8x9w

portal vertex capsomer of the VZV C-Capsid

Method: ELECTRON MICROSCOPY

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

Major capsid protein

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 20	coiled-coil domain of portal × 10 Tri2A × 1 Tri2B × 1 Tri1 × 1 CVC1 × 1 Capsid vertex component 2 × 2 （P10209） Large tegument protein deneddylase × 2 （P10220）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCP_VZVD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–1387； UniProt 14–1394 Author chain C； PDBConstruct 7–1387； UniProt 14–1394

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 20	Major capsid protein × 2 （P09245） coiled-coil domain of portal × 10 Tri2A × 1 Tri2B × 1 Tri1 × 1 CVC1 × 1 Large tegument protein deneddylase × 2 （P10220）	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	7
Chains and sequence ranges	Author chain l； PDBConstruct 1–94； UniProt 1–94 Author chain m； PDBConstruct 1–94； UniProt 1–94

Large tegument protein deneddylase

Human alphaherpesvirus 3

UniProt P10220

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 20	Major capsid protein × 2 （P09245） coiled-coil domain of portal × 10 Tri2A × 1 Tri2B × 1 Tri1 × 1 CVC1 × 1 Capsid vertex component 2 × 2 （P10209）	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	8
Chains and sequence ranges	Author chain n； PDBConstruct 1–47； UniProt 3117–3163 Author chain o； PDBConstruct 1–47； UniProt 3117–3163

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	8x9w
Deposition date deposition_date	2023-12-01
Structure title title	portal vertex capsomer of the VZV C-Capsid
Keywords keywords	VZV, capsid structure, 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.

8x9w__assembly_1__model_1

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

Download this curve (.dat)

8x9w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8x9w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	64.79 Å
Rg (electron density)	63.79 Å
Total Rg	63.33 Å
Atom count	37344
Residues	5160
Excluded volume	657880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8x9w__assembly_1__model_1`	eicosameric （20）	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 (8)

Entity 1 Entity 1 polymer

Description description	Major capsid protein
Molecular weight formula_weight	153965.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	37344

AAAAAATESDRIAGIFNIPAGIIPTGNVLSTIEVCAHRCIFDFFKQIRSDDNSLYSAQFDILLGTYCNTLNFVRFLELGLSVACICTKFPELAYVRDGVIQFEVQQPMIARDGPHPVDQPVHNYMVKRIHKRSLSAAFAIASEALSLLSNTYVDGTEIDSSLRIRAIQQMARNLRTVLDSFERGTADQLLGVLLEKAPPLSLLSPINKFQPEGHLNRVARAALLSDLKRRVCADMFFMTRHAREPRLISAYLSDMVSCTQPSVMVSRITHTNTRGRQVDGVLVTTATLKRQLLQGILQIDDTAADVPVTYGEMVLNGANLVTALVMGKAVRSLDDVGRHLLDITDPNTLNIPSIPPQSNSDSTTAGLPVNARVPADLVIVGDKLVFLEALERRVYQATRVAYPLIGNIDITFIMPMGVFQANSMDRYTRHAGDFSTVSEQDPRQFPPQGIFFYNKDGILTQLTLRDAMGTICHSSLLDVEATLVALRQQHLDRQCYFGVYVAEGTEDTLDVQMGRFMETWADMMPHHPHWVNEHLTILQFIAPSNPRLRFELNPAFDFFVAPGDVDLPGPQRPPEAMPTVNATLRIINGNIPVPLCPISFRDCRGTQLGLGRHTMTPATIKAVKDTFEDRAYPTIFYMLEAVIHGNERNFCALLRLLTQCIRGYWEQSHRVAFVNNFHMLMYITTYLGNGELPEVCINIYRDLLQHVRALRQTITDFTIQGEGHNGETSEALNNILTDDTFIAPILWDCDALIYRDEAARDRLPAIRVSGRNGYQALHFVDMAGHNFQRRDNVLIHGRPVRGDTGQAIPITPHHDREWGILSKIYYYIVIPAFSRGSCCTMGVRYDRLYPALQAVIVPEIPADEEAPTTPEDPRHPLHAHQLVPNSLNVYFHNAHLTVDGDALLTLQELMGDMAERTTAILVSSAPDAGAATATTRNMRIYDGALYHGLIMMAYQAYDETIATGTFFYPVPVNPLFACPEHLASLRGMTNARRVLAKMVPPIPPFLGANHHATIRQPVAYHVTHSKSDFNTLTYSLLGGYFKFTPISLTHQLRTGFHPGIAFTVVRQDRFATEQLLYAERASESYFVGQIQVHHHDAIGGVNFTLTQPRAHVDLGVGYTAVCATAALRCPLTDMGNTAQNLFFSRGGVPMLHDNVTESLRRITASGGRLNPTEPLPIFGGLRPATSAGIARGQASVCEFVAMPVSTDLQYFRTACNPRGRASGMLYMGDRDADIEAIMFDHTQSDVAYTDRATLNPWASQKHSYGDRLYNGTYNLTGASPIYSPCFKFFTPAEVNTNCNTLDRLLMEAKAVASQSSTDTEYQFKRPPGSTEMTQDPCGLFQEAYPPLCSSDAAMLRTAHAGETGADEVHLAQYLIRDASPLRGCLPL

