8xa0

penton capsomer of the VZV C-capsid

Method: ELECTRON MICROSCOPY

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

Large tegument protein deneddylase

Human alphaherpesvirus 3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	Major capsid protein × 5 （Q6QCL5） Capsid vertex component 1 × 1 （P10201） Capsid vertex component 2 × 2 （P10209） Tri2A × 1 Tri2B × 1 Tri1 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LTP_HHV11
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 2； PDBConstruct 1–47； UniProt 3117–3163 Author chain y； PDBConstruct 1–47； UniProt 3117–3163

Major capsid protein

Human alphaherpesvirus 3

UniProt Q6QCL5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	Large tegument protein deneddylase × 2 （P10220） Capsid vertex component 1 × 1 （P10201） Capsid vertex component 2 × 2 （P10209） Tri2A × 1 Tri2B × 1 Tri1 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6QCL5_HHV3
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–1370； UniProt 25–1394 Author chain C； PDBConstruct 1–1370； UniProt 25–1394 Author chain E； PDBConstruct 1–1370； UniProt 25–1394 Author chain F； PDBConstruct 1–1370； UniProt 25–1394 Author chain G； PDBConstruct 1–1370； UniProt 25–1394

Capsid vertex component 1

Human alphaherpesvirus 3

UniProt P10201

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	Large tegument protein deneddylase × 2 （P10220） Major capsid protein × 5 （Q6QCL5） Capsid vertex component 2 × 2 （P10209） Tri2A × 1 Tri2B × 1 Tri1 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CVC1_HHV11
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain h； PDBConstruct 1–696； UniProt 1–696

Capsid vertex component 2

Human alphaherpesvirus 3

UniProt P10209

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	Large tegument protein deneddylase × 2 （P10220） Major capsid protein × 5 （Q6QCL5） Capsid vertex component 1 × 1 （P10201） Tri2A × 1 Tri2B × 1 Tri1 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CVC2_HHV11
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain q； PDBConstruct 1–94； UniProt 1–94 Author chain u； PDBConstruct 1–94； UniProt 1–94

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	8xa0
Deposition date deposition_date	2023-12-01
Last revision last_revision	2024-12-04
Structure title title	penton capsomer of the VZV C-capsid
Keywords keywords	VZV, capsid structure, VIRUS; VIRUS
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.

8xa0__assembly_1__model_1

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

Download this curve (.dat)

8xa0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8xa0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	69.56 Å
Rg (electron density)	69.53 Å
Total Rg	69.48 Å
Atom count	57027
Residues	7398
Excluded volume	1014300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8xa0__assembly_1__model_1`	tridecameric （13）	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 (7)

Entity 1 Entity 1 polymer

Description description	Large tegument protein deneddylase
Molecular weight formula_weight	5500.5 kDa
EC 编号 ec_number	3.4.19.12,3.4.22.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2,y
Atom count atom_count	57027

QRTGRSALAVLIRACYRLQQQLQRTRRALLHHSDAVLTSLHHVRMLL

Source Source

Source organism organism	Human alphaherpesvirus 3
Common name common_name	Varicella-zoster virus
NCBI taxonomy ID ncbi_taxonomy_id	10335
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Major capsid protein
Molecular weight formula_weight	152365.3 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

