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9zdk

The cryo-EM structure of Pakpunavirus P7-1 triplex protein and sheath in contracted state

Method: ELECTRON MICROSCOPY D_max: 249.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zdk
deposition_date	2025-11-25
title	The cryo-EM structure of Pakpunavirus P7-1 triplex protein and sheath in contracted state
keywords	Pakpunavirus P7-1; Cryo-EM, in situ, structure; baseplate; spike; hub; triplex; 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	— Å
rg_electron	106.60 Å
i0	15157400000.00
molecular_weight	1060100.0 kDa
excluded_volume	1330100 Å³
envelope_volume	3650300 Å³
shell_volume	290240 Å³
envelope_diameter	300.4 Å
shell_rg	115.20 Å
envelope_rg	92.75 Å
shape_rg	106.70 Å
total_rg	106.60 Å
total_atoms	74784
n_residues	9810
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	249.7 Å
rg_real	105.20 Å
rg_real_error	0.33 Å
i0_real	1.4470e+10
i0_real_error	2.3270e+08
rg_reciprocal	113.10 Å
i0_reciprocal	15440000000.0000
total_estimate	0.9043
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	166.4 Å
skewness	-0.279
kurtosis	-0.757
angular_range	— – 0.0750 Å⁻¹
current_alpha	1.4550
highest_alpha	1131000000.0000
n_real_points	16
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 1.000; Stabil: 0.945; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	gp88
formula_weight	52425.9 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,B,D,E,G,H,J,K,M,N,P,Q
atom_count	74784

MAGITAEGLTIKDLDQILTDYRNVASQVFADLVSTGDEVDTSGNSALGRLIGVVAPSDEAIWEVIQMVYNSFNPAAATGVALDNLVSFSAISRHAARPTRAQVVLEGNINTVINSPPAKMISSSTGRVFHLLQGVILTPKACSGVGIFPQTVGNDLTYELKMYVDDINTTSIKYTSPATGTVTSESILAGLAADVATNHGNTLTSYEQNGILFIVPIDPFNTKTFEEASNLSIQKVRKLGIAVDDVIGPVPQQALAIDTISIPIAGWDSVINPVPAITGRLRETDDELRERFRNSKFVQATNILESLIDGLMNVEGVEDVRIIENDTDNPDPVHGVPGHSFLPIVLGGIPTEVAQSIWLNKPFGIGSVGDTEVQVVDSRGYTHRVNYQRPVEVPIEIKISVTNTGSMPENIEDILRPRIVAYGTENYKIGDDVIYSRFYAPIMEIPGFQVNSLTIAKKGQTQGMANIEIGFKEVATFAAADITVTTV

Entity 2 polymer

description	gp89
formula_weight	26698.1 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	C,F,I,L,O,R

MAVNQFDREDYLEVARERVTEQFKEKPIFDRFLQVLLSGKFDIQNALEDLQTLRSLDTATGKQLDIIGDIVGRPRGLVYQDIFNYFGFAGTERAGSFGSLSDPTVGAPWYSVGAPTGNAREPSDEEYRMILKAKIIKNRTNSTPEQVIEAYKFVFGVPEVFLEEYAPAAVRIGIGKILTNVERSLLFDLGGAGALLPKTIGVNYTYTEFQAGRVFATEGFPGGQGVGDLNDPTVGGILTNLVT

Entity 3 polymer

description	gp76
formula_weight	46365.9 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	S,T,U,V,W,X

MTVLTDVIDIQISRETAAVAQTNFNVPLFIASHTNFSERARVYNSLKGVAEDFGESDPTYLAAVRYFGQALKPRSLVIGRRQVPSATVSVSVVQEGQSYVLTVNGLPVSYVSQQDDTATLIATGLKAAYDVTPVAGVTVTDNEDGTLTVASNEDWSLKVSSNLTMAAAPSTEGWPAAITAVQGENDEWYALSIDSHADDDIMAVATHIEGTKKVFIGATAQANTKTSAENDIASRLVAAGFQRTALIYHPNADAQFPECAWVGYQLQEQPGSNTWTHKALAAVDAYRLTPTESTNLKNKNVTTFERVGGVNRTFGGAMAGGEWIDVMIFVDWLEARMTERLWFRMANSKKIPYDAVGATILESEIRAQLNEGIRVGGLAEAPAPKVFVPDVLSMSPNMRAQRIFEGIEFEARLAGAIHFVHIRGTVTV

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6. Citations (1)

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resolution	5.00 Å
resolution_method	—
num_particles	7832

fit	/app/data/saxs_computation/zd/9zdk/9zdk.fit
pddf	/app/data/pr_computation/zd/9zdk/9zdk.pr.out
profile	/app/data/saxs_computation/zd/9zdk/9zdk.dat

The cryo-EM structure of Pakpunavirus P7-1 triplex protein and sheath 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

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)