SAXSdb — 5toh

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

Polymerase cofactor VP35

Lake Victoria marburgvirus (strain Musoke-80)

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 60–130 Chain B； UniProt 60–130 Chain C； UniProt 60–130	Fragment：UNP residues 60-130	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；295.5 K；100 mM Sodium cacodylate pH 6.5, 100 mM Mg-acetate and 18% 2-methyl-2,4-pentanediol (MPD), cryo-protected by addition of 25% ethylene glycol	Resolution 2.01 Å R-free 0.266

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 5TOH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4GH9 Crystal structure of Marburg virus VP35 RNA binding domain Deposited 2012-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 204–329（126 aa） Fragment：UNP residues 204-329	Not recorded	ACT ACETATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；2-2.4 M ammonium sulphate, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å R-free 0.217
4GHA Crystal structure of Marburg virus VP35 RNA binding domain bound to 12-bp dsRNA Deposited 2012-08-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 204–329（126 aa） Fragment：Marburg virus VP35 RNA binding domain, UNP residues 204-329 Chain C 204–329（126 aa） Fragment：Marburg virus VP35 RNA binding domain, UNP residues 204-329 Chain E 204–329（126 aa） Fragment：Marburg virus VP35 RNA binding domain, UNP residues 204-329 Chain G 204–329（126 aa） Fragment：Marburg virus VP35 RNA binding domain, UNP residues 204-329	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M Bis-Tris, 2% v/v Tacsimate, 18% PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.250
5TOI Crystal Structure of the Marburg Virus VP35 Oligomerization Domain P4222 Deposited 2016-10-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 60–130（71 aa） Fragment：UNP residues 60-130 Chain B 60–130（71 aa） Fragment：UNP residues 60-130 Chain C 60–130（71 aa） Fragment：UNP residues 60-130	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.5 K；0.2 M K/Na tartrate and 40% 2-methyl-2,4-pentanediol (MPD)	Resolution 2.19 Å R-free 0.342
9IP2 Cryo-EM structure of the RNA-dependent RNA polymerase complex from Marburg virus Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–329（329 aa） Chain C 1–329（329 aa） Chain D 1–329（329 aa） Chain E 1–329（329 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES, 500 mM NaCl, 1 mM TCEP, 6 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å R-free 0.301
9IP4 Cryo-EM structure of the RNA-dependent RNA polymerase complex from Marburg virus Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 57–329（273 aa） Chain C 57–329（273 aa） Chain D 57–329（273 aa） Chain E 57–329（273 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES, 500 mM NaCl, 1 mM TCEP, 6 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.84 Å R-free 0.327

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VP35_MABVM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–72； UniProt 60–130 Author chain B； PDBConstruct 2–72； UniProt 60–130 Author chain C； PDBConstruct 2–72； UniProt 60–130

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	5toh
Deposition date deposition_date	2016-10-17
Structure title title	Crystal Structure of the Marburg Virus VP35 Oligomerization Domain I2
Keywords keywords	polymerase cofactor, coiled coil, oligomerization, trimer, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	25.91 Å
Radius of gyration Rg (electron density) rg_electron	26.94 Å
Forward intensity I(0) i0	7013280.00
Molecular weight molecular_weight	20157.0 kDa
Excluded volume excluded_volume	25569 Å³
Envelope volume envelope_volume	34546 Å³
Hydration-shell volume shell_volume	13240 Å³
Envelope diameter envelope_diameter	105.4 Å
Shell Rg shell_rg	28.07 Å
Envelope Rg envelope_rg	28.13 Å
Shape Rg shape_rg	26.88 Å
Total Rg total_rg	27.31 Å
Total atoms total_atoms	1417
Residues n_residues	175
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	102.7 Å
Rg (real space) rg_real	26.64 Å
Rg uncertainty (real space) rg_real_error	1.42 Å
I(0) (real space) i0_real	7.0130e+06
I(0) uncertainty (real space) i0_real_error	1.0720e+05
Rg (reciprocal space) rg_reciprocal	26.41 Å
I(0) (reciprocal space) i0_reciprocal	7012000.0000
Solution quality estimate total_estimate	0.6458
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	18.5 Å
Skewness Skewness skewness	0.836
Kurtosis Kurtosis kurtosis	0.208
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1367000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.148; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.020; Smooth: 0.929

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	75.690 Å
Unit-cell length b length_b	35.000 Å
Unit-cell length c length_c	105.240 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	53.020 Å
R factor r_factor	0.2410
R_work r_work	0.2390
R_free r_free	0.2660

Description description	Polymerase cofactor VP35
Molecular weight formula_weight	8205.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	1443

Crystal Structure of the Marburg Virus VP35 Oligomerization Domain I2

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

Polymerase cofactor VP35

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Lake Victoria marburgvirus (strain Musoke-80)
通用名 common_name	MARV
NCBI Class编号 ncbi_taxonomy_id	33727
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	26

fit	/app/data/saxs_computation/to/5toh/5toh.fit
pddf	/app/data/pr_computation/to/5toh/5toh.pr.out
profile	/app/data/saxs_computation/to/5toh/5toh.dat