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8xck

Closed state of central tail fiber of bacteriophage lambda

Method: ELECTRON MICROSCOPY Dmax: 198.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tip attachment protein J

Escherichia phage Lambda

UniProt P03749

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 F； UniProt 713–1132 Chain J； UniProt 713–1132 Chain Z； UniProt 713–1132 Not recorded Peptidyl-prolyl cis-trans isomerase A × 3 （P0AFL3） ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.75 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 8XCK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8IYK Tail tip conformation 1 of phage lambda tail Deposited 2023-04-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain F 1–1132（1132 aa）
Chain J 1–1132（1132 aa）
Chain Z 1–1132（1132 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.95 Å
8IYL Tail tip conformation 2 of phage lambda tail Deposited 2023-04-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain E 1–1132（1132 aa）
Chain J 1–1132（1132 aa）
Chain Y 1–1132（1132 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.00 Å
8JVM AHS-CSF domains of phage lambda tail Deposited 2023-06-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain F 830–995（166 aa） Fragment：AHS-CSF domains
Chain J 830–995（166 aa） Fragment：AHS-CSF domains
Chain Z 830–995（166 aa） Fragment：AHS-CSF domains
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.86 Å
8K35 Structure of the bacteriophage lambda tail tip complex Deposited 2023-07-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain A 1–1132（1132 aa）
Chain B 1–1132（1132 aa）
Chain I 1–1132（1132 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8XCG Tail tip complex of bacteriophage lambda in the open state Deposited 2023-12-09 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain F 1–1132（1132 aa）
Chain J 1–1132（1132 aa）
Chain Z 1–1132（1132 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
8XCI Open state of central tail fiber of bacteriophage lambda upon binding to LamB Deposited 2023-12-09 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain F 1–1132（1132 aa）
Chain J 1–1132（1132 aa）
Chain Z 1–1132（1132 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.57 Å
8XCJ Open State of central tail fiber of bacteriophage lambda upon binding to LamB (gpJ713-LamB complex) Deposited 2023-12-09 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 713–1132（420 aa）
Chain J 713–1132（420 aa）
Chain Z 713–1132（420 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9E7M In situ cryoEM structure of bacteriophage Ur-lambda tail tip complex Deposited 2024-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain Ja 1–835（835 aa）
Chain Jb 1–835（835 aa）
Chain Jc 1–835（835 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
9OIK Structure of S. Typhimurium 14028 Gifsy-1 prophage HepS bound to bacteriophage lambda J Tail Tip Deposited 2025-05-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain C 902–933（32 aa）
Chain D 902–933（32 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Sodium Acetate, 16% PEG 4000, 0.1 M Tris pH 8.5
Resolution 1.86 Å R-free 0.209

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

View Construct and Data Evidence
UniProt name TIPJ_LAMBD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain F； PDBConstruct 1–420； UniProt 713–1132 Author chain J； PDBConstruct 1–420； UniProt 713–1132 Author chain Z； PDBConstruct 1–420； UniProt 713–1132

Peptidyl-prolyl cis-trans isomerase A

Escherichia coli

UniProt P0AFL3

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 f； UniProt 1–190 Chain j； UniProt 1–190 Chain z； UniProt 1–190 Not recorded Tip attachment protein J × 3 （P03749） ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.75 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 8XCK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7ZFM Engineered Protein Targeting the Zika Viral Envelope Fusion Loop Deposited 2022-04-01 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 25–187（163 aa）
Not recorded EDO 1,2-ETHANEDIOL × 9 P6G HEXAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 1 ACY ACETIC ACID × 3 SIN SUCCINIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；1.0 M Succinic acid, 0.1 M Hepes pH 7.0 and 1% w/v PEG 2000 MME
Resolution 1.71 Å R-free 0.221
7ZFM Engineered Protein Targeting the Zika Viral Envelope Fusion Loop Deposited 2022-04-01 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 25–187（163 aa）
Not recorded EDO 1,2-ETHANEDIOL × 8 PGE TRIETHYLENE GLYCOL × 1 SIN SUCCINIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；1.0 M Succinic acid, 0.1 M Hepes pH 7.0 and 1% w/v PEG 2000 MME
Resolution 1.71 Å R-free 0.221

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

View Construct and Data Evidence
UniProt name PPIA_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain f； PDBConstruct 1–190； UniProt 1–190 Author chain j； PDBConstruct 1–190； UniProt 1–190 Author chain z； PDBConstruct 1–190； UniProt 1–190

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 8xck

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8xck
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8xck
Deposition date deposition_date2023-12-09
Structure title titleClosed state of central tail fiber of bacteriophage lambda
Keywords keywordsBacteriophage, caudovirales, siphoviridae, phage lambda, host recognition, LamB, cryo-EM, 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_guinier48.50 Å
Radius of gyration Rg (electron density) rg_electron49.92 Å
Forward intensity I(0) i0347169000.00
Molecular weight molecular_weight151640.0 kDa
Excluded volume excluded_volume189600 ų
Envelope volume envelope_volume256750 ų
Hydration-shell volume shell_volume50270 ų
Envelope diameter envelope_diameter206.3 Å
Shell Rg shell_rg43.68 Å
Envelope Rg envelope_rg50.66 Å
Shape Rg shape_rg49.92 Å
Total Rg total_rg49.64 Å
Total atoms total_atoms10671
Residues n_residues1395
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 dmax198.7 Å
Rg (real space) rg_real49.78 Å
Rg uncertainty (real space) rg_real_error3.88 Å
I(0) (real space) i0_real3.4720e+08
I(0) uncertainty (real space) i0_real_error8.6710e+06
Rg (reciprocal space) rg_reciprocal48.50 Å
I(0) (reciprocal space) i0_reciprocal346600000.0000
Solution quality estimate total_estimate0.7040
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.5 Å
Skewness Skewness skewness0.861
Kurtosis Kurtosis kurtosis0.649
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19830000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.351; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.299; Smooth: 0.796
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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)