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6w6w

Cryo-EM structure of CST bound to telomeric single-stranded DNA

Method: ELECTRON MICROSCOPY Dmax: 158.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CST complex subunit CTC1

Homo sapiens

UniProt Q2NKJ3

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–DNA Heteromer Protein × 4 DNA 1 PDB declaration: pentameric（5） Consistent with all polymer counts Chain A； UniProt 2–1217 Chain B； UniProt 2–1217 Not recorded ;DNA (5'-D(P*TP*AP*GP*G)-3') ; × 1 CST complex subunit STN1 × 1 （Q9H668） CST complex subunit TEN1 × 1 （Q86WV5） ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.00 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 6W6W Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5W2L Structure of a central domain of human Ctc1 Deposited 2017-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 716–880（165 aa） Fragment：UNP residues 716-880
Not recorded HG MERCURY (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M MES, pH 6.0, 20% w/v PEG2000 MME
Resolution 1.86 Å R-free 0.249
5W2L Structure of a central domain of human Ctc1 Deposited 2017-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 716–880（165 aa） Fragment：UNP residues 716-880
Not recorded HG MERCURY (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M MES, pH 6.0, 20% w/v PEG2000 MME
Resolution 1.86 Å R-free 0.249
7U5C Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state Deposited 2022-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric
Chain E 1–1217（1217 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric
Chain A 9–1217（1209 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: octameric
Chain A 2–1217（1216 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 mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1217（1217 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 mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: hexameric
Chain A 1–1217（1217 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 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CTC1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 18–1233； UniProt 2–1217 Author chain B； PDBConstruct 18–1233； UniProt 2–1217

CST complex subunit STN1

Homo sapiens

UniProt Q9H668

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–DNA Heteromer Protein × 4 DNA 1 PDB declaration: pentameric（5） Consistent with all polymer counts Chain C； UniProt 2–368 Not recorded CST complex subunit CTC1 × 2 （Q2NKJ3） ;DNA (5'-D(P*TP*AP*GP*G)-3') ; × 1 CST complex subunit TEN1 × 1 （Q86WV5） ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.00 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 6W6W 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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
4JQF Structure of the C-terminal domain of human telomeric Stn1 Deposited 2013-03-20 Different construct Different oligomeric state Different ligand/ion Different experimental method 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
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 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 ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 3
Chains and sequence ranges Author chain C； PDBConstruct 8–374； UniProt 2–368

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–DNA Heteromer Protein × 4 DNA 1 PDB declaration: pentameric（5） Consistent with all polymer counts Chain D； UniProt 3–123 Not recorded CST complex subunit CTC1 × 2 （Q2NKJ3） ;DNA (5'-D(P*TP*AP*GP*G)-3') ; × 1 CST complex subunit STN1 × 1 （Q9H668） ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.00 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 6W6W 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–122（122 aa）
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–122（122 aa）
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
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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TEN1L_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 32–152； UniProt 3–123

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 6w6w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6w6w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6w6w
Deposition date deposition_date2020-03-17
Structure title titleCryo-EM structure of CST bound to telomeric single-stranded DNA
Keywords keywords;Telomere homeostasis, telomere packaging, telomerase terminator, DNA replication, Double-stranded breaks repair, single-stranded DNA-binding proteins, higher-order protein assembly, DNA-induced oligomeriization, STRUCTURAL PROTEIN, STRUCTURAL PROTEIN-DNA complex ;; STRUCTURAL PROTEIN/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier47.61 Å
Radius of gyration Rg (electron density) rg_electron47.32 Å
Forward intensity I(0) i0349676000.00
Molecular weight molecular_weight156020.0 kDa
Excluded volume excluded_volume196260 ų
Envelope volume envelope_volume301260 ų
Hydration-shell volume shell_volume54639 ų
Envelope diameter envelope_diameter162.2 Å
Shell Rg shell_rg49.74 Å
Envelope Rg envelope_rg46.24 Å
Shape Rg shape_rg47.33 Å
Total Rg total_rg47.36 Å
Total atoms total_atoms10981
Residues n_residues1392
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 dmax158.5 Å
Rg (real space) rg_real47.66 Å
Rg uncertainty (real space) rg_real_error1.33 Å
I(0) (real space) i0_real3.4970e+08
I(0) uncertainty (real space) i0_real_error6.1560e+06
Rg (reciprocal space) rg_reciprocal47.61 Å
I(0) (reciprocal space) i0_reciprocal349600000.0000
Solution quality estimate total_estimate0.8748
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary67.2 Å
Skewness Skewness skewness0.208
Kurtosis Kurtosis kurtosis-0.660
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha34380000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.745
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6w6wC01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id6w6wD00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
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8. Citations (1)

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9. Files and Curves (10)