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9xqs

Structure of the inner peripheral region in the phage phiKZ baseplate complex

Method: ELECTRON MICROSCOPY Dmax: 244.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHIKZ087

OrganismNot specified

UniProt Q8SD75

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 × 84 PDB declaration: 84-meric（84） Consistent with protein copy count Chain A； UniProt 1–971 Chain B； UniProt 1–971 Chain U； UniProt 1–971 Chain V； UniProt 1–971 Not recorded PHIKZ128 × 6 （Q8SD34） PHIKZ161 × 12 （Q8SD01） PHIKZ088 × 6 （Q8SD74） PHIKZ182 × 6 （Q8SCY0） PHIKZ049 × 24 （Q8SDB3） PHIKZ029 × 12 （Q8SDD3） PHIKZ062 × 6 （Q8SDA0） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.65 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 Q8SD75_BPDPK
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–971； UniProt 1–971 Author chain B； PDBConstruct 1–971； UniProt 1–971 Author chain U； PDBConstruct 1–971； UniProt 1–971 Author chain V； PDBConstruct 1–971； UniProt 1–971

PHIKZ128

OrganismNot specified

UniProt Q8SD34

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 × 84 PDB declaration: 84-meric（84） Consistent with protein copy count Chain C； UniProt 1–724 Chain D； UniProt 1–724 Not recorded PHIKZ087 × 12 （Q8SD75） PHIKZ161 × 12 （Q8SD01） PHIKZ088 × 6 （Q8SD74） PHIKZ182 × 6 （Q8SCY0） PHIKZ049 × 24 （Q8SDB3） PHIKZ029 × 12 （Q8SDD3） PHIKZ062 × 6 （Q8SDA0） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.65 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 Q8SD34_BPDPK
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–724； UniProt 1–724 Author chain D； PDBConstruct 1–724； UniProt 1–724

PHIKZ161

OrganismNot specified

UniProt Q8SD01

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 × 84 PDB declaration: 84-meric（84） Consistent with protein copy count Chain E； UniProt 1–203 Chain F； UniProt 1–203 Chain G； UniProt 1–203 Chain H； UniProt 1–203 Not recorded PHIKZ087 × 12 （Q8SD75） PHIKZ128 × 6 （Q8SD34） PHIKZ088 × 6 （Q8SD74） PHIKZ182 × 6 （Q8SCY0） PHIKZ049 × 24 （Q8SDB3） PHIKZ029 × 12 （Q8SDD3） PHIKZ062 × 6 （Q8SDA0） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.65 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 Q8SD01_BPDPK
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 1–203； UniProt 1–203 Author chain F； PDBConstruct 1–203； UniProt 1–203 Author chain G； PDBConstruct 1–203； UniProt 1–203 Author chain H； PDBConstruct 1–203； UniProt 1–203

PHIKZ088

OrganismNot specified

UniProt Q8SD74

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 × 84 PDB declaration: 84-meric（84） Consistent with protein copy count Chain I； UniProt 1–349 Chain J； UniProt 1–349 Not recorded PHIKZ087 × 12 （Q8SD75） PHIKZ128 × 6 （Q8SD34） PHIKZ161 × 12 （Q8SD01） PHIKZ182 × 6 （Q8SCY0） PHIKZ049 × 24 （Q8SDB3） PHIKZ029 × 12 （Q8SDD3） PHIKZ062 × 6 （Q8SDA0） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.65 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 Q8SD74_BPDPK
Isoform —
PDB entities 4
Chains and sequence ranges Author chain I； PDBConstruct 1–349； UniProt 1–349 Author chain J； PDBConstruct 1–349； UniProt 1–349

PHIKZ182

OrganismNot specified

UniProt Q8SCY0

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 × 84 PDB declaration: 84-meric（84） Consistent with protein copy count Chain K； UniProt 1–664 Chain L； UniProt 1–664 Not recorded PHIKZ087 × 12 （Q8SD75） PHIKZ128 × 6 （Q8SD34） PHIKZ161 × 12 （Q8SD01） PHIKZ088 × 6 （Q8SD74） PHIKZ049 × 24 （Q8SDB3） PHIKZ029 × 12 （Q8SDD3） PHIKZ062 × 6 （Q8SDA0） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.65 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 Q8SCY0_BPDPK
Isoform —
PDB entities 5
Chains and sequence ranges Author chain K； PDBConstruct 1–664； UniProt 1–664 Author chain L； PDBConstruct 1–664； UniProt 1–664

PHIKZ049

OrganismNot specified

UniProt Q8SDB3

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 × 84 PDB declaration: 84-meric（84） Consistent with protein copy count Chain M； UniProt 1–138 Chain N； UniProt 1–138 Chain O； UniProt 1–138 Chain P； UniProt 1–138 Chain Q； UniProt 1–138 Chain R； UniProt 1–138 Chain S； UniProt 1–138 Chain T； UniProt 1–138 Not recorded PHIKZ087 × 12 （Q8SD75） PHIKZ128 × 6 （Q8SD34） PHIKZ161 × 12 （Q8SD01） PHIKZ088 × 6 （Q8SD74） PHIKZ182 × 6 （Q8SCY0） PHIKZ029 × 12 （Q8SDD3） PHIKZ062 × 6 （Q8SDA0） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.65 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 Q8SDB3_BPDPK
Isoform —
PDB entities 6
Chains and sequence ranges Author chain M； PDBConstruct 1–138； UniProt 1–138 Author chain N； PDBConstruct 1–138； UniProt 1–138 Author chain O； PDBConstruct 1–138； UniProt 1–138 Author chain P； PDBConstruct 1–138； UniProt 1–138 Author chain Q； PDBConstruct 1–138； UniProt 1–138 Author chain R； PDBConstruct 1–138； UniProt 1–138 Author chain S； PDBConstruct 1–138； UniProt 1–138 Author chain T； PDBConstruct 1–138； UniProt 1–138

