SAXSdb — 9zwe

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

Envelope glycoprotein B

Human herpesvirus 2 strain HG52

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain A； UniProt 74–731 Chain B； UniProt 74–731 Chain G； UniProt 74–731	Not recorded	Antibody D48 Heavy Chain × 3 Antibody D48 Light Chain × 3 Antibody 2c Heavy Chain × 3 Antibody 2c Light Chain × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.75 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ZWE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9MW5 D1 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycoprotein gB Deposited 2025-01-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 23–727（705 aa） Chain B 23–727（705 aa） Chain C 23–727（705 aa）	Not recorded	NA SODIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.10 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GB_HHV2H
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–658； UniProt 74–731 Author chain B； PDBConstruct 1–658； UniProt 74–731 Author chain G； PDBConstruct 1–658； UniProt 74–731

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	9zwe
Deposition date deposition_date	2026-01-01
Structure title title	Soluble ectodomain of Herpes simplex virus 2 (HSV-2) glycoprotein B (gB) in the prefusion conformation in complex with 2c and D48 Fabs
Keywords keywords	prefusion, ectodomain, viral fusion protein, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	53.91 Å
Radius of gyration Rg (electron density) rg_electron	54.05 Å
Forward intensity I(0) i0	1765920000.00
Molecular weight molecular_weight	348220.0 kDa
Excluded volume excluded_volume	434340 Å³
Envelope volume envelope_volume	614380 Å³
Hydration-shell volume shell_volume	96051 Å³
Envelope diameter envelope_diameter	176.9 Å
Shell Rg shell_rg	54.93 Å
Envelope Rg envelope_rg	53.67 Å
Shape Rg shape_rg	54.01 Å
Total Rg total_rg	54.20 Å
Total atoms total_atoms	48423
Residues n_residues	3024
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	175.2 Å
Rg (real space) rg_real	53.77 Å
Rg uncertainty (real space) rg_real_error	1.37 Å
I(0) (real space) i0_real	1.7660e+09
I(0) uncertainty (real space) i0_real_error	3.7020e+07
Rg (reciprocal space) rg_reciprocal	54.02 Å
I(0) (reciprocal space) i0_reciprocal	1767000000.0000
Solution quality estimate total_estimate	0.8743
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	72.5 Å
Skewness Skewness skewness	0.178
Kurtosis Kurtosis kurtosis	-0.455
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	90060000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.684

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Envelope glycoprotein B
Molecular weight formula_weight	83540.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,G
Atom count atom_count	48423

EATPPPDANATVAAGHATLRAHLREIKVENADAQFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGNRTSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNMETTAFHRDDHETDMELKPAKVATRCSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTSYAADRFKQVDGFYARDLTTKARATSPTTRNLLTTPKFTVAWDWVPKRPAVCTMTKWQEVDEMLRAEYGGSFRFSSDAISTTFTTNLTEYSLSRVDLGDCIGRDAREAIDRMFARKYNATHIKVGQPQYYLATGGFLIAYQPLLSNTLAELYVREYMREQDRKPRNATPAPLREAPSANASVERIKTTSSIEFARLQFTYNHIQRHVNDMLGRIAVAWCELQNHELTLWNEARKLNPNAIASATVGRRVSARMLGDVMAVSTCVPVAPDNVIVQNSMRVSSRPGTCYSRPLVSFRYEDQGPLIEGQLGENNELRLTRDALEPCTVGHRRYFIFGGGYVYFEEYAYSHQLSRADVTTVPPFIDLNITMLCDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIRADANAAMFAGGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK

来源 Source

来源生物 organism	Human herpesvirus 2 strain HG52
NCBI Class编号 ncbi_taxonomy_id	10315
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Antibody D48 Heavy Chain
Molecular weight formula_weight	24402.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,C,L

EVQLVETGGGVVRPGRSLRLSCTTSGFSFSGSAMHWVRQAPGKGLEWVAVISHDGNIIQYHDSVKGRFTISRDNSKNVLLLQMNSLRVDDTAMYYCARDVWLLPATISYAFDFWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Antibody D48 Light Chain
Molecular weight formula_weight	23476.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,D,M

VIWMTQSPPSLSASIGDTVTITCRASQGISNSIAWYQRRPGKAPELLVYAAYRLQSGVPSRLSGSGSGAEYTLTIKNMQPEDFATYYCQQYYDNPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Antibody 2c Heavy Chain
Molecular weight formula_weight	24262.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,E,N

QVTLKESGPGILLPSQTLSLTCSFSGFSLSTSGMSVGWIRQPSGKGLEWLGHIWWNNDKYYKPALKSRLTISKDTSNKQVFLKIASVVTADTATYYCARIYYGYRPYAMDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	Antibody 2c Light Chain
Molecular weight formula_weight	24022.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,F,O

DVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPWSFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

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8. Citations (1)

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

Resolution resolution	2.75 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	227517

fit	/app/data/saxs_computation/zw/9zwe/9zwe.fit
pddf	/app/data/pr_computation/zw/9zwe/9zwe.pr.out
profile	/app/data/saxs_computation/zw/9zwe/9zwe.dat

Soluble ectodomain of Herpes simplex virus 2 (HSV-2) glycoprotein B (gB) in the prefusion conformation in complex with 2c and D48 Fabs

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

Envelope glycoprotein B

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)