9zd8

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

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

No usable UniProt protein identity is available for this entry.

The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.

Assembly Composition of the Current Entry

Assembly	Physical composition	Protein state	蛋白 / DNA / RNA / 其他Polymer	Data consistency
1	Protein heterocomplex	Heteromer	63 / 0 / 0 / 0	Consistent with protein count

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9zd8
Deposition date deposition_date	2025-11-25
Structure title title	The cryo-EM structure of Pakpunavirus P7-1 baseplate in extended status
Keywords keywords	Pakpunavirus P7-1; Cryo-EM, in situ, structure; baseplate; VIRAL PROTEIN, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9zd8__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9zd8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9zd8__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	84.70 Å
Rg (electron density)	84.53 Å
Total Rg	84.58 Å
Atom count	107757
Residues	13914
Excluded volume	1916100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9zd8__assembly_1__model_1`	63-meric （63）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	gp88
Molecular weight formula_weight	52425.9 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

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

MAGITAEGLTIKDLDQILTDYRNVASQVFADLVSTGDEVDTSGNSALGRLIGVVAPSDEAIWEVIQMVYNSFNPAAATGVALDNLVSFSAISRHAARPTRAQVVLEGNINTVINSPPAKMISSSTGRVFHLLQGVILTPKACSGVGIFPQTVGNDLTYELKMYVDDINTTSIKYTSPATGTVTSESILAGLAADVATNHGNTLTSYEQNGILFIVPIDPFNTKTFEEASNLSIQKVRKLGIAVDDVIGPVPQQALAIDTISIPIAGWDSVINPVPAITGRLRETDDELRERFRNSKFVQATNILESLIDGLMNVEGVEDVRIIENDTDNPDPVHGVPGHSFLPIVLGGIPTEVAQSIWLNKPFGIGSVGDTEVQVVDSRGYTHRVNYQRPVEVPIEIKISVTNTGSMPENIEDILRPRIVAYGTENYKIGDDVIYSRFYAPIMEIPGFQVNSLTIAKKGQTQGMANIEIGFKEVATFAAADITVTTV

Entity 2 Entity 2 polymer

Description description	gp89
Molecular weight formula_weight	26698.1 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

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

MAVNQFDREDYLEVARERVTEQFKEKPIFDRFLQVLLSGKFDIQNALEDLQTLRSLDTATGKQLDIIGDIVGRPRGLVYQDIFNYFGFAGTERAGSFGSLSDPTVGAPWYSVGAPTGNAREPSDEEYRMILKAKIIKNRTNSTPEQVIEAYKFVFGVPEVFLEEYAPAAVRIGIGKILTNVERSLLFDLGGAGALLPKTIGVNYTYTEFQAGRVFATEGFPGGQGVGDLNDPTVGGILTNLVT

Entity 3 Entity 3 polymer

Description description	gp83
Molecular weight formula_weight	28575.0 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

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

MTIAIKRENGDLIWFDAVTEFGRQYRGSVSSNPIETGGKITDHITTENPVFTLTAVVSDADFNLNRPVINDNEAQTYKINNKEFVNTQPVTIPAVISTSRLDPSRIFPEVITQFIPPEIPSATVLPQKGDKVAYDIERQLIDMQRNAEVFSLLDFRDGIIWDQIERCIFTDLSFTENAETGSSLQPRMTIEAVTFTDTRYVEVRVNKGRKTAKKEKRDTKEGDTGASNATSQDSPTFKRSQMKEAQIRTQVAR

Entity 4 Entity 4 polymer

Description description	gp79
Molecular weight formula_weight	17714.9 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

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

MANTVLTYSPSDVKIVLCGYALTGVVSFEMSWLSRPYTMVRGIRGHHTRVFNRDLSAQIRIEVLQTSVSNDAFFSLVEQDRRTQSARITLSVKDTHGSTMMSTDNAYVNGYPSITFTDGIENRVWTIDVLDWTDGTVGGNQQVGFDVFGTVQGALSYLR

Entity 5 Entity 5 polymer

Description description	gp78
Molecular weight formula_weight	18265.0 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

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

MITTYSPRDVVVTLAGIHSVTGYAEGEFIRIVKDIKPFIKHGSMDGEIARVYNKDQGWRVELTIMQSSPTNDILSMLYNVDIATRMGKFPLMIKDTKGSTSFLALTAWVEDLPRVSFSGQLETRTWILGCSEVAMNIGGNVDQSLVEQAILLGSSLLPALTQFGGF

Entity 6 Entity 6 polymer

Description description	gp84
Molecular weight formula_weight	14001.8 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

