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9qgp

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

Method: ELECTRON MICROSCOPY D_max: 340.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qgp
deposition_date	2025-03-14
title	Cryo-EM structure of the PlPVC1 sheath, 6-fold symmetrized (C6), in contracted 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	88.00 Å
rg_electron	87.55 Å
i0	11999200000.00
molecular_weight	957150.0 kDa
excluded_volume	1205200 Å³
envelope_volume	2114900 Å³
shell_volume	193800 Å³
envelope_diameter	263.0 Å
shell_rg	101.10 Å
envelope_rg	80.12 Å
shape_rg	87.55 Å
total_rg	87.67 Å
total_atoms	67578
n_residues	8646
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	340.4 Å
rg_real	91.58 Å
rg_real_error	2.84 Å
i0_real	1.2080e+10
i0_real_error	2.6840e+08
rg_reciprocal	89.28 Å
i0_reciprocal	12040000000.0000
total_estimate	0.7922
solution_quality	GOOD a GOOD solution
n_peaks	4
r_peak_primary	151.3 Å
skewness	0.259
kurtosis	0.081
angular_range	— – 0.0900 Å⁻¹
current_alpha	0.5607
highest_alpha	595300000.0000
n_real_points	19
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.273; Stabil: 0.883; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.893

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Phage tail sheath family protein
formula_weight	39009.8 kDa
src_method	man
entity_count	12

Polymer

type	polypeptide(L)
strand_id	2A,2B,2C,2D,2E,2F,2G,2H,2I,2J,2K,2L
atom_count	67578

MTTITTYPGVYIEEDASLSLSVSSSATAVPVFAVAGDNPLISGKPYIRISNWLEYLTLKNEQFDPANTLDISLRAYFINGGGYCYLVQTTDLEKQVPKLDDVTLLVAAGENITTAVSTLCKPGKGLFAIFDGPTTELKSDGTSNSDYDPNPFAAVYYPWLTADWTTTIDIPPSAAIAGVYCSVDSTRGVWKAPANVPIQGGLQPKYPVTDDLQAQYNQGKALNMIRTFPKSGTLVWGARTLEDNDNWRYIPVRRLFNSAERDIKNAMSFAVFEPNSQPTWERVRSAVNNYLYSLWQQGGLAGNKPDDAYFVQIGKDITMTDDDIKQGKMIIKIGMAAVRPAEFIILQFTQNTAQ

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 2 polymer

description	Phage tail sheath family protein
formula_weight	51330.9 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	3A,3B,3C,3D,3E,3F

MPTIPTYPGVYIEEDASLNLSVNQGNTAIPVFIGLFSPKNTNLKSQVTRVNSWLDFTNLFNAGCIAPITIKSTKRASMPAPTLLENVKGDTAVVATPGISVDADNKDPTYTYKVIVNYTTSSDALKLYFQNGGGPCYILPQLDRLTQGFLDSIPELIKQALEITLIVCPEWDSGYQSKIYNSLTSSLLNAGYFLIADNQDKNTALITEVASQTATYYPAVKVSQLIQAEDSQIAVSGYEDAKTKSDEVKNLAQLKEKNPTVYQQAVQKIQAIQDEIAANGNIIPVSAVMAGIYCATDASRGVWKAPANIVLSGISDVAERLTDDEQGEMNSKGINAIRYFSHKGFVVWGARTLQNDDNWRYIPVRRLFNAAERDIKQAMQSVVFEPNSQPTWERVKSAIDNYLYSLWQQGALAGNKPQEAYFVQIGKDVTMSDDDIKQGKMIVKVGMAAVRPAEFIILQFSQQVAQ

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 3 polymer

description	Phage tail sheath family protein
formula_weight	44076.1 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	4A,4B,4C,4D,4E,4F

MEITQPSVTITENLIFPKQNDSFIGIPVFIGYTSSPVDKTAIKLHSLADFARSFPESGLMYYSVRHFFENGGQQAYVLSLGTEQQLSDFSSLITALQQAWLAQTIAAENDITLIITPDVIRFDQTEISDTQRDLWLQLWQSVLNLCKSRRGIMGLLDAPDDPTLAAKCLQQFSSADRQWGVVYWPLLKSAYQDNTQNPIVLSPTAAVAAVIQRNDNQQGVWTAPANIALSKVISPVRAYIEANALFNPDGTSLNLVRSFPGKGIRIWGCRTLENTHDSPWSYIQTRRLVSYIEAYMTQLGRAFVFEPNNAITWMKFKGQAHNWLRQLWLKGGLRGTQEDQAFEVLLGVDESMREADLRAGKMIIKIRLAVLIPAEFIELNLTFDTRTGTIPS

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	3.10 Å
resolution_method	—
num_particles	30862

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

Cryo-EM structure of the PlPVC1 sheath, 6-fold symmetrized (C6), in contracted 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)