SAXSdb — 1dgi

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1. Structure Basics

entry_id	1dgi
deposition_date	1999-11-24
title	Cryo-EM structure of human poliovirus(serotype 1)complexed with three domain CD155
keywords	CD155, PVR, HUMAN POLIOVIRUS, POLIOVIRUS-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	44.84 Å
rg_electron	46.64 Å
i0	243470000.00
molecular_weight	127260.0 kDa
excluded_volume	155120 Å³
envelope_volume	156440 Å³
shell_volume	34516 Å³
envelope_diameter	178.2 Å
shell_rg	39.57 Å
envelope_rg	49.43 Å
shape_rg	46.93 Å
total_rg	46.34 Å
total_atoms	1
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	129.2 Å
rg_real	40.57 Å
rg_real_error	0.68 Å
i0_real	2.3260e+08
i0_real_error	4.2810e+06
rg_reciprocal	44.85 Å
i0_reciprocal	243000000.0000
total_estimate	0.6352
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	36.9 Å
skewness	0.760
kurtosis	0.042
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0828
highest_alpha	17630000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.651; Stabil: 0.929; Sysdev: 0.000; Positv: 1.000; Valcen: 0.845; Smooth: 0.706

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	POLIOVIRUS RECEPTOR
formula_weight	32928.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R
atom_count	1155

DVVVQAPTQVPGFLGDSVTLPCYLQVPNMEVTHVSQLTWARHGESGSMAVFHQTQGPSYSESKRLEFVAARLGAELRNASLRMFGLRVEDEGNYTCLFVTFPQGSRSVDIWLRVLAKPQNTAEVQKVQLTGEPVPMARCVSTGGRPPAQITWHSDLGGMPNTSQVPGFLSGTVTVTSLWILVPSSQVDGKNVTCKVEHESFEKPQLLTVNLTVYYPPEVSISGYDNNWYLGQNEATLTCDARSNPEPTGYNWSTTMGPLPPFAVAQGAQLLIRPVDKPINTTLICNVTNALGARQAELTVQV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	VP1
formula_weight	31874.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	1

GSSSTAATSRDALPNTEASGPTHSKEIPALTAVETGATNPLVPSDTVQTRHVVQHRSRSESSIESFFARGACVTIMTVDNPASTTNKDKLFAVWKITYKDTVQLRRKLEFFTYSRFDMELTFVVTANFTETNNGHALNQVYQIMYVPPGAPVPEKWDDYTWQTSSNPSIFYTYGTAPARISVPYVGISNAYSHFYDGFSKVPLKDQSAALGDSLYGAASLNDFGILAVRVVNDHNPTKVTSKIRVYLKPKHIRVWCPRPPRAVAYYGPGVDYKDGTLTPLSTKDLTTY

Source

organism	Human poliovirus 1
ncbi_taxonomy_id	12080
host_organism	Homo sapiens

Entity 3 polymer

description	VP2
formula_weight	29664.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	2

EACGYSDRVLQLTLGNSTITTQEAANSVVAYGRWPEYLRDSEANPVDQPTEPDVAACRFYTLDTVSWTKESRGWWWKLPDALRDMGLFGQNMYYHYLGRSGYTVHVQCNASKFHQGALGVFAVPEMCLAGDSNTTTMHTSYQNANPGEKGGTFTGTFTPDNNQTSPARRFCPVDYLLGNGTLLGNAFVFPHQIINLRTNNCATLVLPYVNSLSIDSMVKHNNWGIAILPLAPLNFASESSPEIPITLTIAPMCCEFNGLRNITLPRLQ

Source

organism	Human poliovirus 1
ncbi_taxonomy_id	12080
host_organism	Homo sapiens

Entity 4 polymer

description	VP3
formula_weight	26235.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	3

GLPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEIDTMIPFDLSATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTFLFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQTIDDSFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQKA

Source

organism	Human poliovirus 1
ncbi_taxonomy_id	12080
host_organism	Homo sapiens

Entity 5 polymer

description	VP4
formula_weight	6983.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	4

XGAQVSSQKVGAHENSSTINYTTINYYRDSASNAASKQDFSQDPSKFTEPIKDVLIKTAPMLN

Source

organism	Human poliovirus 1
ncbi_taxonomy_id	12080
host_organism	Homo sapiens

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6. Citations (3)

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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	22.000 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	22.00 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	1156

fit	/app/data/saxs_computation/dg/1dgi/1dgi.fit
pddf	/app/data/pr_computation/dg/1dgi/1dgi.pr.out
profile	/app/data/saxs_computation/dg/1dgi/1dgi.dat

Cryo-EM structure of human poliovirus(serotype 1)complexed with three domain CD155

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

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

6. Citations (3)

7. Files & Curves (10)

Files (7)

Curves (3)