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8xcg

Tail tip complex of bacteriophage lambda in the open state

Method: ELECTRON MICROSCOPY Dmax: 153.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tail tip protein M

Escherichia phage Lambda

UniProt P03737

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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain E； UniProt 1–109 Chain K； UniProt 1–109 Chain M； UniProt 1–109 Chain Y； UniProt 1–109 Chain e； UniProt 1–109 Chain m； UniProt 1–109 Not recorded Tip attachment protein J × 3 （P03749） Tail tip assembly protein I × 3 （P03730） Tail tip protein L × 3 （P03738） SF4 IRON/SULFUR CLUSTER × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.46 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 8XCG 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain E 1–109（109 aa）
Chain K 1–109（109 aa）
Chain M 1–109（109 aa）
Chain Y 1–109（109 aa）
Chain e 1–109（109 aa）
Chain m 1–109（109 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain D 1–109（109 aa）
Chain F 1–109（109 aa）
Chain M 1–109（109 aa）
Chain X 1–109（109 aa）
Chain Z 1–109（109 aa）
Chain m 1–109（109 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
8K35 Structure of the bacteriophage lambda tail tip complex Deposited 2023-07-14 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain C 1–109（109 aa）
Chain D 1–109（109 aa）
Chain E 1–109（109 aa）
Chain F 1–109（109 aa）
Chain H 1–109（109 aa）
Chain O 1–109（109 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
9E7M In situ cryoEM structure of bacteriophage Ur-lambda tail tip complex Deposited 2024-11-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain Ma 1–109（109 aa）
Chain Mb 1–109（109 aa）
Chain Mc 1–109（109 aa）
Chain Md 1–109（109 aa）
Chain Me 1–109（109 aa）
Chain Mf 1–109（109 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

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TIPM_LAMBD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain E； PDBConstruct 1–109； UniProt 1–109 Author chain K； PDBConstruct 1–109； UniProt 1–109 Author chain M； PDBConstruct 1–109； UniProt 1–109 Author chain Y； PDBConstruct 1–109； UniProt 1–109 Author chain e； PDBConstruct 1–109； UniProt 1–109 Author chain m； PDBConstruct 1–109； UniProt 1–109

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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain F； UniProt 1–1132 Chain J； UniProt 1–1132 Chain Z； UniProt 1–1132 Not recorded Tail tip protein M × 6 （P03737） Tail tip assembly protein I × 3 （P03730） Tail tip protein L × 3 （P03738） SF4 IRON/SULFUR CLUSTER × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.46 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 8XCG 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 oligomeric state 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 oligomeric state 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 ligand/ion 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 oligomeric state 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
8XCI Open state of central tail fiber of bacteriophage lambda upon binding to LamB Deposited 2023-12-09 Different oligomeric state Different ligand/ion 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 construct Different oligomeric state Different ligand/ion 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
8XCK Closed state of central tail fiber of bacteriophage lambda Deposited 2023-12-09 Different construct Different oligomeric state Different ligand/ion 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 2.75 Å
9E7M In situ cryoEM structure of bacteriophage Ur-lambda tail tip complex Deposited 2024-11-03 Different construct Different oligomeric state 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 ligand/ion 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 2
Chains and sequence ranges Author chain F； PDBConstruct 1–1132； UniProt 1–1132 Author chain J； PDBConstruct 1–1132； UniProt 1–1132 Author chain Z； PDBConstruct 1–1132； UniProt 1–1132

Tail tip assembly protein I

Escherichia phage Lambda

UniProt P03730

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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain I； UniProt 1–223 Chain P； UniProt 1–223 Chain h； UniProt 1–223 Not recorded Tail tip protein M × 6 （P03737） Tip attachment protein J × 3 （P03749） Tail tip protein L × 3 （P03738） SF4 IRON/SULFUR CLUSTER × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.46 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 8XCG 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain I 1–223（223 aa）
Chain P 1–223（223 aa）
Chain h 1–223（223 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain I 1–223（223 aa）
Chain N 1–223（223 aa）
Chain f 1–223（223 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
8K35 Structure of the bacteriophage lambda tail tip complex Deposited 2023-07-14 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain K 1–223（223 aa）
Chain Q 1–223（223 aa）
Chain x 1–223（223 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
9E7M In situ cryoEM structure of bacteriophage Ur-lambda tail tip complex Deposited 2024-11-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain Ia 133–222（90 aa）
Chain Ib 133–222（90 aa）
Chain Ic 133–222（90 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

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TIPI_LAMBD
Isoform —
PDB entities 3
Chains and sequence ranges Author chain I； PDBConstruct 1–223； UniProt 1–223 Author chain P； PDBConstruct 1–223； UniProt 1–223 Author chain h； PDBConstruct 1–223； UniProt 1–223

Tail tip protein L

Escherichia phage Lambda

UniProt P03738

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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain L； UniProt 1–232 Chain N； UniProt 1–232 Chain f； UniProt 1–232 Not recorded Tail tip protein M × 6 （P03737） Tip attachment protein J × 3 （P03749） Tail tip assembly protein I × 3 （P03730） SF4 IRON/SULFUR CLUSTER × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.46 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 8XCG 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain L 1–232（232 aa）
Chain N 1–232（232 aa）
Chain f 1–232（232 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain G 1–232（232 aa）
Chain L 1–232（232 aa）
Chain d 1–232（232 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
8K35 Structure of the bacteriophage lambda tail tip complex Deposited 2023-07-14 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain G 1–232（232 aa）
Chain J 1–232（232 aa）
Chain N 1–232（232 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
9E7M In situ cryoEM structure of bacteriophage Ur-lambda tail tip complex Deposited 2024-11-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain La 1–232（232 aa）
Chain Lb 1–232（232 aa）
Chain Lc 1–232（232 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

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TIPL_LAMBD
Isoform —
PDB entities 4
Chains and sequence ranges Author chain L； PDBConstruct 1–232； UniProt 1–232 Author chain N； PDBConstruct 1–232； UniProt 1–232 Author chain f； PDBConstruct 1–232； UniProt 1–232

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 8xcg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8xcg
Deposition date deposition_date2023-12-09
Structure title titleTail tip complex of bacteriophage lambda in the open state
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_guinier49.58 Å
Radius of gyration Rg (electron density) rg_electron49.04 Å
Forward intensity I(0) i02082040000.00
Molecular weight molecular_weight369490.0 kDa
Excluded volume excluded_volume457850 ų
Envelope volume envelope_volume697400 ų
Hydration-shell volume shell_volume114700 ų
Envelope diameter envelope_diameter161.9 Å
Shell Rg shell_rg57.11 Å
Envelope Rg envelope_rg46.93 Å
Shape Rg shape_rg49.04 Å
Total Rg total_rg49.33 Å
Total atoms total_atoms25941
Residues n_residues3312
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 dmax153.8 Å
Rg (real space) rg_real49.15 Å
Rg uncertainty (real space) rg_real_error0.83 Å
I(0) (real space) i0_real2.0820e+09
I(0) uncertainty (real space) i0_real_error3.4630e+07
Rg (reciprocal space) rg_reciprocal49.57 Å
I(0) (reciprocal space) i0_reciprocal2083000000.0000
Solution quality estimate total_estimate0.8617
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary67.3 Å
Skewness Skewness skewness0.097
Kurtosis Kurtosis kurtosis-0.311
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha309500000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.778
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)