real space) i0_real_error2.9940e+06
Rg (reciprocal space) rg_reciprocal33.92
I(0) (reciprocal space) i0_reciprocal182300000.0000
Solution quality estimate total_estimate0.8823
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.4
Skewness Skewness skewness0.378
Kurtosis Kurtosis kurtosis-0.368
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19970000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.941

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd1d3i1_
Class classi — Low resolution protein structures
Fold Fold foldi.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
Family Family familyi.6.1.1 — Viruses and virus-receptor complexes
Domain ID domain_idd1d3i2_
Class classi — Low resolution protein structures
Fold Fold foldi.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
Family Family familyi.6.1.1 — Viruses and virus-receptor complexes
Domain ID domain_idd1d3i3_
Class classi — Low resolution protein structures
Fold Fold foldi.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
Family Family familyi.6.1.1 — Viruses and virus-receptor complexes
Domain ID domain_idd1d3i4_
Class classi — Low resolution protein structures
Fold Fold foldi.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
Family Family familyi.6.1.1 — Viruses and virus-receptor complexes
Domain ID domain_idd1d3ii_
Class classi — Low resolution protein structures
Fold Fold foldi.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
Family Family familyi.6.1.1 — Viruses and virus-receptor complexes

8. Citations (6)

9. Files and Curves (10)