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1d3e

;CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 16 (HRV16) 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: 124.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d3e
deposition_date	1999-09-29
title	;CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 16 (HRV16) 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, HRV16, 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

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	34.25 Å
rg_electron	34.15 Å
i0	186859000.00
molecular_weight	110050.0 kDa
excluded_volume	134200 Å³
envelope_volume	119030 Å³
shell_volume	33073 Å³
envelope_diameter	131.1 Å
shell_rg	35.95 Å
envelope_rg	32.74 Å
shape_rg	34.14 Å
total_rg	34.26 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

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3. P(r) Analysis (GNOM)

dmax	124.7 Å
rg_real	34.37 Å
rg_real_error	1.17 Å
i0_real	1.8690e+08
i0_real_error	3.4140e+06
rg_reciprocal	34.30 Å
i0_reciprocal	186800000.0000
total_estimate	0.8473
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.9 Å
skewness	0.496
kurtosis	-0.068
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	22190000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.707; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.952

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4. Crystallography & Experiment

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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 16 COAT PROTEIN VP1)
formula_weight	32314.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	1

APVAAYVDEVLNEVLVVPNINQSHPTTSNAAPVLDAAETGHTNKIQPEDTIETRYVQSSQTLDEMSVESFLGRSGCIHESVLDIVDNYNDQSFTKWNINLQEMAQIRRKFEMFTYARFDSEITMVPSVAAKDGHIGHIVMQYMYVPPGAPIPTTRDDYAWQSGTNASVFWQHGQPFPRFSLPFLSIASAYYMFYDGYDGDTYKSRYGTVVTNDMGTLCSRIVTSEQLHKVKVVTRIYHKAKHTKAWCPRPPRAVQYSHTHTTNYKLSSEVHNDVAIRPRTNLTTV

Entity 3 polymer

description	PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2)
formula_weight	27910.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	2

SDRIIQITRGDSTITSQDVANAVVGYGVWPHYLTPQDATAIDKPTQPDTSSNRFYTLDSKMWNSTSKGWWWKLPDALKDMGIFGENMFYHFLGRSGYTVHVQCNASKFHQGTLLVVMIPEHQLATVNKGNVNAGYKYTHPGEAGREVGTAAAAEKQPSDDNWLNFDGTLLGNLLIFPHQFINLRSNNSATLIVPYVNAVPMDSMVRHNNWSLVIIPVCQLQSNNISNIVPITVSISPMCAEFSGARAKTVVQ

Entity 4 polymer

description	PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3)
formula_weight	26314.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	3

GLPVYVTPGSGQFMTTDDMQSPCALPWYHPTKEIFIPGEVKNLIEMCQVDTLIPINSTQSNIGNVSMYTVTLSPQTKLAEEIFAIKVDIASHPLATTLIGEIASYFTHWTGSLRFSFMFCGTANTTLKVLLAYTPPGIGKPRSRKEAMLGTHVVWDVGLQSTVSLVVPWISASQYRFTTPDTYSSAGYITCWYQTNFVVPPNTPNTAEMLCFVSGCKDFCLRMARDTDLHKQTGPITQ

Entity 5 polymer

description	PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4)
formula_weight	7374.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	4

GAQVSRQNVGTHSTQNMVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ

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6. Citations (5)

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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	28.000 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	28.00 Å
resolution_method	;COMMON-LINES AND POLAR-FOURIER-TRANSFORM FULLER ET AL. 1996, J.STRUC.BIOL.c 116, 48-55; BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130 ;
num_particles	44

fit	/app/data/saxs_computation/d3/1d3e/1d3e.fit
pddf	/app/data/pr_computation/d3/1d3e/1d3e.pr.out
profile	/app/data/saxs_computation/d3/1d3e/1d3e.dat

;CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 16 (HRV16) 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 (5)

7. Files & Curves (10)

Files (7)

Curves (3)