SAXSdb — 9yka

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

BALF4

human gammaherpesvirus 4

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 × 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain A； UniProt 1–688 Chain B； UniProt 1–688 Chain C； UniProt 1–688	Not recorded	AMMO2 fab heavy chain × 3 AMMO2 fab light chain × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.90 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 9YKA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7FBI Cryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5 Deposited 2021-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 22–674（653 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8YY6 Structure of a murine monoclonal antibody Fab5 targeting Epstein-Barr virus gB Deposited 2024-04-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 23–683（661 aa） Chain B 23–683（661 aa） Chain C 23–683（661 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	R4R670_EBVG
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–688； UniProt 1–688 Author chain B； PDBConstruct 1–688； UniProt 1–688 Author chain C； PDBConstruct 1–688； UniProt 1–688

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	9yka
Deposition date deposition_date	2025-10-06
Structure title title	Cryo-EM structure of post-fusion EBV gB in complex with AMMO2 fab
Keywords keywords	Post-fusion, AMMO2, fab, VIRAL PROTEIN; VIRAL PROTEIN
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	39.96 Å
Radius of gyration Rg (electron density) rg_electron	39.44 Å
Forward intensity I(0) i0	393297000.00
Molecular weight molecular_weight	158620.0 kDa
Excluded volume excluded_volume	197210 Å³
Envelope volume envelope_volume	267210 Å³
Hydration-shell volume shell_volume	58028 Å³
Envelope diameter envelope_diameter	129.8 Å
Shell Rg shell_rg	43.98 Å
Envelope Rg envelope_rg	39.02 Å
Shape Rg shape_rg	39.46 Å
Total Rg total_rg	39.65 Å
Total atoms total_atoms	11157
Residues n_residues	1380
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	127.0 Å
Rg (real space) rg_real	39.79 Å
Rg uncertainty (real space) rg_real_error	1.13 Å
I(0) (real space) i0_real	3.9330e+08
I(0) uncertainty (real space) i0_real_error	6.4510e+06
Rg (reciprocal space) rg_reciprocal	39.90 Å
I(0) (reciprocal space) i0_reciprocal	393300000.0000
Solution quality estimate total_estimate	0.9056
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.8 Å
Skewness Skewness skewness	0.145
Kurtosis Kurtosis kurtosis	-0.579
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25910000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.927

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	AMMO2 fab heavy chain
Molecular weight formula_weight	14393.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,H,D
Atom count atom_count	11157

QVQLVQSGAEVKKPGSSIKVSCKTSGGPFSTYGINWVRQAPGQGLEWMGWIIPVFDTSSFAQRFQDRLSITADASTSTAYMELRSLRSEDTAVYYCARDRVLGAHGANPLNGHHYGMDVWGQGTTVTVSSAST

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 2 Entity 2 polymer

Description description	AMMO2 fab light chain
Molecular weight formula_weight	23134.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,I,E

DIQITQSPSSVSASVGDRVTITCRANLGISDWLAWYQQKPGRAPKLLIYAASSLESGVPSRFSGSGSGIYFTLTISSLQPEDVATYFCQQANSFPLSFGGGTRVDIARTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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	BALF4
Molecular weight formula_weight	81665.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MTRRRVLSVVVLLAALACRLGAQTPEQPAPPATTVQPTATRQQTSFPFRVCELSSHGDLFRFSSDIQCPSFGTRENHTEGLLMVFKDNIIPYSFKVRSYTKIVTNILIYNGHRADSVTNRHEEKFSVESYETDQMDTIYQCYNAVKMTKDGLTRVYVDRDGVNITVNLKPTGGLANGVRRYASQTELYDAPGRVEATYRTRTTVNCLITDMMAKSNSPFEFFVTTTGQTVEMSPFYDGKNTETFHERADSFHVRTNYKIVDYDNRGTNPQGERRAFLDKGTYTLSWKLENRTAYCPLQHWQTFDSTIATETGKSIHFVTDEGTSSFVTNTTVGIELPDAFKCIEEQVNKTMHEKYEAVQDRYTKGQEAITYFITSGGLLLAWLPLTPRSLATVKNLTELTTPTSSPPSSPSPPAPPAARGSTSAAVLGGSGGNAGNATTPVPPAAPGKSLGTLNNPATVQIQFAYDSLRRQINRMLGDLARAWCLEQKRQNMVLRELTKINPTTVMSSIYGKAVAAKRLGDVISVSQCVPVNQATVTLRKSMRVPGSETMCYSRPLVSFSFINDTKTYEGQLGTDNEIFLTKKMTEVCQATSQYYFQSGNEIHVYNDYHHFKTIELDGIATLQTFISLNTSLIENIDFASLELYSRDEQRASNVFDLEGIFREYNFQAQNIAGLRKDLDNAVSNGRNQGGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRAAASSLEVLFQGPG

来源 Source

来源生物 organism	human gammaherpesvirus 4
通用名 common_name	Epstein-Barr virus
NCBI Class编号 ncbi_taxonomy_id	10376
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	6

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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	triclinic

Resolution resolution	2.90 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	154000

fit	/app/data/saxs_computation/yk/9yka/9yka.fit
pddf	/app/data/pr_computation/yk/9yka/9yka.pr.out
profile	/app/data/saxs_computation/yk/9yka/9yka.dat

Cryo-EM structure of post-fusion EBV gB in complex with AMMO2 fab

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

BALF4

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

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 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)