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9zd8

The cryo-EM structure of Pakpunavirus P7-1 baseplate in extended status

Method: ELECTRON MICROSCOPY D_max: 294.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zd8
deposition_date	2025-11-25
title	The cryo-EM structure of Pakpunavirus P7-1 baseplate in extended status
keywords	Pakpunavirus P7-1; Cryo-EM, in situ, structure; baseplate; 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	84.70 Å
rg_electron	84.53 Å
i0	31846800000.00
molecular_weight	1529100.0 kDa
excluded_volume	1916100 Å³
envelope_volume	3268700 Å³
shell_volume	308230 Å³
envelope_diameter	288.5 Å
shell_rg	91.41 Å
envelope_rg	82.46 Å
shape_rg	84.53 Å
total_rg	84.58 Å
total_atoms	107757
n_residues	13914
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	294.4 Å
rg_real	86.93 Å
rg_real_error	1.35 Å
i0_real	3.1600e+10
i0_real_error	6.2450e+08
rg_reciprocal	85.96 Å
i0_reciprocal	31970000000.0000
total_estimate	0.9037
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	98.1 Å
skewness	0.355
kurtosis	-0.061
angular_range	— – 0.0900 Å⁻¹
current_alpha	1.1900
highest_alpha	7594000000.0000
n_real_points	19
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 0.912; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; Smooth: 0.677

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	gp88
formula_weight	52425.9 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	0,L,M,N,V,W,X,f,g,h,o,u
atom_count	107757

MAGITAEGLTIKDLDQILTDYRNVASQVFADLVSTGDEVDTSGNSALGRLIGVVAPSDEAIWEVIQMVYNSFNPAAATGVALDNLVSFSAISRHAARPTRAQVVLEGNINTVINSPPAKMISSSTGRVFHLLQGVILTPKACSGVGIFPQTVGNDLTYELKMYVDDINTTSIKYTSPATGTVTSESILAGLAADVATNHGNTLTSYEQNGILFIVPIDPFNTKTFEEASNLSIQKVRKLGIAVDDVIGPVPQQALAIDTISIPIAGWDSVINPVPAITGRLRETDDELRERFRNSKFVQATNILESLIDGLMNVEGVEDVRIIENDTDNPDPVHGVPGHSFLPIVLGGIPTEVAQSIWLNKPFGIGSVGDTEVQVVDSRGYTHRVNYQRPVEVPIEIKISVTNTGSMPENIEDILRPRIVAYGTENYKIGDDVIYSRFYAPIMEIPGFQVNSLTIAKKGQTQGMANIEIGFKEVATFAAADITVTTV

Entity 2 polymer

description	gp89
formula_weight	26698.1 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	1,O,Y,i,p,v

MAVNQFDREDYLEVARERVTEQFKEKPIFDRFLQVLLSGKFDIQNALEDLQTLRSLDTATGKQLDIIGDIVGRPRGLVYQDIFNYFGFAGTERAGSFGSLSDPTVGAPWYSVGAPTGNAREPSDEEYRMILKAKIIKNRTNSTPEQVIEAYKFVFGVPEVFLEEYAPAAVRIGIGKILTNVERSLLFDLGGAGALLPKTIGVNYTYTEFQAGRVFATEGFPGGQGVGDLNDPTVGGILTNLVT

Entity 3 polymer

description	gp83
formula_weight	28575.0 kDa
src_method	nat
entity_count	6

Polymer

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

MTIAIKRENGDLIWFDAVTEFGRQYRGSVSSNPIETGGKITDHITTENPVFTLTAVVSDADFNLNRPVINDNEAQTYKINNKEFVNTQPVTIPAVISTSRLDPSRIFPEVITQFIPPEIPSATVLPQKGDKVAYDIERQLIDMQRNAEVFSLLDFRDGIIWDQIERCIFTDLSFTENAETGSSLQPRMTIEAVTFTDTRYVEVRVNKGRKTAKKEKRDTKEGDTGASNATSQDSPTFKRSQMKEAQIRTQVAR

Entity 4 polymer

description	gp79
formula_weight	17714.9 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	G,Q,a,k,q,w

MANTVLTYSPSDVKIVLCGYALTGVVSFEMSWLSRPYTMVRGIRGHHTRVFNRDLSAQIRIEVLQTSVSNDAFFSLVEQDRRTQSARITLSVKDTHGSTMMSTDNAYVNGYPSITFTDGIENRVWTIDVLDWTDGTVGGNQQVGFDVFGTVQGALSYLR

Entity 5 polymer

description	gp78
formula_weight	18265.0 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	H,R,b,l,r,x

MITTYSPRDVVVTLAGIHSVTGYAEGEFIRIVKDIKPFIKHGSMDGEIARVYNKDQGWRVELTIMQSSPTNDILSMLYNVDIATRMGKFPLMIKDTKGSTSFLALTAWVEDLPRVSFSGQLETRTWILGCSEVAMNIGGNVDQSLVEQAILLGSSLLPALTQFGGF

