← Back to search

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 D_max: 114.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1d3i
deposition_date	1999-09-29
title	;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 ;
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
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	33.90 Å
rg_electron	33.49 Å
i0	182260000.00
molecular_weight	109410.0 kDa
excluded_volume	133650 Å³
envelope_volume	118210 Å³
shell_volume	33103 Å³
envelope_diameter	123.2 Å
shell_rg	35.89 Å
envelope_rg	31.88 Å
shape_rg	33.47 Å
total_rg	33.64 Å
total_atoms	—
n_residues	—
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	114.1 Å
rg_real	33.94 Å
rg_real_error	0.87 Å
i0_real	1.8230e+08
i0_real_error	2.9940e+06
rg_reciprocal	33.92 Å
i0_reciprocal	182300000.0000
total_estimate	0.8823
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.4 Å
skewness	0.378
kurtosis	-0.368
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	19970000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.941

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	PROTEIN (INTERCELLULAR ADHESION MOLECULE-1)
formula_weight	20438.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I
atom_count	989

QTSVSPSKVILPRGGSVLVTCSTSCDQPKLLGIETPLPKKELLLPGNNRKVYELSNVQEDSQPMCYSNCPDGQSTAKTFLTVYWTPERVELAPLPSWQPVGKNLTLRCQVEGGAPRANLTVVLLRGEKELKREPAVGEPAEVTTTVLVRRDHHGANFSCRTELDLRPQGLELFENTSAPYQLQTF

Entity 2 polymer

description	PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1)
formula_weight	32560.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	1

GLGDELEEVIVEKTKQTVASISSGPKHTQKVPILTANETGATMPVLPSDSIETRTTYMHFNGSETDVECFLGRAACVHVTEIQNKDATGIDNHREAKLFNDWKINLSSLVQLRKKLELFTYVRFDSEYTILATASQPDSANYSSNLVVQAMYVPPGAPNPKEWDDYTWQSASNPSVFFKVGDTSRFSVPYVGLASAYNCFYDGYSHDDAETQYGITVLNHMGSMAFRIVNEHDEHKTLVKIRVYHRAKHVEAWIPRAPRALPYTSIGRTNYPKNTEPVIKKRKGDIKSY

Entity 3 polymer

description	PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2)
formula_weight	28501.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	2

SPNVEACGYSDRVQQITLGNSTITTQEAANAVVCYAEWPEYLPDVDASDVNKTSKPDTSVCRFYTLDSKTWTTGSKGWCWKLPDALKDMGVFGQNMFFHSLGRSGYTVHVQCNATKFHSGCLLVVVIPEHQLASHEGGNVSVKYTFTHPGERGIDLSSANEVGGPVKDVLYNMNGTLLGNLLIFPHQFINLRTNNTATIVIPYINSVPIDSMTRHNNVSLMVIPIAPLTVPTGATPSLPITVTIAPMCTEFSGIRSKSIVPQ

Entity 4 polymer

description	PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3)
formula_weight	26236.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	3

GLPTTTLPGSGQFLTTDDRQSPSALPNYEPTPRIHIPGKVHNLLEIIQVDTLIPMNNTHTKDEVNSYLIPLNANRQNEQVFGTNLFIGDGVFKTTLLGEIVQYYTHWSGSLRFSLMYTGPALSSAKLILAYTPPGARGPQDRREAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYTDPDTYTSAGFLSCWYQTSLILPPETTGQVYLLSFISACPDFKLRLMKDTQTISQTVALTE

Entity 5 polymer

description	PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4)
formula_weight	7183.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	4

GAQVSTQKSGSHENQNILTNGSNQTFTVINYYKDAASTSSAGQSLSMDPSKFTEPVKDLMLKGAPALN

▶

6. Citations (6)

▶

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	1

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	26.000 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	26.00 Å
resolution_method	;MODEL-BASED, POLAR-FOURIER-TRANSFORM (FULLER ET AL. 1996, J.STRUC.BIOL.116, 48-55; BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130) ;
num_particles	36

fit	/app/data/saxs_computation/d3/1d3i/1d3i.fit
pddf	/app/data/pr_computation/d3/1d3i/1d3i.pr.out
profile	/app/data/saxs_computation/d3/1d3i/1d3i.dat

;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 ;

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

6. Citations (6)

7. Files & Curves (10)

Files (7)

Curves (3)