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9x5r

Cryo-EM structure of Borna disease virus RNA-directed RNA polymerase in complex with Suramin

Method: ELECTRON MICROSCOPY Dmax: 96.0 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RNA-directed RNA polymerase L

Borna disease virus-V

UniProt P52639

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–1711 Not recorded Phosphoprotein × 1 （P0C799） ZINC ION × 1 ;8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID ; × 3 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 2.70 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 9X5R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9H1G Structure of the borna disease virus 1 replication complex Deposited 2024-10-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–1711（1711 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
9H1Q Structure of the borna disease virus 1 replication core complex - reaction complex Deposited 2024-10-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–1711（1711 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9H1Y Structure of the borna disease virus 1 replication full-length complex - reaction complex Deposited 2024-10-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–1711（1711 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
9X1V Cryo-EM structure of Borna disease virus RNA polymerase complex Deposited 2025-10-03 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–1711（1711 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.72 Å
9X28 Cryo-EM structure of Borna disease virus RNA polymerase L protein Deposited 2025-10-04 Different oligomeric state Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1711（1711 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.83 Å

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

View Construct and Data Evidence
UniProt name L_BDVV
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1711； UniProt 1–1711

Phosphoprotein

Borna disease virus-V

UniProt P0C799

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–201 Not recorded RNA-directed RNA polymerase L × 1 （P52639） ZINC ION × 1 ;8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID ; × 3 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 2.70 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 9X5R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8BS7 Multimerisation domain of Borna disease virus 1 Deposited 2022-11-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–201（201 aa）
Chain B 1–201（201 aa）
Chain C 1–201（201 aa）
Chain D 1–201（201 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M (NH4)2-tartarate and 20% w/v PEG3350
Resolution 3.20 Å R-free 0.387
8BS7 Multimerisation domain of Borna disease virus 1 Deposited 2022-11-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 1–201（201 aa）
Chain F 1–201（201 aa）
Chain G 1–201（201 aa）
Chain H 1–201（201 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M (NH4)2-tartarate and 20% w/v PEG3350
Resolution 3.20 Å R-free 0.387
9H1G Structure of the borna disease virus 1 replication complex Deposited 2024-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–201（201 aa）
Chain C 1–201（201 aa）
Chain D 1–201（201 aa）
Chain E 1–201（201 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
9H1Q Structure of the borna disease virus 1 replication core complex - reaction complex Deposited 2024-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–201（201 aa）
Chain C 1–201（201 aa）
Chain D 1–201（201 aa）
Chain E 1–201（201 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9H1Y Structure of the borna disease virus 1 replication full-length complex - reaction complex Deposited 2024-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–201（201 aa）
Chain C 1–201（201 aa）
Chain D 1–201（201 aa）
Chain E 1–201（201 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
9X1V Cryo-EM structure of Borna disease virus RNA polymerase complex Deposited 2025-10-03 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–201（201 aa）
Chain C 1–201（201 aa）
Chain D 1–201（201 aa）
Chain E 1–201（201 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.72 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PHOSP_BDVV
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–201； UniProt 1–201

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9x5r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9x5r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9x5r
Deposition date deposition_date2025-10-13
Structure title titleCryo-EM structure of Borna disease virus RNA-directed RNA polymerase in complex with Suramin
Keywords keywordsPolymerase, Complex, Inhibitor, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.59 Å
Radius of gyration Rg (electron density) rg_electron31.64 Å
Forward intensity I(0) i0301468000.00
Molecular weight molecular_weight141550.0 kDa
Excluded volume excluded_volume178190 ų
Envelope volume envelope_volume222760 ų
Hydration-shell volume shell_volume55866 ų
Envelope diameter envelope_diameter103.0 Å
Shell Rg shell_rg40.71 Å
Envelope Rg envelope_rg31.19 Å
Shape Rg shape_rg31.63 Å
Total Rg total_rg32.43 Å
Total atoms total_atoms9940
Residues n_residues1231
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax96.0 Å
Rg (real space) rg_real32.29 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real3.0150e+08
I(0) uncertainty (real space) i0_real_error3.9990e+06
Rg (reciprocal space) rg_reciprocal32.42 Å
I(0) (reciprocal space) i0_reciprocal301500000.0000
Solution quality estimate total_estimate0.9062
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.1 Å
Skewness Skewness skewness0.048
Kurtosis Kurtosis kurtosis-0.561
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha88240000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.958
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)