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3iyh

P22 procapsid coat protein structures reveal a novel mechanism for capsid maturation: Stability without auxiliary proteins or chemical cross-links

Method: ELECTRON MICROSCOPY Dmax: 162.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Coat protein

OrganismNot specified

UniProt P26747

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 × 360 PDB declaration: 360-MERIC（360） Consistent with protein copy count Chain A； UniProt 1–430 Chain B； UniProt 1–430 Chain C； UniProt 1–430 Chain D； UniProt 1–430 Chain E； UniProt 1–430 Chain F； UniProt 1–430 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：20 mM sodium phosphate buffer, pH = 7.6；pH 7.6；20 mM sodium phosphate buffer, pH = 7.6 cryo-EM vitrification conditions：blot 2-3 seconds before plunging；89 K；Cryogen ETHANE Resolution 8.20 Å
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–430 Chain B； UniProt 1–430 Chain C； UniProt 1–430 Chain D； UniProt 1–430 Chain E； UniProt 1–430 Chain F； UniProt 1–430 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：20 mM sodium phosphate buffer, pH = 7.6；pH 7.6；20 mM sodium phosphate buffer, pH = 7.6 cryo-EM vitrification conditions：blot 2-3 seconds before plunging；89 K；Cryogen ETHANE Resolution 8.20 Å
3 Protein homooligomer Homooligomer Protein × 30 PDB declaration: 30-meric（30） Consistent with protein copy count Chain A； UniProt 1–430 Chain B； UniProt 1–430 Chain C； UniProt 1–430 Chain D； UniProt 1–430 Chain E； UniProt 1–430 Chain F； UniProt 1–430 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：20 mM sodium phosphate buffer, pH = 7.6；pH 7.6；20 mM sodium phosphate buffer, pH = 7.6 cryo-EM vitrification conditions：blot 2-3 seconds before plunging；89 K；Cryogen ETHANE Resolution 8.20 Å
4 Protein homooligomer Homooligomer Protein × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain A； UniProt 1–430 Chain B； UniProt 1–430 Chain C； UniProt 1–430 Chain D； UniProt 1–430 Chain E； UniProt 1–430 Chain F； UniProt 1–430 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：20 mM sodium phosphate buffer, pH = 7.6；pH 7.6；20 mM sodium phosphate buffer, pH = 7.6 cryo-EM vitrification conditions：blot 2-3 seconds before plunging；89 K；Cryogen ETHANE Resolution 8.20 Å
5 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–430 Chain B； UniProt 1–430 Chain C； UniProt 1–430 Chain D； UniProt 1–430 Chain E； UniProt 1–430 Chain F； UniProt 1–430 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：20 mM sodium phosphate buffer, pH = 7.6；pH 7.6；20 mM sodium phosphate buffer, pH = 7.6 cryo-EM vitrification conditions：blot 2-3 seconds before plunging；89 K；Cryogen ETHANE Resolution 8.20 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 3IYH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2M5S High-resolution NMR structure and cryo-EM imaging support multiple functional roles for the accessory I-domain of phage P22 coat protein Deposited 2013-03-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 223–345（123 aa） Fragment：;This domain has previously been called the 'extra-density domain' and 'telokin-like domain' in the literature based on cryo-EM models ;
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；310.15 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] protein, 20 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] protein, 20 mM sodium phosphate, 1% H2O/99% D2O | 1% H2O/99% D2O
Resolution not provided
3IYI P22 expanded head coat protein structures reveal a novel mechanism for capsid maturation: Stability without auxiliary proteins or chemical cross-links Deposited 2009-12-14 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 420 PDB declaration: 420-meric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM sodium phosphate buffer, pH = 7.6；pH 7.6；20 mM sodium phosphate buffer, pH = 7.6
cryo-EM vitrification conditions Blot for 2-3 seconds before plunging；89 K；Cryogen ETHANE
Resolution 9.10 Å
3IYI P22 expanded head coat protein structures reveal a novel mechanism for capsid maturation: Stability without auxiliary proteins or chemical cross-links Deposited 2009-12-14 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM sodium phosphate buffer, pH = 7.6；pH 7.6；20 mM sodium phosphate buffer, pH = 7.6
cryo-EM vitrification conditions Blot for 2-3 seconds before plunging；89 K；Cryogen ETHANE
Resolution 9.10 Å
3IYI P22 expanded head coat protein structures reveal a novel mechanism for capsid maturation: Stability without auxiliary proteins or chemical cross-links Deposited 2009-12-14 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 35 PDB declaration: 35-meric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM sodium phosphate buffer, pH = 7.6；pH 7.6；20 mM sodium phosphate buffer, pH = 7.6
cryo-EM vitrification conditions Blot for 2-3 seconds before plunging；89 K；Cryogen ETHANE
Resolution 9.10 Å
3IYI P22 expanded head coat protein structures reveal a novel mechanism for capsid maturation: Stability without auxiliary proteins or chemical cross-links Deposited 2009-12-14 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 42 PDB declaration: 42-meric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM sodium phosphate buffer, pH = 7.6；pH 7.6；20 mM sodium phosphate buffer, pH = 7.6
cryo-EM vitrification conditions Blot for 2-3 seconds before plunging；89 K；Cryogen ETHANE
Resolution 9.10 Å
3IYI P22 expanded head coat protein structures reveal a novel mechanism for capsid maturation: Stability without auxiliary proteins or chemical cross-links Deposited 2009-12-14 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM sodium phosphate buffer, pH = 7.6；pH 7.6；20 mM sodium phosphate buffer, pH = 7.6
cryo-EM vitrification conditions Blot for 2-3 seconds before plunging；89 K；Cryogen ETHANE
Resolution 9.10 Å
5UU5 Bacteriophage P22 mature virion capsid protein Deposited 2017-02-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 420 PDB declaration: 420-meric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50 mM Tris, pH 7.6, 1 mM MgCl2, 25 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE；single blot, one second duration
Resolution 3.30 Å
5UU5 Bacteriophage P22 mature virion capsid protein Deposited 2017-02-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50 mM Tris, pH 7.6, 1 mM MgCl2, 25 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE；single blot, one second duration
Resolution 3.30 Å
5UU5 Bacteriophage P22 mature virion capsid protein Deposited 2017-02-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 35 PDB declaration: 35-meric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50 mM Tris, pH 7.6, 1 mM MgCl2, 25 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE；single blot, one second duration
Resolution 3.30 Å
5UU5 Bacteriophage P22 mature virion capsid protein Deposited 2017-02-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 42 PDB declaration: 42-meric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50 mM Tris, pH 7.6, 1 mM MgCl2, 25 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE；single blot, one second duration
Resolution 3.30 Å
5UU5 Bacteriophage P22 mature virion capsid protein Deposited 2017-02-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50 mM Tris, pH 7.6, 1 mM MgCl2, 25 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE；single blot, one second duration
Resolution 3.30 Å
8GN5 Designed pH-responsive P22 VLP Deposited 2022-08-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 4–428（425 aa）
Chain B 4–428（425 aa）
Chain C 4–428（425 aa）
Chain D 4–428（425 aa）
Mutation：S43H, E54H, E153H, N287H Mutation：S43H, E54H, E153H, N287H Mutation：S43H, E54H, E153H, N287H Mutation：S43H, E54H, E153H, N287H No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
8I1T The asymmetric unit of P22 empty capsid Deposited 2023-01-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8I1V The asymmetric unit of P22 procapsid Deposited 2023-01-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8U10 In situ cryo-EM structure of bacteriophage P22 gp1:gp4:gp5:gp10:gp9 N-term complex in conformation 1 at 3.2A resolution Deposited 2023-08-30 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 58 PDB declaration: 58-meric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Chain H 1–430（430 aa）
Chain I 1–430（430 aa）
Chain J 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8U11 In situ cryo-EM structure of bacteriophage P22 gp1:gp5:gp4: gp10: gp9 N-term complex in conformation 2 at 3.1A resolution Deposited 2023-08-30 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 58 PDB declaration: 58-meric
Chain A 1–430（430 aa）
Chain B 1–430（430 aa）
Chain C 1–430（430 aa）
Chain D 1–430（430 aa）
Chain E 1–430（430 aa）
Chain F 1–430（430 aa）
Chain G 1–430（430 aa）
Chain H 1–430（430 aa）
Chain I 1–430（430 aa）
Chain J 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9PGG Cryo-EM structure of bacteriophage P22 gp1-gp5-gp4 complex at 2.76 angstrom Deposited 2025-07-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric
Chain Aa 1–430（430 aa）
Chain Ab 1–430（430 aa）
Chain Ac 1–430（430 aa）
Chain Ad 1–430（430 aa）
Chain Ae 1–430（430 aa）
Chain Af 1–430（430 aa）
Chain Ag 1–430（430 aa）
Chain Ah 1–430（430 aa）
Chain Ai 1–430（430 aa）
Chain Aj 1–430（430 aa）
Chain Ak 1–430（430 aa）
Chain Al 1–430（430 aa）
Chain Am 1–430（430 aa）
Chain An 1–430（430 aa）
Chain Ao 1–430（430 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å

