SAXSdb — 4jqf

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

CST complex subunit STN1

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 191–368	Fragment：unp residues 191-368	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8.5；289.15 K；1.6 M Ammonium phosphate dibasic, 100 mM Tris, 3% Ethylene glycol, pH 8.5, VAPOR DIFFUSION, Microbatch Crystallization, temperature 289.15K	Resolution 1.60 Å R-free 0.219

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 4JQF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4JOI Crystal structure of the human telomeric Stn1-Ten1 complex Deposited 2013-03-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 19–184（166 aa） Fragment：Stn1 N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；0.8 M AmSO4, 0.1 M citric acid pH 4.0 and 5% jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.05 Å R-free 0.249
4JOI Crystal structure of the human telomeric Stn1-Ten1 complex Deposited 2013-03-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 19–184（166 aa） Fragment：Stn1 N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；0.8 M AmSO4, 0.1 M citric acid pH 4.0 and 5% jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.05 Å R-free 0.249
6W6W Cryo-EM structure of CST bound to telomeric single-stranded DNA Deposited 2020-03-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric	Chain C 2–368（367 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7U5C Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state Deposited 2022-03-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric	Chain F 1–368（368 aa）	Not recorded	ZN ZINC ION × 4 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
8D0B Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback template Deposited 2022-05-26	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric	Chain B 7–368（362 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；CHAPSO is only added just before sample vitrification. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
8D0K Human CST-DNA polymerase alpha/primase preinitiation complex bound to 4xTEL-foldback template - PRIM2C advanced PIC Deposited 2022-05-26	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric	Chain B 2–368（367 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；CHAPSO is only added just before sample vitrification. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.27 Å
8SOJ Cryo-EM structure of human CST bound to POT1(ESDL)/TPP1 in the absence of telomeric ssDNA Deposited 2023-04-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–368（368 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8SOK Cryo-EM structure of human CST bound to POT1(ESDL)/TPP1 in the presence of telomeric ssDNA Deposited 2023-04-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: hexameric	Chain B 1–368（368 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–179； UniProt 191–368

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	4jqf
Deposition date deposition_date	2013-03-20
Structure title title	Structure of the C-terminal domain of human telomeric Stn1
Keywords keywords	Wing-helix-turn-helix (wHTH) motif, Protein binding, Pol alpha, Ctc1, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	19.67 Å
Radius of gyration Rg (electron density) rg_electron	18.85 Å
Forward intensity I(0) i0	6885470.00
Molecular weight molecular_weight	19203.0 kDa
Excluded volume excluded_volume	24064 Å³
Envelope volume envelope_volume	28828 Å³
Hydration-shell volume shell_volume	13968 Å³
Envelope diameter envelope_diameter	67.8 Å
Shell Rg shell_rg	23.48 Å
Envelope Rg envelope_rg	19.06 Å
Shape Rg shape_rg	18.83 Å
Total Rg total_rg	19.69 Å
Total atoms total_atoms	1350
Residues n_residues	168
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	69.0 Å
Rg (real space) rg_real	19.83 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	6.8850e+06
I(0) uncertainty (real space) i0_real_error	9.6130e+04
Rg (reciprocal space) rg_reciprocal	19.81 Å
I(0) (reciprocal space) i0_reciprocal	6885000.0000
Solution quality estimate total_estimate	0.8134
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.5 Å
Skewness Skewness skewness	0.518
Kurtosis Kurtosis kurtosis	-0.238
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2464000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.644; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.688; Smooth: 0.949

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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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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4jqfA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	980 — CST, Suppressor of Cdc13 homolog, complex subunit STN1, N-terminal domain

Domain ID domain_id	4jqfA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	28.805 Å
Unit-cell length b length_b	76.572 Å
Unit-cell length c length_c	114.422 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1985
R_work r_work	0.1974
R_free r_free	0.2190

Description description	CST complex subunit STN1
Molecular weight formula_weight	20473.3 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	1516

Structure of the C-terminal domain of human telomeric Stn1

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

CST complex subunit STN1

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	166

fit	/app/data/saxs_computation/jq/4jqf/4jqf.fit
pddf	/app/data/pr_computation/jq/4jqf/4jqf.pr.out
profile	/app/data/saxs_computation/jq/4jqf/4jqf.dat