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11bp

The cryo-EM structure of Pakpunavirus P7-1 empty particle neck (portal:H-t-T)

Method: ELECTRON MICROSCOPY D_max: 163.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11bp
deposition_date	2026-02-16
title	The cryo-EM structure of Pakpunavirus P7-1 empty particle neck (portal:H-t-T)
keywords	;Pakpunavirus P7-1; Cryo-EM, in situ, structure; neck; portal protein; H-t-T; collar protein; gateway protein; VIRAL PROTEIN, VIRAL PROTEIN, VIRUS ;; VIRUS
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	60.71 Å
rg_electron	59.91 Å
i0	9544050000.00
molecular_weight	816020.0 kDa
excluded_volume	1016500 Å³
envelope_volume	1470100 Å³
shell_volume	188610 Å³
envelope_diameter	173.0 Å
shell_rg	72.22 Å
envelope_rg	58.79 Å
shape_rg	59.94 Å
total_rg	60.02 Å
total_atoms	57276
n_residues	7104
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	163.7 Å
rg_real	60.21 Å
rg_real_error	0.58 Å
i0_real	9.5440e+09
i0_real_error	1.4630e+08
rg_reciprocal	61.10 Å
i0_reciprocal	9557000000.0000
total_estimate	0.8457
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	81.9 Å
skewness	0.040
kurtosis	-0.577
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	1637000000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.998; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Portal protein
formula_weight	54362.6 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L
atom_count	57276

MAETEKTAPGIPRLRLGEIGSTGLKQVNGTILEERRPELRFPRACRTFQMMAEDPTIKSALDLFEMMMSRVDWEVDLGVDPDEAMKARGKFLKECMHDMEHSWYSFIKEVTSFYTYGFSVHEMVFKRREGYPVSKYNDNKFGIKKLPIRSQSTITKWLYSEDGRNFLGCEQSLANVVNGDRYVNLGNKDGTVEIPAKKMLLFRVDAKRDSPEGNSPLRACYNAWRYRVEIEEQESVGVTRDMNGMPTLYLPPRYMSEDATEAERAVYEYYKRVIRNIQMNEQSGLILPQAFDPESRQPLFKFELTSSQGSKMYDTDAIIRRWDNKILQALFADMLKMGQDQVGSYSLAGAKTNIMAMAIESRLREIKDVLDNKLIPTLFALNGDYSPDLPKLQYGELDEIDLEEFSKGIQRIGSVGGLERDREVYNKIRKALKIKPRPDDEPVDVDNIMGGQSQAGKAGVGNGASTSAAGRDNAAANNA

Entity 2 polymer

description	Head to Tail protein gp72
formula_weight	18142.6 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	M,N,O,P,Q,R,S,T,U,V,W,X

MAYTGDPANNPIDRLREIVGDVWEPPMLSDETYQWVLDKNEGNERRAALELMRMMLFRLTRGMRERTGDIEVYGAEYFNNYLKALQLILKDPNIAISLAVPYAGGISKSDMLANDLDPDNVTREFYIGFARREKLYNQCNPGPQDLSMGCDYLGKLQF

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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	4.100 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.10 Å
resolution_method	—
num_particles	853

fit	/app/data/saxs_computation/1b/11bp/11bp.fit
pddf	/app/data/pr_computation/1b/11bp/11bp.pr.out
profile	/app/data/saxs_computation/1b/11bp/11bp.dat

The cryo-EM structure of Pakpunavirus P7-1 empty particle neck (portal:H-t-T)

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 (2)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)