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

MSTTYIDTLPLYQDRKYRYAVAIEGISRVLQFYWNSRSRQWHMDIFDEELNPILTGLAVVPQYPIMADYAMQHIGFNGYFLLMPVNLEQVQYKHDASDIVPQFFELLYVNVDLEDDVE

Entity 7 Entity 7 polymer

Description description	gp87
Molecular weight formula_weight	14196.2 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

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

MDLFVNPDTHDLVFINGEAPVTQRMVDIVAQRLKIKLYTFLGEWFLDDRIGIPYFERILGKSRSLPAVDAIFQSEIMRDPGVLEITSWQSGIDPHTREYSMEFTVRTTDNTESLPITFRMIGV

Entity 8 Entity 8 polymer

Description description	gp86
Molecular weight formula_weight	26712.2 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Z,j

MRRTGLQELLNLHSSTEGSKQYTAIPCVVLRVLDDFRRLSVDVRPVVNDLYKDGTSEEQPEILSVPVIMPGTANTLISFPLNVGDTVLCVFSQRTMDVFKGSATGQPHTPNDLRKFNMADAIAIPGLFTFPRSMNDPARHSWPHDTKDLTIAHNLMTGQEAEVRIKANGDILINSRKTISINAQNVNVKCASLTVDAAHTTWNGNIAHTGNYVQTGGTSTFNGIPFHTHKHGGVMPGGGVTAVPQA

Entity 9 Entity 9 polymer

Description description	gp85
Molecular weight formula_weight	33881.9 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,T,d

MKQYDRVYKLTLGNTESGQGVEITNLHPDGSLNREGLQFRFDISKSSDNKKSGNSATVEIYNLSIATLNILETEYLTCRLEVGYKEMGTSVVLDGNVVETSTRKSGNDYVTQLILGEGYTALTETKLKGTVSPGKTVKDVIEEIRLQMPGVDRGAYTGLNCNNPIMYGYQLRGLAKDALNSVCEANNIEWNISGNVLNVTDVNGPTTKSVQMAPLVNRETGLIDIPFYASASGTAQKKDQRRRRGVQFKCLLNPELTPGVLVRVESDRLSGTFRINNVRISGGYRDNEWYTECWCSDLNQEDIDQ

Entity 10 Entity 10 polymer

Description description	gp88
Molecular weight formula_weight	86017.3 kDa
Source method src_method	nat
Copy count entity_count	9

Polymer Polymer

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

MITERIAQLTGELKFTVDSRPLTAFDKKLAGVEARLREFSKLTNKRFGVKLTLDTKTLREELAKAATQRVVLKNIAVDAAAVRLISEKLQERLNATPIRLKSVRLDLSGIRDQKNFVKTALGQTKVDLPVELGLAQASRTLYEWKKRTESRFKIHLNADISRSKLLQNARNTLRDVQGRLNGLAVATPQIRLSVDRAHLRREIQDVLEQIRREVRIRIDLESSIRGGGAGGSRGTAGHIRQGMGMGIGSELAGWGRGFIPGLGGAFAIMQLNRANQELQGQRLAMQAVGGGVQGGQELQATLRDISQRLGLDDRAIGSSYVKMMAAGQASNFDKTQVDGIFQSMAEYGRVMGLDGEAMKGSFRAVEQMMGKGQIMSEELKGQLAERFPAAVALMAKSQDMTIAELMKTMEKGELKSDALIPFARTLAEEARKGGALDAAMQGTAAQQGRFQFGWNRTIEAFAAGGFDRGMSDFFKIAAQGMKEALPLVTALGGGFEALMRPVNALVGIGGELGSQWENIAKQFNMTGTGLTLTTAQTLALLTPMGRLISAISWGALALEDFIVFLEGGDSVFGDFLNNNVQAAETFEKLASESSELKNNLDGIFSVVPGLAEALKGLEFNEMLVSTMRELAAIMEFFNSVVERFAIAGKYRDAKIAEAGGDRSTIMSNIDTMYAMFNPEDAKDKATFIGDRLVAQNIDAIQTETHTRATQSLTPDQFGYMMQRGQVRNEMEGALKKSAIDISFNLNVSGIDAQGNVMTTEAQERVREIVSNVLEEEISRASASYKESQ

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	10400

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Assembly Composition of the Current Entry

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9zd8__assembly_1__model_1

9zd8__assembly_1__model_1 | I(q)

9zd8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 polymer

Polymer Polymer

Entity 10 Entity 10 polymer

Polymer Polymer

7. Citations (1)