SAXSdb — 4gh9

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

Polymerase cofactor VP35

Marburg virus

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 204–329	Fragment：UNP residues 204-329	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

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 4GH9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 ligand/ion 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
5TOH Crystal Structure of the Marburg Virus VP35 Oligomerization Domain I2 Deposited 2016-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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；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
5TOI Crystal Structure of the Marburg Virus VP35 Oligomerization Domain P4222 Deposited 2016-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 21–146； UniProt 204–329

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	4gh9
Deposition date deposition_date	2012-08-07
Structure title title	Crystal structure of Marburg virus VP35 RNA binding domain
Keywords keywords	Viral polymerase, Interferon inhibition, double stranded viral RNA, VIRAL PROTEIN, RNA BINDING PROTEIN; VIRAL PROTEIN,RNA BINDING 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	15.87 Å
Radius of gyration Rg (electron density) rg_electron	14.37 Å
Forward intensity I(0) i0	3532930.00
Molecular weight molecular_weight	13704.0 kDa
Excluded volume excluded_volume	17396 Å³
Envelope volume envelope_volume	19456 Å³
Hydration-shell volume shell_volume	11740 Å³
Envelope diameter envelope_diameter	50.9 Å
Shell Rg shell_rg	19.75 Å
Envelope Rg envelope_rg	14.70 Å
Shape Rg shape_rg	14.36 Å
Total Rg total_rg	15.57 Å
Total atoms total_atoms	967
Residues n_residues	122
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	51.1 Å
Rg (real space) rg_real	15.81 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	3.5330e+06
I(0) uncertainty (real space) i0_real_error	4.3510e+04
Rg (reciprocal space) rg_reciprocal	15.82 Å
I(0) (reciprocal space) i0_reciprocal	3533000.0000
Solution quality estimate total_estimate	0.8110
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.1 Å
Skewness Skewness skewness	0.220
Kurtosis Kurtosis kurtosis	-0.338
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	548700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Polymerase cofactor VP35
Molecular weight formula_weight	16302.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1084

MAHHHHHHVDDDDKENLYFQSKPNLSAKDLALLLFTHLPGNNTPFHILAQVLSKIAYKSGKSGAFLDAFHQILSEGENAQAALTRLSRTFDAFLGVVPPVIRVKNFQTVPRPCQKSLRAVPPNPTIDKGWVCVYSSEQGETRALKI

来源 Source

来源生物 organism	Marburg virus
通用名 common_name	MARV
NCBI Class编号 ncbi_taxonomy_id	33727
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	117

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4gh9a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.388 — Filoviridae VP35-like
Superfamily Superfamily superfamily	d.388.1 — Filoviridae VP35-like
Family Family family	d.388.1.1 — Filoviridae VP35

CATH v4.4 (2 domains)

Domain ID domain_id	4gh9A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	950 — Filoviridae VP35, C-terminal inhibitory domain, helical subdomain

Domain ID domain_id	4gh9A02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	70 — Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain

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8. Citations (1)

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Unit-cell length a length_a	42.524 Å
Unit-cell length b length_b	90.880 Å
Unit-cell length c length_c	65.925 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	26.682 Å
R factor r_factor	0.1635
R_work r_work	0.1608
R_free r_free	0.2167

fit	/app/data/saxs_computation/gh/4gh9/4gh9.fit
pddf	/app/data/pr_computation/gh/4gh9/4gh9.pr.out
profile	/app/data/saxs_computation/gh/4gh9/4gh9.dat

Crystal structure of Marburg virus VP35 RNA binding domain

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