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9c4f

Infectious B19V capsid

Method: ELECTRON MICROSCOPY Dmax: 185.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid protein 2

OrganismNot specified

UniProt Q784T0

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–554 Chain B； UniProt 1–554 Chain C； UniProt 1–554 Chain D； UniProt 1–554 Chain E； UniProt 1–554 Not recorded Inter-alpha-trypsin inhibitor heavy chain H4 × 1 （Q14624） ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.20 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 9C4F Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9C27 Infectious B19V capsid Deposited 2024-05-30 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric
Chain A 1–554（554 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9C27 Infectious B19V capsid Deposited 2024-05-30 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–554（554 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9C27 Infectious B19V capsid Deposited 2024-05-30 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–554（554 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9C27 Infectious B19V capsid Deposited 2024-05-30 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–554（554 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9C27 Infectious B19V capsid Deposited 2024-05-30 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–554（554 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9C2T Infectious B19V capsid Deposited 2024-05-31 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 2–554（553 aa）
Chain B 2–554（553 aa）
Chain C 2–554（553 aa）
Chain D 2–554（553 aa）
Chain E 2–554（553 aa）
Chain F 2–554（553 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

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

View Construct and Data Evidence
UniProt name Q784T0_PAVHB
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–554； UniProt 1–554 Author chain B； PDBConstruct 1–554； UniProt 1–554 Author chain C； PDBConstruct 1–554； UniProt 1–554 Author chain D； PDBConstruct 1–554； UniProt 1–554 Author chain E； PDBConstruct 1–554； UniProt 1–554

Inter-alpha-trypsin inhibitor heavy chain H4

OrganismNot specified

UniProt Q14624

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain I； UniProt 1–930 Not recorded Capsid protein 2 × 5 （Q784T0） ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.20 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 9C4F Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9C4N Infectious B19V capsid Deposited 2024-06-04 Different oligomeric state Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain Y 1–930（930 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

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

View Construct and Data Evidence
UniProt name ITIH4_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain I； PDBConstruct 1–930； UniProt 1–930

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 9c4f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9c4f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9c4f
Deposition date deposition_date2024-06-04
Structure title titleInfectious B19V capsid
Keywords keywordsB19, Virion, Capsid, 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_guinier52.75 Å
Radius of gyration Rg (electron density) rg_electron52.23 Å
Forward intensity I(0) i01320190000.00
Molecular weight molecular_weight305170.0 kDa
Excluded volume excluded_volume381870 ų
Envelope volume envelope_volume552960 ų
Hydration-shell volume shell_volume86336 ų
Envelope diameter envelope_diameter195.2 Å
Shell Rg shell_rg55.91 Å
Envelope Rg envelope_rg53.65 Å
Shape Rg shape_rg52.25 Å
Total Rg total_rg52.28 Å
Total atoms total_atoms21560
Residues n_residues2774
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 dmax185.9 Å
Rg (real space) rg_real52.80 Å
Rg uncertainty (real space) rg_real_error1.76 Å
I(0) (real space) i0_real1.3200e+09
I(0) uncertainty (real space) i0_real_error2.5250e+07
Rg (reciprocal space) rg_reciprocal52.70 Å
I(0) (reciprocal space) i0_reciprocal1320000000.0000
Solution quality estimate total_estimate0.8700
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary62.0 Å
Skewness Skewness skewness0.370
Kurtosis Kurtosis kurtosis-0.225
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha93480000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.862
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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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9. Files and Curves (10)