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

IPAGIIPTGNVLSTIEVCIFFCIFDFFKQIRSDDNSLYSAQFDILLGTYCNTLNFVRFLELGLSVACICTKFPELAYVRDGVIQFEVQQPMIARDGPHPVDQPVHNYMVKRIHKRSLSAAFAIASEALSLLSNTYVAATEIDSSLRIRAIQQMARNLRTVSDSFERGTADQLLGVLLEKAPPLSLLSPINKFQPEGHLNRVARAALLSDLKRRVCADMFFMTRHAREPRLISAYLSDMVSCTQPSVMVSRITHTNTRGRQVDGVLVTTATLKRQLLQGILQIDDTAADVPVTYGEMVLQGTNLVTALVMGKAVRGMDDVARHLLDITDPNTLNIPSIPPQSNSDSTTAGLPVNARVPADLVIVGDKLVFLEALERRVYQATRVAYPLIGNIDITFIMPMGVFQANSMDRYTRHAGDFSTVSEQDPRQFPPQGIFFYNKDGILTQLTLRDAMGTICHSSLLDVEATLVALRQQHLDRQCYFGVYVAEGTEDTLDVQMGRFMETWADMMPHHPHWVNEHLTILQFIAPSNPRLRFELNPAFDFFVAPGDVDLPGPQRPPEAMPTVNATLRIINGNIPVPLCPISFRDCRGTQLGLGRHTMTPATIKAVKDTFEDRAYPTIFYMLEAVIHGNERNFCALLRLLTQCIRGYWEQSHRVAFVNNFHMLMYITTYLGNGELPEVCINIYRDLLQHVRALRQTITDFTIQGEGHNGETSEALNNILTDDTFIAPILWDCDALIYRDEAARDRLPAIRVSGRNGYQALHFVDMAGHNFQRRDNVLIHGRPVRGDTGQAIPITPHHDREWGILSKIYYYIVIPAFSRGSCCTMGVRYDRLYPALQAVIVPEIPADEEAPTTPEDPRHPLHAHQLVPNSLNVYFHNAHLTVDGDALLTLQELMGDMAERTTAILVSSAPDAGAATATTRNMRIYDGALYHGLIMMAYQAYDETIATGTFFYPVPVNPLFACPEHLASLRGMTNARRVLAKMVPPIPPFLGANHHATIRQPVAYHVTHSKSDFNTLTYSLLGGYFKFTPISLTHQLRTGFHPGIAFTVVRQDRFATEQLLYAERASESYFVGQIQVHHHDAIGGVNFTLTQPRAHVDLGVGYTAVCATAALRCPLTDMGNTAQNLFFSRGGVPMLHDNVTESLRRITASGGRLNPTEPLPIFGGLRPATSAGIARGQASVCEFVAMPVSTDLQYFRTACNPRGRASGMLYMGDRDADIEAIMFDHTQSDVAYTDRATLNPWASQKHSYGDRLYNGTYNLTGASPIYSPCFKFFTPAEVNTNCNTLDRLLMEAKAVASQSSTDTEYQFKRPPGSTEMTQDPCGLFQEAYPPLCSSDAAMLRTAHAGETGADEVHLAQYLIRDASPLRGCLPL

Source Source

Source organism organism	Human alphaherpesvirus 3
Common name common_name	Varicella-zoster virus
NCBI taxonomy ID ncbi_taxonomy_id	10335
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Capsid vertex component 1
Molecular weight formula_weight	73998.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	h

MNAHLANEVQYDLGHARVGPSSLVHVIISSECLAAAGIPLAALMRGRPGLGTAANFQVEIQTRAHATGDCTPWCTAFAAYVPADAVGELLAPVVPAHPGLLPRASSAGGLFVSLPVVCDAQGVYDPYAVAALRLAWGSGASCARVILFSYDELVPPNTRYAADSTRIMRVCRHLCRYVALLGAAAPPAAKEAAAHLSMGLGESASPRPQPLARPHAGAPADPPIVGASDPPISPEEQLTAPGGDTTAAQDVSIAQENEEILALVQRAVQDVTRRHPVRARTGRAACGVASGLRQGALVHQAVSGGAMGAADADAVLAGLEPPGGGRFVAPAPHGPGGEDILNDVLTLTPGTAKPRSLVEWLDRGWEALAGGDRPDWLWSRRSISVVLRHHYGTKQRFVVVSYENSVAWGGRRARPPLLSSALATALTEACAAERVVRPHQLSPAGQAELLLRFPALEVPLRHPRPVLPPFDIAAEVAFTARIHLACLRALGQAIRAALQGGPRISQRLRYDFGPDQRAWLGEVTRRFPILLENLMRAVEGTAPDAFFHTAYALAVLAHLGGRGGRGRRVVPLGDDLPARFADSDGHYVFDYYSTSGDTLRLNNRPIAVAMDGDVSKREQSKCRFMEAVPSTAPRRVCEQYLPGESYAYLCLGFNRRLCGIVVFPGGFAFTINIAAYLSLSDPVARAAVLRFCRKVS