Entity 6 polymer

description	gp84
formula_weight	14001.8 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	I,S,c,m,s,y

MSTTYIDTLPLYQDRKYRYAVAIEGISRVLQFYWNSRSRQWHMDIFDEELNPILTGLAVVPQYPIMADYAMQHIGFNGYFLLMPVNLEQVQYKHDASDIVPQFFELLYVNVDLEDDVE

Entity 7 polymer

description	gp87
formula_weight	14196.2 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	K,U,e,n,t,z

MDLFVNPDTHDLVFINGEAPVTQRMVDIVAQRLKIKLYTFLGEWFLDDRIGIPYFERILGKSRSLPAVDAIFQSEIMRDPGVLEITSWQSGIDPHTREYSMEFTVRTTDNTESLPITFRMIGV

Entity 8 polymer

description	gp86
formula_weight	26712.2 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	P,Z,j

MRRTGLQELLNLHSSTEGSKQYTAIPCVVLRVLDDFRRLSVDVRPVVNDLYKDGTSEEQPEILSVPVIMPGTANTLISFPLNVGDTVLCVFSQRTMDVFKGSATGQPHTPNDLRKFNMADAIAIPGLFTFPRSMNDPARHSWPHDTKDLTIAHNLMTGQEAEVRIKANGDILINSRKTISINAQNVNVKCASLTVDAAHTTWNGNIAHTGNYVQTGGTSTFNGIPFHTHKHGGVMPGGGVTAVPQA

Entity 9 polymer

description	gp85
formula_weight	33881.9 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	J,T,d

MKQYDRVYKLTLGNTESGQGVEITNLHPDGSLNREGLQFRFDISKSSDNKKSGNSATVEIYNLSIATLNILETEYLTCRLEVGYKEMGTSVVLDGNVVETSTRKSGNDYVTQLILGEGYTALTETKLKGTVSPGKTVKDVIEEIRLQMPGVDRGAYTGLNCNNPIMYGYQLRGLAKDALNSVCEANNIEWNISGNVLNVTDVNGPTTKSVQMAPLVNRETGLIDIPFYASASGTAQKKDQRRRRGVQFKCLLNPELTPGVLVRVESDRLSGTFRINNVRISGGYRDNEWYTECWCSDLNQEDIDQ

Entity 10 polymer

description	gp88
formula_weight	86017.3 kDa
src_method	nat
entity_count	9

Polymer

type	polypeptide(L)
strand_id	4,2,3,5,6,7,8,9,AA

MITERIAQLTGELKFTVDSRPLTAFDKKLAGVEARLREFSKLTNKRFGVKLTLDTKTLREELAKAATQRVVLKNIAVDAAAVRLISEKLQERLNATPIRLKSVRLDLSGIRDQKNFVKTALGQTKVDLPVELGLAQASRTLYEWKKRTESRFKIHLNADISRSKLLQNARNTLRDVQGRLNGLAVATPQIRLSVDRAHLRREIQDVLEQIRREVRIRIDLESSIRGGGAGGSRGTAGHIRQGMGMGIGSELAGWGRGFIPGLGGAFAIMQLNRANQELQGQRLAMQAVGGGVQGGQELQATLRDISQRLGLDDRAIGSSYVKMMAAGQASNFDKTQVDGIFQSMAEYGRVMGLDGEAMKGSFRAVEQMMGKGQIMSEELKGQLAERFPAAVALMAKSQDMTIAELMKTMEKGELKSDALIPFARTLAEEARKGGALDAAMQGTAAQQGRFQFGWNRTIEAFAAGGFDRGMSDFFKIAAQGMKEALPLVTALGGGFEALMRPVNALVGIGGELGSQWENIAKQFNMTGTGLTLTTAQTLALLTPMGRLISAISWGALALEDFIVFLEGGDSVFGDFLNNNVQAAETFEKLASESSELKNNLDGIFSVVPGLAEALKGLEFNEMLVSTMRELAAIMEFFNSVVERFAIAGKYRDAKIAEAGGDRSTIMSNIDTMYAMFNPEDAKDKATFIGDRLVAQNIDAIQTETHTRATQSLTPDQFGYMMQRGQVRNEMEGALKKSAIDISFNLNVSGIDAQGNVMTTEAQERVREIVSNVLEEEISRASASYKESQ

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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	3.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.60 Å
resolution_method	—
num_particles	10400

fit	/app/data/saxs_computation/zd/9zd8/9zd8.fit
pddf	/app/data/pr_computation/zd/9zd8/9zd8.pr.out
profile	/app/data/saxs_computation/zd/9zd8/9zd8.dat

The cryo-EM structure of Pakpunavirus P7-1 baseplate in extended status

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 (10)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 polymer

Polymer

Entity 9 polymer

Polymer

Entity 10 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)