PHIKZ029

OrganismNot specified

UniProt Q8SDD3

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 × 84 PDB declaration: 84-meric（84） Consistent with protein copy count Chain W； UniProt 1–695 Chain X； UniProt 1–695 Chain Y； UniProt 1–695 Chain Z； UniProt 1–695 Not recorded PHIKZ087 × 12 （Q8SD75） PHIKZ128 × 6 （Q8SD34） PHIKZ161 × 12 （Q8SD01） PHIKZ088 × 6 （Q8SD74） PHIKZ182 × 6 （Q8SCY0） PHIKZ049 × 24 （Q8SDB3） PHIKZ062 × 6 （Q8SDA0） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.65 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 9XQS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J0H Fitting of the bacteriophage phiKZ gp29PR structure into the cryo-EM density map of the phiKZ extended tail sheath Deposited 2011-08-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain B 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain C 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain D 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain E 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain F 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；liquid ethane
Resolution 18.00 Å
3J0I Fitting of the phiKZ gp29PR structure into the cryo-EM density map of the phiKZ polysheath Deposited 2011-08-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain B 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain C 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain D 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain E 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Chain F 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；liquid ethane
Resolution 19.00 Å
3SPE Crystal structure of the tail sheath protein protease resistant fragment from bacteriophage phiKZ Deposited 2011-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 96–390（295 aa） Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390)
Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8 M Na/K Phosphate, pH 5.0 with 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.286
3SPE Crystal structure of the tail sheath protein protease resistant fragment from bacteriophage phiKZ Deposited 2011-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 96–390（295 aa） Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390)
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8 M Na/K Phosphate, pH 5.0 with 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.286
3SPE Crystal structure of the tail sheath protein protease resistant fragment from bacteriophage phiKZ Deposited 2011-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 96–390（295 aa） Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390)
Chain B 96–390（295 aa） Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390)
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8 M Na/K Phosphate, pH 5.0 with 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.286
9XPF The structure of sheath and tube proteins of phage Phikz Deposited 2025-11-16 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain A 1–695（695 aa）
Chain B 1–695（695 aa）
Chain C 1–695（695 aa）
Chain D 1–695（695 aa）
Chain E 1–695（695 aa）
Chain F 1–695（695 aa）
Chain M 1–695（695 aa）
Chain N 1–695（695 aa）
Chain O 1–695（695 aa）
Chain P 1–695（695 aa）
Chain Q 1–695（695 aa）
Chain R 1–695（695 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
9XPS The neck structure of the Phage Phikz Deposited 2025-11-17 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-meric
Chain x 1–695（695 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8SDD3_BPDPK
Isoform —
PDB entities 7
Chains and sequence ranges Author chain W； PDBConstruct 1–695； UniProt 1–695 Author chain X； PDBConstruct 1–695； UniProt 1–695 Author chain Y； PDBConstruct 1–695； UniProt 1–695 Author chain Z； PDBConstruct 1–695； UniProt 1–695

PHIKZ062

OrganismNot specified

UniProt Q8SDA0

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 × 84 PDB declaration: 84-meric（84） Consistent with protein copy count Chain a； UniProt 1–136 Chain b； UniProt 1–136 Not recorded PHIKZ087 × 12 （Q8SD75） PHIKZ128 × 6 （Q8SD34） PHIKZ161 × 12 （Q8SD01） PHIKZ088 × 6 （Q8SD74） PHIKZ182 × 6 （Q8SCY0） PHIKZ049 × 24 （Q8SDB3） PHIKZ029 × 12 （Q8SDD3） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.65 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 Q8SDA0_BPDPK
Isoform —
PDB entities 8
Chains and sequence ranges Author chain a； PDBConstruct 1–136； UniProt 1–136 Author chain b； PDBConstruct 1–136； UniProt 1–136

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 9xqs

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9xqs
Deposition date deposition_date2025-11-18
Structure title titleStructure of the inner peripheral region in the phage phiKZ baseplate complex
Keywords keywordsbaseplate, inner peripheral, 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_guinier93.93 Å
Radius of gyration Rg (electron density) rg_electron93.88 Å
Forward intensity I(0) i022780500000.00
Molecular weight molecular_weight1300600.0 kDa
Excluded volume excluded_volume1631800 ų
Envelope volume envelope_volume3227900 ų
Hydration-shell volume shell_volume283490 ų
Envelope diameter envelope_diameter335.3 Å
Shell Rg shell_rg93.43 Å
Envelope Rg envelope_rg90.33 Å
Shape Rg shape_rg93.87 Å
Total Rg total_rg93.90 Å
Total atoms total_atoms91692
Residues n_residues11498
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 dmax244.3 Å
Rg (real space) rg_real89.99 Å
Rg uncertainty (real space) rg_real_error0.63 Å
I(0) (real space) i0_real2.1810e+10
I(0) uncertainty (real space) i0_real_error3.4310e+08
Rg (reciprocal space) rg_reciprocal93.38 Å
I(0) (reciprocal space) i0_reciprocal22740000000.0000
Solution quality estimate total_estimate0.9172
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary100.6 Å
Skewness Skewness skewness0.188
Kurtosis Kurtosis kurtosis-0.656
Angular range angular_range— – 0.0850 Å−1
Current regularization parameter α current_alpha0.5700
Highest regularization parameter α highest_alpha4262000000.0000
Real-space data points n_real_points18
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 1.000; Stabil: 0.980; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)