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9cm9

Cryo-EM model derived from localized reconstruction of Ad657-hexon-FX complex at 3.86A resolution

Method: ELECTRON MICROSCOPY Dmax: 191.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Hexon protein

OrganismNot specified

UniProt A0A348FV85

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain J； UniProt 1–959 Chain K； UniProt 1–959 Chain L； UniProt 1–959 Not recorded Coagulation factor X × 1 （Q5JVE7） CA CALCIUM ION × 7 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 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 9CM9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10DK Structure of an adenovirus hexon with Zwitterionic insertion in HVR5 Deposited 2026-01-13 Different construct 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 1–958（958 aa）
Chain B 1–958（958 aa）
Chain C 1–958（958 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；20mM HEPES pH 7.2 300 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
10DP Human adenovirus hexon and polyclonal antibody complex Deposited 2026-01-13 Different construct 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 3–958（956 aa）
Chain B 3–958（956 aa）
Chain C 3–958（956 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；20mM HEPES pH 7.2 300 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9CMO Cryo-EM model derived from localized reconstruction of Ad657-hexon-FII complex at 4.14A resolution Deposited 2024-07-15 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 1–959（959 aa）
Chain K 1–959（959 aa）
Chain L 1–959（959 aa）
Not recorded CA CALCIUM ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.17 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A348FV85_9ADEN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain J； PDBConstruct 1–959； UniProt 1–959 Author chain K； PDBConstruct 1–959； UniProt 1–959 Author chain L； PDBConstruct 1–959； UniProt 1–959

Coagulation factor X

OrganismNot specified

UniProt Q5JVE7

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain Z； UniProt 1–488 Non-standard monomer：Yes (specific site not provided by mmCIF) Hexon protein × 3 （A0A348FV85） CA CALCIUM ION × 7 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q5JVE7_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain Z； PDBConstruct 1–488； UniProt 1–488

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 9cm9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9cm9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9cm9
Deposition date deposition_date2024-07-13
最后修订 last_revision2024-11-27
Structure title titleCryo-EM model derived from localized reconstruction of Ad657-hexon-FX complex at 3.86A resolution
Keywords keywordsAdenovirus, Hexon, Coagulation factor X, Coagulation factor II, Prothrombin, Complex, Interactions, VIRUS, 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_guinier54.17 Å
Radius of gyration Rg (electron density) rg_electron54.61 Å
Forward intensity I(0) i01923160000.00
Molecular weight molecular_weight357670.0 kDa
Excluded volume excluded_volume443560 ų
Envelope volume envelope_volume666770 ų
Hydration-shell volume shell_volume105040 ų
Envelope diameter envelope_diameter210.0 Å
Shell Rg shell_rg54.90 Å
Envelope Rg envelope_rg56.56 Å
Shape Rg shape_rg54.55 Å
Total Rg total_rg54.84 Å
Total atoms total_atoms25178
Residues n_residues3153
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 dmax191.8 Å
Rg (real space) rg_real54.84 Å
Rg uncertainty (real space) rg_real_error2.21 Å
I(0) (real space) i0_real1.9230e+09
I(0) uncertainty (real space) i0_real_error3.9520e+07
Rg (reciprocal space) rg_reciprocal53.62 Å
I(0) (reciprocal space) i0_reciprocal1920000000.0000
Solution quality estimate total_estimate0.7496
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary59.5 Å
Skewness Skewness skewness0.877
Kurtosis Kurtosis kurtosis0.561
Angular range angular_range— – 0.1450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha192700000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.493; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.276
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)