SAXSdb — 8x9y

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

Small capsomere-interacting 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 18	Tri1 × 2 Major capsid protein × 6 （P09245） Tri2A × 2 Tri2B × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	U5NQG6_HHV3
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–94； UniProt 14–107 Author chain G； PDBConstruct 1–94； UniProt 14–107 Author chain M； PDBConstruct 1–94； UniProt 14–107 Author chain S； PDBConstruct 1–94； UniProt 14–107 Author chain Y； PDBConstruct 1–94； UniProt 14–107 Author chain k； PDBConstruct 1–94； UniProt 14–107

Major capsid protein

Human alphaherpesvirus 3

UniProt P09245

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	Tri1 × 2 Small capsomere-interacting protein × 6 （U5NQG6） Tri2A × 2 Tri2B × 2	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	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–1369； UniProt 26–1394 Author chain C； PDBConstruct 1–1369； UniProt 26–1394 Author chain H； PDBConstruct 1–1369； UniProt 26–1394 Author chain I； PDBConstruct 1–1369； UniProt 26–1394 Author chain J； PDBConstruct 1–1369； UniProt 26–1394 Author chain K； PDBConstruct 1–1369； UniProt 26–1394

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	8x9y
Deposition date deposition_date	2023-12-01
Last revision last_revision	2025-04-30
Structure title title	E-hexon 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.

8x9y__assembly_1__model_1

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

Download this curve (.dat)

8x9y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8x9y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	70.91 Å
Rg (electron density)	70.63 Å
Total Rg	70.80 Å
Atom count	79700
Residues	10372
Excluded volume	1416500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8x9y__assembly_1__model_1`	octadecameric （18）	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 (5)

Entity 1 Entity 1 polymer

Description description	Tri1
Molecular weight formula_weight	42776.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z,E
Atom count atom_count	79700

SIQVTPRSIVINRMNNIQINPTSIGNPNNGLHMTYNNAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAASIQVTPRSIVINRMNNIQINPTSIGNPQVTIRLPLNNFKSTTQLIQQVSLTDFFRPDIEHAGSTVLILRHPTDLPALARHRAPPGRQTERLAEAWGQLLEASRAYVTSLSFIAACRAEEYTDKQAAEANRTAIVSAYGCSRMGARLIRFSECLRAMVQCHVFPHRFISFFGSLLEYTIQDNLCNITAVAKGPQEAARTDKTSTRRVTANIPACVFWDVDKDLHLSADGLKHVFLVFVYTQRRQREGVRLHLALSQLNEQCFGRGIGFLLGARICMYAAYTLIGTIPSESVRYTRRMERFGGYNVPTIWLEGVVWGGTNTWNEC

Source Source

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

Entity 2 Entity 2 polymer

Description description	Small capsomere-interacting protein
Molecular weight formula_weight	10185.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,G,M,S,Y,k

SNPTTFSVEAIAAYTPVALIRLLNASGPLQPGHRVDIADARSIYTVGAAASAARARANHNANTIRRTAMFAETDPMTWLRPTVGLRRTFNPRII

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	Major capsid protein
Molecular weight formula_weight	152267.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,H,I,J,K

