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9zd7

The cryo-EM structure of Pakpunavirus P7-1 short tail fiber (gp92) bound to the extended baseplate

Method: ELECTRON MICROSCOPY D_max: 449.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zd7
deposition_date	2025-11-25
title	The cryo-EM structure of Pakpunavirus P7-1 short tail fiber (gp92) bound to the extended baseplate
keywords	Pakpunavirus P7-1; Cryo-EM, in situ, structure; tail fiber; 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	148.80 Å
i0	85477500000.00
molecular_weight	2484200.0 kDa
excluded_volume	3101700 Å³
envelope_volume	7406500 Å³
shell_volume	452470 Å³
envelope_diameter	530.4 Å
shell_rg	111.30 Å
envelope_rg	150.60 Å
shape_rg	148.80 Å
total_rg	148.50 Å
total_atoms	174969
n_residues	22896
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	449.1 Å
rg_real	146.40 Å
rg_real_error	2.70 Å
i0_real	8.4160e+10
i0_real_error	2.3550e+09
rg_reciprocal	114.10 Å
i0_reciprocal	76650000000.0000
total_estimate	0.8713
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	134.7 Å
skewness	0.677
kurtosis	-0.453
angular_range	— – 0.0500 Å⁻¹
current_alpha	1.1920
highest_alpha	13790000000.0000
n_real_points	11
gnom_version	4.1.3
quality_criteria	AN1: 0.013; Oscil: 0.698; Stabil: 0.939; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.421

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

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	174969

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	13870.6 kDa
src_method	nat
entity_count	6

Polymer

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

STTYIDTLPLYQDRKYRYAVAIEGISRVLQFYWNSRSRQWHMDIFDEELNPILTGLAVVPQYPIMADYAMQHIGFNGYFLLMPVNLEQVQYKHDASDIVPQFFELLYVNVDLEDDVE

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	tail tip 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

Entity 11 polymer

description	short tail fiber gp92
formula_weight	53102.2 kDa
src_method	nat
entity_count	18

Polymer

type	polypeptide(L)
strand_id	AE,AF,AG,AB,AC,AD,AH,AI,AJ,AK,AL,AM,AN,AO,AP,AQ,AR,AS

MPNIMKPTGINAIWSENGQKVDPGAVKVGLGWVTELPPYQTANFIEYKQDLFNAHVNQHGIPEWDSVTEYQGNLSYTQGANGIIYKCLRTHSDKIPTDPLNITAGYWRVAFEDAGEAAKVQANLDRHVTNYNTLSGIGNVVIARQNLSVYSKAEGDARYAMKHGNGSNVFSVATATQPTHAIPLSQLSTLVPPATETVAGVMAVATTIETEAGANDTKAVSPLKAAQVYLKKKDNLSGLSNVTAARANLGLSDTATMPSSTFLKAGSNLADVPNKALARSNLGITSSATQPETYFLRSAQNLADVPNKAQARVNLGLTGMATTDPAAVMMKADNLAGLANTATARSNLGLGTASTRNTGDFLSSGDNLSDLTNVQAARNNLGLKGAATLDVWGLPANTTAMDFQSNQSDISRGWARLPNGLLLQWGTGPGLSDDTRTNIQLPVPARILNVQVTVMGTFNNSIGPGAFMTDMWSNTGFRVSCNWGNWSYPFNWFAITSTL

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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	4.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.20 Å
resolution_method	—
num_particles	10400

fit	/app/data/saxs_computation/zd/9zd7/9zd7.fit
pddf	/app/data/pr_computation/zd/9zd7/9zd7.pr.out
profile	/app/data/saxs_computation/zd/9zd7/9zd7.dat

The cryo-EM structure of Pakpunavirus P7-1 short tail fiber (gp92) bound to the extended baseplate

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 (11)

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

Entity 11 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)