Source Source

Source organism organism	Human alphaherpesvirus 3
Common name common_name	Varicella-zoster virus
NCBI taxonomy ID ncbi_taxonomy_id	10335
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Capsid vertex component 2
Molecular weight formula_weight	10890.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	q,u

MDPYCPFDALDVWEHRRFIVADSRNFITPEFPRDFWMSPVFNLPRETAAEQVVVLQAQRTAAAAALENAAMQAAELPVDIERRLRPIERNVHEI

Source Source

Source organism organism	Human alphaherpesvirus 3
Common name common_name	Varicella-zoster virus
NCBI taxonomy ID ncbi_taxonomy_id	10335
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	Tri2A
Molecular weight formula_weight	27729.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

AMPFEIEVLLPGELSPAETSALQKCEGKIITFSTLRHRASLVDIALSSYYINGAPPDTLSLLEAYRMRFAAVITRVIPGKLLAHAIGVGTPTPGLFIQNTSPVDLCNGDYICLLPPVYGSADSIRLDSVGLEIVFPLTIPQTLMREIIAKVVARAVEDLNLMFSINEGCLLILALIPRLLALLIPRLLALVTREAAQLIHPEAPMLMLPIYETISSWISTSSRLGDTLGTRAILRVCVFDGPSTVHPGDRTAVIQV

Source Source

Source organism organism	Human alphaherpesvirus 3
Common name common_name	Varicella-zoster virus
NCBI taxonomy ID ncbi_taxonomy_id	10335
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	Tri2B
Molecular weight formula_weight	28721.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

AMPFEIEVLLPGEISPAETSALQKCEGKIITFSTLRHRASLVDIALSSYYINGAPPDTLSLLEAYRMRFAAVITRVIPGKLLAHAIGVGTPTPGLFIQNTSPVDLCNGDYICLLPPVFGSADEIRLDSVGLEIVFPLTIPQTLMREIIAKVVARAVERTAADVICYNGRRYELETNLQHRDGSDAAIRTLVLNLMFSINEGTTLILTLITRLLRFPIYEAISSWISTSSRLGDTLGTRAILRVCVFDGPSTVHPGDRTAVIQV

Source Source

Source organism organism	Human alphaherpesvirus 3
Common name common_name	Varicella-zoster virus
NCBI taxonomy ID ncbi_taxonomy_id	10335
Host organism host_organism	Homo sapiens

Entity 7 Entity 7 polymer

Description description	Tri1
Molecular weight formula_weight	32268.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z

FKSTTQLIQQVSLTDFFRPDIEHAGSTVLILRHPTDLPALARHRAPPGRQTERLAEAWGQLLEASRAYVTSLSFIAACRAEEYTDKQAAEANRTAIVSAYGCSRMGARLIRFSECLRAMVQCHVFPHRFISFFGSLLEYTIQDNLCNITAVAKGPQEAARTDKTSTRRVTANIPACVFWDVDKDLHLSADGLKHVFLVFVYTQRRQREGVRLHLALSQLNEQCFGRGIGFLLGARICMYAAYTLIGTIPSESVRYTRRMERFGGYNVPTIWLEGVVWGGTNTWNEC

Source Source

Source organism organism	Human alphaherpesvirus 3
Common name common_name	Varicella-zoster virus
NCBI taxonomy ID ncbi_taxonomy_id	10335
Host organism host_organism	Homo sapiens

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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	4.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	417864

penton capsomer of the VZV C-capsid

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

Large tegument protein deneddylase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Major capsid protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Capsid vertex component 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Capsid vertex component 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8xa0__assembly_1__model_1

8xa0__assembly_1__model_1 | I(q)

8xa0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

7. Citations (1)