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8xot

Prohead portal of bacteriophage lambda

Method: ELECTRON MICROSCOPY Dmax: 142.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Portal protein B

Escherichia phage Lambda

UniProt P03710

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 × 12 PDB declaration: 12-meric（12） Consistent with protein copy count Chain B； UniProt 1–533 Chain B1； UniProt 1–533 Chain B2； UniProt 1–533 Chain B3； UniProt 1–533 Chain B4； UniProt 1–533 Chain B5； UniProt 1–533 Chain b； UniProt 1–533 Chain b1； UniProt 1–533 Chain b2； UniProt 1–533 Chain b3； UniProt 1–533 Chain b4； UniProt 1–533 Chain b5； UniProt 1–533 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen NITROGEN Resolution 3.51 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 8XOT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8K38 The structure of bacteriophage lambda portal-adaptor 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 1–533（533 aa）
Chain B 1–533（533 aa）
Chain C 1–533（533 aa）
Chain D 1–533（533 aa）
Chain E 1–533（533 aa）
Chain F 1–533（533 aa）
Chain G 1–533（533 aa）
Chain H 1–533（533 aa）
Chain I 1–533（533 aa）
Chain J 1–533（533 aa）
Chain K 1–533（533 aa）
Chain L 1–533（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K39 Structure of the bacteriophage lambda portal vertex Deposited 2023-07-14 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain U 1–533（533 aa）
Chain V 1–533（533 aa）
Chain W 1–533（533 aa）
Chain X 1–533（533 aa）
Chain Y 1–533（533 aa）
Chain Z 1–533（533 aa）
Chain a 1–533（533 aa）
Chain b 1–533（533 aa）
Chain c 1–533（533 aa）
Chain d 1–533（533 aa）
Chain e 1–533（533 aa）
Chain f 1–533（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8XOU Prohead portal vertex of bacteriophage lambda Deposited 2024-01-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain B 1–533（533 aa）
Chain B1 1–533（533 aa）
Chain B2 1–533（533 aa）
Chain B3 1–533（533 aa）
Chain B4 1–533（533 aa）
Chain B5 1–533（533 aa）
Chain b 1–533（533 aa）
Chain b1 1–533（533 aa）
Chain b2 1–533（533 aa）
Chain b3 1–533（533 aa）
Chain b4 1–533（533 aa）
Chain b5 1–533（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 5.58 Å
8XOW Mature virion portal of bacteriophage lambda Deposited 2024-01-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain B 1–533（533 aa）
Chain B1 1–533（533 aa）
Chain B2 1–533（533 aa）
Chain B3 1–533（533 aa）
Chain B4 1–533（533 aa）
Chain B5 1–533（533 aa）
Chain b 1–533（533 aa）
Chain b1 1–533（533 aa）
Chain b2 1–533（533 aa）
Chain b3 1–533（533 aa）
Chain b4 1–533（533 aa）
Chain b5 1–533（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.32 Å
8XPM Mature virion portal of phage lambda with DNA Deposited 2024-01-04 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 66 PDB declaration: 68-meric
Chain B 1–533（533 aa）
Chain B1 1–533（533 aa）
Chain B2 1–533（533 aa）
Chain B3 1–533（533 aa）
Chain B4 1–533（533 aa）
Chain B5 1–533（533 aa）
Chain b 1–533（533 aa）
Chain b1 1–533（533 aa）
Chain b2 1–533（533 aa）
Chain b3 1–533（533 aa）
Chain b4 1–533（533 aa）
Chain b5 1–533（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.90 Å
8XQB Mature virion portal vertex of bacteriophage lambda Deposited 2024-01-05 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 71 PDB declaration: 71-meric
Chain B 1–533（533 aa）
Chain B1 1–533（533 aa）
Chain B2 1–533（533 aa）
Chain B3 1–533（533 aa）
Chain B4 1–533（533 aa）
Chain B5 1–533（533 aa）
Chain b 1–533（533 aa）
Chain b1 1–533（533 aa）
Chain b2 1–533（533 aa）
Chain b3 1–533（533 aa）
Chain b4 1–533（533 aa）
Chain b5 1–533（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 4.07 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PORTL_LAMBD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 1–533； UniProt 1–533 Author chain B1； PDBConstruct 1–533； UniProt 1–533 Author chain B2； PDBConstruct 1–533； UniProt 1–533 Author chain B3； PDBConstruct 1–533； UniProt 1–533 Author chain B4； PDBConstruct 1–533； UniProt 1–533 Author chain B5； PDBConstruct 1–533； UniProt 1–533 Author chain b； PDBConstruct 1–533； UniProt 1–533 Author chain b1； PDBConstruct 1–533； UniProt 1–533 Author chain b2； PDBConstruct 1–533； UniProt 1–533 Author chain b3； PDBConstruct 1–533； UniProt 1–533 Author chain b4； PDBConstruct 1–533； UniProt 1–533 Author chain b5； PDBConstruct 1–533； UniProt 1–533

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 8xot

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8xot
Deposition date deposition_date2024-01-02
Structure title titleProhead portal of bacteriophage lambda
Keywords keywordscaudovirales, siphoviridae, portal vertex, portal, capsid, connector/neck, tail, delivery device, B-DNA, 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_guinier55.33 Å
Radius of gyration Rg (electron density) rg_electron54.59 Å
Forward intensity I(0) i06118100000.00
Molecular weight molecular_weight632960.0 kDa
Excluded volume excluded_volume780190 ų
Envelope volume envelope_volume1076800 ų
Hydration-shell volume shell_volume151140 ų
Envelope diameter envelope_diameter152.5 Å
Shell Rg shell_rg66.70 Å
Envelope Rg envelope_rg53.51 Å
Shape Rg shape_rg54.63 Å
Total Rg total_rg54.69 Å
Total atoms total_atoms44532
Residues n_residues5688
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 dmax142.3 Å
Rg (real space) rg_real54.94 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real6.1180e+09
I(0) uncertainty (real space) i0_real_error8.9410e+07
Rg (reciprocal space) rg_reciprocal55.64 Å
I(0) (reciprocal space) i0_reciprocal6124000000.0000
Solution quality estimate total_estimate0.8464
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary81.3 Å
Skewness Skewness skewness-0.028
Kurtosis Kurtosis kurtosis-0.691
Angular range angular_range— – 0.1400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4464000000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 1.000; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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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)