Major capsid protein
Lederbergvirus
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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count | Chain A; UniProt 4–428 Chain B; UniProt 4–428 Chain C; UniProt 4–428 Chain D; UniProt 4–428 | Mutation:S43H, E54H, E153H, N287H | No other associated polymer | ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4;PBS buffer pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE | Resolution 4.02 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 8GN5 | 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 |
| 3IYH P22 procapsid 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 experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer;Protein × 360 PDB declaration: 360-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)
|
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 2-3 seconds before plunging;89 K;Cryogen ETHANE
|
Resolution 8.20 Å |
| 3IYH P22 procapsid 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 experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer;Protein × 6 PDB declaration: hexameric |
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)
|
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 2-3 seconds before plunging;89 K;Cryogen ETHANE
|
Resolution 8.20 Å |
| 3IYH P22 procapsid 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 experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer;Protein × 30 PDB declaration: 30-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)
|
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 2-3 seconds before plunging;89 K;Cryogen ETHANE
|
Resolution 8.20 Å |
| 3IYH P22 procapsid 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 experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer;Protein × 36 PDB declaration: 36-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)
|
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 2-3 seconds before plunging;89 K;Cryogen ETHANE
|
Resolution 8.20 Å |
| 3IYH P22 procapsid 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 experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer;Protein × 6 PDB declaration: hexameric |
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)
|
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 2-3 seconds before plunging;89 K;Cryogen ETHANE
|
Resolution 8.20 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 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
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 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
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 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
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 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
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 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
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 |
| 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 21 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | CAPSD_BPP22 |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A; PDBConstruct 1–425; UniProt 4–428 Author chain B; PDBConstruct 1–425; UniProt 4–428 Author chain C; PDBConstruct 1–425; UniProt 4–428 Author chain D; PDBConstruct 1–425; UniProt 4–428 |