PAGIIPTGNVLSTIEVCAHRCIFDFFKQIRSDDNSLYSAQFDILLGTYCNTLNFVRFLELGLSVACICTKFPELAYVRDGVIQFEVQQPMIARDGPHPVDQPVHNYMVKRIHKRSLSAAFAIASEALSLLSNTYVDGTEIDSSLRIRAIQQMARNLRTVLDSFERGTADQLLGVLLEKAPPLSLLSPINKFQPEGHLNRVARAALLSDLKRRVCADMFFMTRHAREPRLISAYLSDMVSCTQPSVMVSRITHTNTRGRQVDGVLVTTATLKRQLLQGILQIDDTAADVPVTYGEMVLQGTNLVTALVMGKAVRGMDDVARHLLDITDPNTLNIPSIPPQSNSDSTTAGLPVNARVPADLVIVGDKLVFLEALERRVYQATRVAYPLIGNIDITFIMPMGVFQANSMDRYTRHAGDFSTVSEQDPRQFPPQGIFFYNKDGILTQLTLRDAMGTICHSSLLDVEATLVALRQQHLDRQCYFGVYVAEGTEDTLDVQMGRFMETWADMMPHHPHWVNEHLTILQFIAPSNPRLRFELNPAFDFFVAPGDVDLPGPQRPPEAMPTVNATLRIINGNIPVPLCPISFRDCRGTQLGLGRHTMTPATIKAVKDTFEDRAYPTIFYMLEAVIHGNERNFCALLRLLTQCIRGYWEQSHRVAFVNNFHMLMYITTYLGNGELPEVCINIYRDLLQHVRALRQTITDFTIQGEGHNGETSEALNNILTDDTFIAPILWDCDALIYRDEAARDRLPAIRVSGRNGYQALHFVDMAGHNFQRRDNVLIHGRPVRGDTGQAIPITPHHDREWGILSKIYYYIVIPAFSRGSCCTMGVRYDRLYPALQAVIVPEIPADEEAPTTPEDPRHPLHAHQLVPNSLNVYFHNAHLTVDGDALLTLQELMGDMAERTTAILVSSAPDAGAATATTRNMRIYDGALYHGLIMMAYQAYDETIATGTFFYPVPVNPLFACPEHLASLRGMTNARRVLAKMVPPIPPFLGANHHATIRQPVAYHVTHSKSDFNTLTYSLLGGYFKFTPISLTHQLRTGFHPGIAFTVVRQDRFATEQLLYAERASESYFVGQIQVHHHDAIGGVNFTLTQPRAHVDLGVGYTAVCATAALRCPLTDMGNTAQNLFFSRGGVPMLHDNVTESLRRITASGGRLNPTEPLPIFGGLRPATSAGIARGQASVCEFVAMPVSTDLQYFRTACNPRGRASGMLYMGDRDADIEAIMFDHTQSDVAYTDRATLNPWASQKHSYGDRLYNGTYNLTGASPIYSPCFKFFTPAEVNTNCNTLDRLLMEAKAVASQSSTDTEYQFKRPPGSTEMTQDPCGLFQEAYPPLCSSDAAMLRTAHAGETGADEVHLAQYLIRDASPLRGCLPL

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	Tri2A
Molecular weight formula_weight	27729.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,R

AMPFEIEVLLPGELSPAETSALQKCEGKIITFSTLRHRASLVDIALSSYYINGAPPDTLSLLEAYRMRFAAVITRVIPGKLLAHAIGVGTPTPGLFIQNTSPVDLCNGDYICLLPPVYGSADSIRLDSVGLEIVFPLTIPQTLMREIIAKVVARAVEDLNLMFSINEGCLLILALIPRLLALLIPRLLALVTREAAQLIHPEAPMLMLPIYETISSWISTSSRLGDTLGTRAILRVCVFDGPSTVHPGDRTAVIQV

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	Tri2B
Molecular weight formula_weight	28721.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,V

AMPFEIEVLLPGEISPAETSALQKCEGKIITFSTLRHRASLVDIALSSYYINGAPPDTLSLLEAYRMRFAAVITRVIPGKLLAHAIGVGTPTPGLFIQNTSPVDLCNGDYICLLPPVFGSADEIRLDSVGLEIVFPLTIPQTLMREIIAKVVARAVERTAADVICYNGRRYELETNLQHRDGSDAAIRTLVLNLMFSINEGTTLILTLITRLLRFPIYEAISSWISTSSRLGDTLGTRAILRVCVFDGPSTVHPGDRTAVIQV

Source Source

Source organism organism	Human alphaherpesvirus 3
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	3.700 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.70 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1796810

E-hexon capsomer of the VZV C-Capsid

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

Small capsomere-interacting protein

State in the Current Structure

Other States of the Same Protein in the Database

Major capsid protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8x9y__assembly_1__model_1

8x9y__assembly_1__model_1 | I(q)

8x9y__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 (5)

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

7. Citations (1)

E-hexon capsomer of the VZV C-Capsid

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

Small capsomere-interacting 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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8x9y__assembly_1__model_1

8x9y__assembly_1__model_1 | I(q)

8x9y__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 (5)

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

7. Citations (1)