SAXSdb — 8k38

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Portal protein B

OrganismNot specified

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain A； UniProt 1–533 Chain B； UniProt 1–533 Chain C； UniProt 1–533 Chain D； UniProt 1–533 Chain E； UniProt 1–533 Chain F； UniProt 1–533 Chain G； UniProt 1–533 Chain H； UniProt 1–533 Chain I； UniProt 1–533 Chain J； UniProt 1–533 Chain K； UniProt 1–533 Chain L； UniProt 1–533	Not recorded	Head completion protein × 12 （P68660）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.20 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 8K38	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8K39 Structure of the bacteriophage lambda portal vertex Deposited 2023-07-14	Different oligomeric state 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
8XOT Prohead portal of bacteriophage lambda Deposited 2024-01-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: 12-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 3.51 Å
8XOU Prohead portal vertex of bacteriophage lambda Deposited 2024-01-02	Different oligomeric state Different experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 A； PDBConstruct 1–533； UniProt 1–533 Author chain B； PDBConstruct 1–533； UniProt 1–533 Author chain C； PDBConstruct 1–533； UniProt 1–533 Author chain D； PDBConstruct 1–533； UniProt 1–533 Author chain E； PDBConstruct 1–533； UniProt 1–533 Author chain F； PDBConstruct 1–533； UniProt 1–533 Author chain G； PDBConstruct 1–533； UniProt 1–533 Author chain H； PDBConstruct 1–533； UniProt 1–533 Author chain I； PDBConstruct 1–533； UniProt 1–533 Author chain J； PDBConstruct 1–533； UniProt 1–533 Author chain K； PDBConstruct 1–533； UniProt 1–533 Author chain L； PDBConstruct 1–533； UniProt 1–533

Head completion protein

OrganismNot specified

UniProt P68660

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain M； UniProt 1–68 Chain N； UniProt 1–68 Chain O； UniProt 1–68 Chain P； UniProt 1–68 Chain Q； UniProt 1–68 Chain R； UniProt 1–68 Chain S； UniProt 1–68 Chain T； UniProt 1–68 Chain U； UniProt 1–68 Chain V； UniProt 1–68 Chain W； UniProt 1–68 Chain X； UniProt 1–68	Not recorded	Portal protein B × 12 （P03710）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.20 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 8K38	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HYW SOLUTION STRUCTURE OF BACTERIOPHAGE LAMBDA GPW Deposited 2001-01-22	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 1–68（68 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 200mM NaCl；Pressure ambient NMR sample composition 1.5mM gpW U-15N, 13C; 10mM phosphate buffer NA, 200mM NaCl,90% H2O,10% D2O \| 90% H2O/10% D2O	Resolution not provided
8XOW Mature virion portal of bacteriophage lambda Deposited 2024-01-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain W 1–68（68 aa） Chain W1 1–68（68 aa） Chain W2 1–68（68 aa） Chain W3 1–68（68 aa） Chain W4 1–68（68 aa） Chain W5 1–68（68 aa） Chain w 1–68（68 aa） Chain w1 1–68（68 aa） Chain w2 1–68（68 aa） Chain w3 1–68（68 aa） Chain w4 1–68（68 aa） Chain w5 1–68（68 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain W 1–68（68 aa） Chain W1 1–68（68 aa） Chain W2 1–68（68 aa） Chain W3 1–68（68 aa） Chain W4 1–68（68 aa） Chain W5 1–68（68 aa） Chain w 1–68（68 aa） Chain w1 1–68（68 aa） Chain w2 1–68（68 aa） Chain w3 1–68（68 aa） Chain w4 1–68（68 aa） Chain w5 1–68（68 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 71 PDB declaration: 71-meric	Chain W 1–68（68 aa） Chain W1 1–68（68 aa） Chain W2 1–68（68 aa） Chain W3 1–68（68 aa） Chain W4 1–68（68 aa） Chain W5 1–68（68 aa） Chain w 1–68（68 aa） Chain w1 1–68（68 aa） Chain w2 1–68（68 aa） Chain w3 1–68（68 aa） Chain w4 1–68（68 aa） Chain w5 1–68（68 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

