SAXSdb — 1j8i

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

Lymphotactin

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 22–114	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；283 K；Ionic strength (raw mmCIF value) 200 mM sodium chloride NMR sample composition：1.3mM Human Lymphotactin, U-15N,13C; 20 mM phosphate buffer pH 6.0, 200 mM NaCl \| 90% H2O/10% D2O NMR sample composition：1 mM Human Lymphotactin, U-15N; 20 mM phosphate buffer pH 6.0, 200 mM NaCl \| 90% H2O/10% D2O NMR sample composition：1 mM Human Lymphotactin, 20 mM phosphate buffer pH 6.0, 200 mM NaCl \| 100% D2O	Resolution not provided

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 1J8I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1J9O SOLUTION STRUCTURE OF HUMAN LYMPHOTACTIN Deposited 2001-05-28	Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–114（93 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；283 K；Ionic strength (raw mmCIF value) 200mM NaCl NMR sample composition 1.3mM human lymphotactin U-15N-13C; 20 mM phosphate buffer, 200mM NaCl \| 90% H2O/10% D2O NMR sample composition 1mM human lymphotactin U-15N; 20 mM phosphate buffer, 200mM NaCl \| 90% H2O/10% D2O NMR sample composition 1mM human lymphotactin; 20 mM phosphate buffer, 200mM NaCl \| 100% D2O	Resolution not provided
2HDM Solution structure of V21C/V59C Lymphotactin/XCL1 Deposited 2006-06-20	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–114（92 aa）	Mutation：V21C, V59C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure AMBIENT NMR sample composition 1 mM CC3 hLtn, U-15N, 13C; 20 mM phospate buffer, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2JP1 Solution structure of the alternative conformation of XCL1/Lymphotactin Deposited 2007-04-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–114（93 aa） Chain B 22–114（93 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；313 K；Ionic strength (raw mmCIF value) 22；Pressure AMBIENT NMR sample composition 1.0 mM XCL1 U-15N/13C, 20 mM sodium phosphate, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 0.6 mM XCL1 U-15N/13C, 0.6 mM XCL1 unlabeled, 20 mM sodium phosphate, 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
2N54 Solution structure of a disulfide stabilized XCL1 dimer Deposited 2015-07-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–114（93 aa） Chain B 22–114（93 aa）	Mutation：A57C, A70C Mutation：A57C, A70C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；313 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition 1 mM [U-99% 13C; U-99% 15N] XCL1, 20 mM potassium phosphate, 0.02 % [U-100% 15N] sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2NYZ Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The C- Chemokine XCL1 Deposited 2006-11-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 22–114（93 aa） Chain E 22–114（93 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；10% PEG 8000, 100 mM TRIS, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.272
9AST Cryo-EM structure of XCR1 signaling complex Deposited 2024-02-26	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 22–114（93 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å

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

View Construct and Data Evidence

UniProt name	XCL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–93； UniProt 22–114

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	1j8i
Deposition date deposition_date	2001-05-21
Structure title title	Solution Structure of Human Lymphotactin
Keywords keywords	Chemokine, CYTOKINE; CYTOKINE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	22.81 Å
Radius of gyration Rg (electron density) rg_electron	23.48 Å
Forward intensity I(0) i0	648807000.00
Molecular weight molecular_weight	205280.0 kDa
Excluded volume excluded_volume	255020 Å³
Envelope volume envelope_volume	125670 Å³
Hydration-shell volume shell_volume	30664 Å³
Envelope diameter envelope_diameter	143.5 Å
Shell Rg shell_rg	37.49 Å
Envelope Rg envelope_rg	41.59 Å
Shape Rg shape_rg	23.51 Å
Total Rg total_rg	23.85 Å
Total atoms total_atoms	29300
Residues n_residues	1860
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	46.4 Å
Rg (real space) rg_real	16.08 Å
Rg uncertainty (real space) rg_real_error	0.10 Å
I(0) (real space) i0_real	5.4150e+08
I(0) uncertainty (real space) i0_real_error	5.2620e+06
Rg (reciprocal space) rg_reciprocal	23.73 Å
I(0) (reciprocal space) i0_reciprocal	648700000.0000
Solution quality estimate total_estimate	0.5999
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	16.9 Å
Skewness Skewness skewness	0.464
Kurtosis Kurtosis kurtosis	-0.379
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	4.8830
Highest regularization parameter α highest_alpha	305200.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.078; Oscil: 0.965; Stabil: 0.976; Sysdev: 0.000; Positv: 1.000; Valcen: 0.975; 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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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1j8ia_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

CATH v4.4 (1 domains)

Domain ID domain_id	1j8iA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Description description	Lymphotactin
Molecular weight formula_weight	10286.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	29300

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/j8/1j8i/1j8i.fit
pddf	/app/data/pr_computation/j8/1j8i/1j8i.pr.out
profile	/app/data/saxs_computation/j8/1j8i/1j8i.dat

Solution Structure of Human Lymphotactin

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

Lymphotactin

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)