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9zbs

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

Method: ELECTRON MICROSCOPY D_max: 222.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zbs
deposition_date	2025-11-21
title	The cryo-EM structure of Pakpunavirus P7-1 neck (portal:H-t-T:collar:gateway)
keywords	;Pakpunavirus P7-1; Cryo-EM, in situ, structure; neck; portal protein; H-t-T; collar protein; gateway protein; VIRAL PROTEIN, VIRAL PROTEIN ;; VIRAL PROTEIN
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	75.90 Å
rg_electron	76.16 Å
i0	15149700000.00
molecular_weight	1031400.0 kDa
excluded_volume	1284700 Å³
envelope_volume	1957400 Å³
shell_volume	209780 Å³
envelope_diameter	274.5 Å
shell_rg	75.92 Å
envelope_rg	79.10 Å
shape_rg	76.22 Å
total_rg	75.95 Å
total_atoms	72366
n_residues	9006
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	222.3 Å
rg_real	74.32 Å
rg_real_error	0.97 Å
i0_real	1.4920e+10
i0_real_error	2.8140e+08
rg_reciprocal	74.54 Å
i0_reciprocal	15100000000.0000
total_estimate	0.8352
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	74.1 Å
skewness	0.532
kurtosis	-0.191
angular_range	— – 0.1050 Å⁻¹
current_alpha	0.0956
highest_alpha	1741000000.0000
n_real_points	22
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.117

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	72366

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

Entity 3 polymer

description	Head-tail joining protein
formula_weight	14369.5 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	Y,Z,a,b,c,d

MLYPTFSMTNFVKLDLIRRGQPGDDGFGRPTPPVETVVTITANVQPIEKSTDTRILPEADRSKACFKVYSRGEEIRQLKEGPGGWSADRFMWEGELYEVMKVINYSMGILNHYKAICMRVERNSTA

Entity 4 polymer

description	Tail completion protein
formula_weight	21305.1 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	e,f,g,h,i,j

MIHTELENSLYLMVKELFPDWRVIQAYTNNQEPQTPYLAIDIKRLDELGRENVSNMSDPISPSHGTIQVQQDFAAKVVFELIGKYGETASVSDMAMAITRAMRTPAGHAAQRKFNLSLFKLPSTRRVPMLRETDMYMFYQVTCEFGFSVIETTTQEFAAGADIHGVYYDAGRPGHIIESHIDINFEH

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6. Citations (1)

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resolution	3.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.60 Å
resolution_method	—
num_particles	10400

fit	/app/data/saxs_computation/zb/9zbs/9zbs.fit
pddf	/app/data/pr_computation/zb/9zbs/9zbs.pr.out
profile	/app/data/saxs_computation/zb/9zbs/9zbs.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Refinement

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)