SAXSdb — 4joi

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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 19–184	Fragment：Stn1 N-terminal domain	CST complex subunit TEN1 × 1 （Q86WV5）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 19–184	Fragment：Stn1 N-terminal domain	CST complex subunit TEN1 × 1 （Q86WV5）	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

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 4JOI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4JQF Structure of the C-terminal domain of human telomeric Stn1 Deposited 2013-03-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 191–368（178 aa） Fragment：unp residues 191-368	Not recorded	No recorded non-water small molecule	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
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 7 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 1–166； UniProt 19–184 Author chain B； PDBConstruct 1–166； UniProt 19–184

CST complex subunit TEN1

Homo sapiens

UniProt Q86WV5

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–122	Not recorded	CST complex subunit STN1 × 1 （Q9H668）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–122	Not recorded	CST complex subunit STN1 × 1 （Q9H668）	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

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 4JOI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 D 3–123（121 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 G 1–123（123 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 C 3–123（121 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 C 3–123（121 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 C 1–123（123 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 C 1–123（123 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

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

View Construct and Data Evidence

UniProt name	TEN1L_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–122； UniProt 1–122 Author chain D； PDBConstruct 1–122； UniProt 1–122

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	4joi
Deposition date deposition_date	2013-03-18
Structure title title	Crystal structure of the human telomeric Stn1-Ten1 complex
Keywords keywords	OB fold, 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	32.15 Å
Radius of gyration Rg (electron density) rg_electron	31.82 Å
Forward intensity I(0) i0	55481200.00
Molecular weight molecular_weight	59843.0 kDa
Excluded volume excluded_volume	75524 Å³
Envelope volume envelope_volume	102500 Å³
Hydration-shell volume shell_volume	28224 Å³
Envelope diameter envelope_diameter	107.4 Å
Shell Rg shell_rg	36.87 Å
Envelope Rg envelope_rg	31.51 Å
Shape Rg shape_rg	31.78 Å
Total Rg total_rg	32.43 Å
Total atoms total_atoms	4211
Residues n_residues	518
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	102.8 Å
Rg (real space) rg_real	32.38 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	5.5480e+07
I(0) uncertainty (real space) i0_real_error	1.0220e+06
Rg (reciprocal space) rg_reciprocal	32.29 Å
I(0) (reciprocal space) i0_reciprocal	55480000.0000
Solution quality estimate total_estimate	0.8440
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.378
Kurtosis Kurtosis kurtosis	-0.726
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11670000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.787; Smooth: 0.657

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CST complex subunit STN1
Molecular weight formula_weight	19139.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4376

LDPVFLAFAKLYIRDILDMKESRQVPGVFLYNGHPIKQVDVLGTVIGVRERDAFYSYGVDDSTGVINCICWKKLNTESVSAAPSAARELSLTSQLKKLQETIEQKTKIEIGDTIRVRGSIRTYREEREIHATTYYKVDDPVWNIQIARMLELPTIYRKVYDQPFHS

来源 Source

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

Entity 2 Entity 2 polymer

Description description	CST complex subunit TEN1
Molecular weight formula_weight	13740.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,C

MLPKPGTYYLPWEVSAGQVPDGSTLRTFGRLCLYDMIQSRVTLMAQHGSDQHQVLVCTKLVEPFHAQVGSLYIVLGELQHQQDRGSVVKARVLTCVEGMNLPLLEQAIREQRLYKQERGGSQ

来源 Source

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	165

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4joiA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	4joiB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	4joiC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	4joiD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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8. Citations (1)

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Unit-cell length a length_a	130.613 Å
Unit-cell length b length_b	58.101 Å
Unit-cell length c length_c	87.458 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2127
R_work r_work	0.2108
R_free r_free	0.2486

fit	/app/data/saxs_computation/jo/4joi/4joi.fit
pddf	/app/data/pr_computation/jo/4joi/4joi.pr.out
profile	/app/data/saxs_computation/jo/4joi/4joi.dat

Crystal structure of the human telomeric Stn1-Ten1 complex

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

CST complex subunit TEN1

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)