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	coiled-coil domain of portal
Molecular weight formula_weight	7422.1 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,H,I,J,K,L,Q,R,S,T

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Source Source

Source organism organism	Human alphaherpesvirus 3
NCBI taxonomy ID ncbi_taxonomy_id	10335
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Tri2A
Molecular weight formula_weight	32225.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

AMPFEIEVLLPGELSPAETSALQKCEGKIITFSTLRHRASLVDIALSSYYINGAPPDTLSLLEAYRMRFAAVITRVIPGKLLAHAIGVGTPTPGLFIQNTSPVDLCNGDYICLLPPVFGSADSIRLDSVGLEIVFPLTIPQTLMREIIAKVVARAVEDLNPDPDLNVLYYNGARLSLVADVQQLASDAAIRTLVLNLMFSINEGCLLILALIPRLLALGYVNALLQMQSVTREAAQLIHPEAPMLMRRLPIYETISSWISTSSRLGDTLGTRAILRVCVFDGPSTVHPGDRTAVIQV

Source Source

Source organism organism	Human alphaherpesvirus 3
NCBI taxonomy ID ncbi_taxonomy_id	10335
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Tri2B
Molecular weight formula_weight	33420.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

AMPFEIEVLLPGEISPAETSALQKCEGKIITFSTLRHRASLVDIALSSYYINGAPPDTLSLLEAYRMRFAAVITRVIPGKLLAHAIGVGTPTPGLFIQNTSPVDLCNGDYICLLPPVFGSADEIRLDSVGLEIVFPLTIPQTLMREIIAKVVARAVERTAAGRTPGELPGADVICYNGRRYELETNLQHRDGSDAAIRTLVLNLMFSINEGTTLILTLITRLLVQGAHDGYVNLLIQTANCVRETGQPMPRIQDGHRRFPIYEAISSWISTSSRLGDTLGTRAILRVCVFDGPSTVHPGDRTAVIQV

Source Source

Source organism organism	Human alphaherpesvirus 3
NCBI taxonomy ID ncbi_taxonomy_id	10335
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	Tri1
Molecular weight formula_weight	32583.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

TTQLIQQVSLTDFFRPDIEHAGSTVLILRHPTDLPHLARHRAPPGRQTERLAEAWGQLLEASESGCARAYVTSLSFIAACRAEEYTDKQAAEANRTAIVSAYGCSRMGARLIRFSECLRAMVQCHVFPHRFISFFGSLLEYTIQDNLCNITAVAKGPQEAARTDKTSTRRVTANIPACVFWDVDKDLHLSADGLKHVFLVFVYTQRRQREGVRLHLALSQLNEQCFGRGIGFLLGARICMYAAYTLIGTIPSESVRYTRRMERFGGYNVPTIWLEGVVWGGTNTWNECY

Source Source

Source organism organism	Human alphaherpesvirus 3
NCBI taxonomy ID ncbi_taxonomy_id	10335
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	CVC1
Molecular weight formula_weight	59751.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	k

MNAHLANEVQYDLGHPSSLVHVIISSECLAAAGIPLAALMRANFQVEIQTRAHATGDCTPWCTAFAAYVPADAVGELLAPVVPAHPGLLPRASSAGGLFVSLPVVCDAQGVYDPYAVAALRLAWGSGASCARVILFSYDELVPPNTRYAADSTRIMRVCRHLCRYVALLGAAAPPAAKEAAAHLSMGLPPISPEEQLTAPGGDTTAAQDVSIAQENEEILALVQRRSLVEWLDRGWEALAGGDRPDWLWSRRSISVVLRHHYGTKQRFVVVSYENSVAWGGRRARPPLLSSALATALTEACAAERVVRPHQLSPAGQAELLLRFPALEVPLRHPRPVLPPFDIAAEVAFTARIHLACLRALGQAIRAALQGGPRISQRLRYDFGPDQRAWLGEVTRRFPILLENLMRAVEGTAPDAFFHTAYALAVLAHLGGRVVPLGDDLPARFADSDGHYVFDYYSTSGDTLRLNNRPIAVAMDEQSKCRFMEAPRRVCEQYLPGESYAYLCLGFNRRLCGIVVFPGGFAFTINIAAYLSLSDPVARAAVLRFCRKVS

Source Source

Source organism organism	Human alphaherpesvirus 3
NCBI taxonomy ID ncbi_taxonomy_id	10335
Host organism host_organism	Homo sapiens

Entity 7 Entity 7 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	l,m

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 8 Entity 8 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	n,o

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

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

Resolution resolution	4.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	28556

portal vertex capsomer of the VZV C-Capsid

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

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 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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8x9w__assembly_1__model_1

8x9w__assembly_1__model_1 | I(q)

8x9w__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 (8)

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

Entity 8 Entity 8 polymer

Polymer Polymer

Source Source

7. Citations (1)