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

View Construct and Data Evidence

UniProt name	HCP_LAMBD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–68； UniProt 1–68 Author chain N； PDBConstruct 1–68； UniProt 1–68 Author chain O； PDBConstruct 1–68； UniProt 1–68 Author chain P； PDBConstruct 1–68； UniProt 1–68 Author chain Q； PDBConstruct 1–68； UniProt 1–68 Author chain R； PDBConstruct 1–68； UniProt 1–68 Author chain S； PDBConstruct 1–68； UniProt 1–68 Author chain T； PDBConstruct 1–68； UniProt 1–68 Author chain U； PDBConstruct 1–68； UniProt 1–68 Author chain V； PDBConstruct 1–68； UniProt 1–68 Author chain W； PDBConstruct 1–68； UniProt 1–68 Author chain X； PDBConstruct 1–68； UniProt 1–68

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8k38
Deposition date deposition_date	2023-07-14
Structure title title	The structure of bacteriophage lambda portal-adaptor
Keywords keywords	Complex, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	57.16 Å
Radius of gyration Rg (electron density) rg_electron	56.39 Å
Forward intensity I(0) i0	7742890000.00
Molecular weight molecular_weight	713560.0 kDa
Excluded volume excluded_volume	880200 Å³
Envelope volume envelope_volume	1258900 Å³
Hydration-shell volume shell_volume	170060 Å³
Envelope diameter envelope_diameter	168.3 Å
Shell Rg shell_rg	69.80 Å
Envelope Rg envelope_rg	55.42 Å
Shape Rg shape_rg	56.40 Å
Total Rg total_rg	56.63 Å
Total atoms total_atoms	50172
Residues n_residues	6396
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	172.8 Å
Rg (real space) rg_real	56.71 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	7.7430e+09
I(0) uncertainty (real space) i0_real_error	1.4190e+08
Rg (reciprocal space) rg_reciprocal	57.52 Å
I(0) (reciprocal space) i0_reciprocal	7752000000.0000
Solution quality estimate total_estimate	0.8846
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	76.8 Å
Skewness Skewness skewness	-0.036
Kurtosis Kurtosis kurtosis	-0.663
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1648000000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.795

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Portal protein B
Molecular weight formula_weight	59529.6 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	50172

MKTPTIPTLLGPDGMTSLREYAGYHGGGSGFGGQLRSWNPPSESVDAALLPNFTRGNARADDLVRNNGYAANAIQLHQDHIVGSFFRLSHRPSWRYLGIGEEEARAFSREVEAAWKEFAEDDCCCIDVERKRTFTMMIREGVAMHAFNGELFVQATWDTSSSRLFRTQFRMVSPKRISNPNNTGDSRNCRAGVQINDSGAALGYYVSEDGYPGWMPQKWTWIPRELPGGRASFIHVFEPVEDGQTRGANVFYSVMEQMKMLDTLQNTQLQSAIVKAMYAATIESELDTQSAMDFILGANSQEQRERLTGWIGEIAAYYAAAPVRLGGAKVPHLMPGDSLNLQTAQDTDNGYSVFEQSLLRYIAAGLGVSYEQLSRNYAQMSYSTARASANESWAYFMGRRKFVASRQASQMFLCWLEEAIVRRVVTLPSKARFSFQEARSAWGNCDWIGSGRMAIDGLKEVQEAVMLIEAGLSTYEKECAKRGDDYQEIFAQQVRETMERRAAGLKPPAWAAAAFESGLRQSTEEEKSDSRAA

Entity 2 Entity 2 polymer

Description description	Head completion protein
Molecular weight formula_weight	7625.7 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O,P,Q,R,S,T,U,V,W,X

MTRQEELAAARAALHDLMTGKRVATVQKDGRRVEFTATSVSDLKKYIAELEVQTGMTQRRRGPAGFYV

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	72868

fit	/app/data/saxs_computation/k3/8k38/8k38.fit
pddf	/app/data/pr_computation/k3/8k38/8k38.pr.out
profile	/app/data/saxs_computation/k3/8k38/8k38.dat

The structure of bacteriophage lambda portal-adaptor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Portal protein B

State in the Current Structure

Other States of the Same Protein in the Database

Head completion protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)