9 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VG05_BPP22
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–430； UniProt 1–430 Author chain B； PDBConstruct 1–430； UniProt 1–430 Author chain C； PDBConstruct 1–430； UniProt 1–430 Author chain D； PDBConstruct 1–430； UniProt 1–430 Author chain E； PDBConstruct 1–430； UniProt 1–430 Author chain F； PDBConstruct 1–430； UniProt 1–430

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 3iyh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3iyh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3iyh
Deposition date deposition_date2009-12-14
Structure title titleP22 procapsid coat protein structures reveal a novel mechanism for capsid maturation: Stability without auxiliary proteins or chemical cross-links
Keywords keywordsHK97-like fold, Capsid protein, Late protein, Virion, VIRUS; VIRUS
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier49.49 Å
Radius of gyration Rg (electron density) rg_electron49.32 Å
Forward intensity I(0) i0966223000.00
Molecular weight molecular_weight256490.0 kDa
Excluded volume excluded_volume313280 ų
Envelope volume envelope_volume315590 ų
Hydration-shell volume shell_volume56238 ų
Envelope diameter envelope_diameter173.5 Å
Shell Rg shell_rg50.32 Å
Envelope Rg envelope_rg46.33 Å
Shape Rg shape_rg49.54 Å
Total Rg total_rg49.34 Å
Total atoms total_atoms—
Residues n_residues—
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 dmax162.7 Å
Rg (real space) rg_real49.41 Å
Rg uncertainty (real space) rg_real_error1.30 Å
I(0) (real space) i0_real9.6620e+08
I(0) uncertainty (real space) i0_real_error1.6430e+07
Rg (reciprocal space) rg_reciprocal49.49 Å
I(0) (reciprocal space) i0_reciprocal966300000.0000
Solution quality estimate total_estimate0.8954
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.8 Å
Skewness Skewness skewness0.218
Kurtosis Kurtosis kurtosis-0.580
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha85070000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.918
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)