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9qgn

Cryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in extended state

Method: ELECTRON MICROSCOPY D_max: 164.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qgn
deposition_date	2025-03-14
title	Cryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in extended state
keywords	Contractile injection system, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
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	57.05 Å
rg_electron	56.28 Å
i0	5133200000.00
molecular_weight	615960.0 kDa
excluded_volume	775180 Å³
envelope_volume	1178300 Å³
shell_volume	163340 Å³
envelope_diameter	166.0 Å
shell_rg	68.04 Å
envelope_rg	54.19 Å
shape_rg	56.27 Å
total_rg	56.59 Å
total_atoms	43476
n_residues	5562
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	164.5 Å
rg_real	56.62 Å
rg_real_error	0.81 Å
i0_real	5.1330e+09
i0_real_error	9.2230e+07
rg_reciprocal	57.40 Å
i0_reciprocal	5139000000.0000
total_estimate	0.8433
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	82.2 Å
skewness	-0.003
kurtosis	-0.595
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	1189000000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.133

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	DUF4255 domain-containing protein
formula_weight	33299.5 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	43476

MTIIIASDNAIIEINQALNTILSQYLNITGQNIDIRFDLPEINSIQSEPTVSVFLYEIHEDLQLRSAESRRYNPSTNTLLPGWVNINCNYLITYWDASKPSSDSSSPDSQPNNQAAQVMTRILNALINNRQLTGLPGAYTRIIPQQENLNSLGNFWQALGNRPRLSLLYSITVPMKLKNIEDNVIPVSKISASVDQKPNLDNSQINQALIDKLCVELGGTEDVRLALAKVNLTTKPDTENNQNQENESVIVEVSGITSVTYLPQIKDTLTKWKSSQEAIVKINGVSIVVSKENADKLIGI

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 2 polymer

description	Phage tail protein
formula_weight	16574.6 kDa
src_method	man
entity_count	12

Polymer

type	polypeptide(L)
strand_id	1A,1B,1C,1D,1E,1F,1G,1H,1I,1J,1K,1L

MAITPEQIAVEYPIPTYRFVVSVGDEQIPFNNVSGLDVHYDVIEYKDGIGNYYKMPGQRQSINITLRKGVFPGDTKLFDWINSIQLNQVEKKDIAISLTNEAGTEILMTWNVANAFPTSFTSPSFDATSNEIAVQEIALTADRVTIQAA

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 3 polymer

description	Phage tail sheath family protein
formula_weight	39009.8 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	2A,2B,2C,2D,2E,2F

MTTITTYPGVYIEEDASLSLSVSSSATAVPVFAVAGDNPLISGKPYIRISNWLEYLTLKNEQFDPANTLDISLRAYFINGGGYCYLVQTTDLEKQVPKLDDVTLLVAAGENITTAVSTLCKPGKGLFAIFDGPTTELKSDGTSNSDYDPNPFAAVYYPWLTADWTTTIDIPPSAAIAGVYCSVDSTRGVWKAPANVPIQGGLQPKYPVTDDLQAQYNQGKALNMIRTFPKSGTLVWGARTLEDNDNWRYIPVRRLFNSAERDIKNAMSFAVFEPNSQPTWERVRSAVNNYLYSLWQQGGLAGNKPDDAYFVQIGKDITMTDDDIKQGKMIIKIGMAAVRPAEFIILQFTQNTAQ

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

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6. Citations (1)

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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	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.46 Å
resolution_method	—
num_particles	57353

fit	/app/data/saxs_computation/qg/9qgn/9qgn.fit
pddf	/app/data/pr_computation/qg/9qgn/9qgn.pr.out
profile	/app/data/saxs_computation/qg/9qgn/9qgn.dat

Cryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in extended state

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

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)