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5w2l

Structure of a central domain of human Ctc1

Method: X-RAY DIFFRACTION Dmax: 67.5 Å Quality: EXCELLENT
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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 716–880 Fragment：UNP residues 716-880 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 716–880 Fragment：UNP residues 716-880 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

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 5W2L 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 mutation/modification 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 A 2–1217（1216 aa）
Chain B 2–1217（1216 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 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 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 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 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 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 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 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 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 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 6 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 4–168； UniProt 716–880 Author chain B； PDBConstruct 4–168； UniProt 716–880

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 5w2l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5w2l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5w2l
Deposition date deposition_date2017-06-06
Structure title titleStructure of a central domain of human Ctc1
Keywords keywordsTelomere, CST complex, Ctc1, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.53 Å
Radius of gyration Rg (electron density) rg_electron21.12 Å
Forward intensity I(0) i019549700.00
Molecular weight molecular_weight32289.0 kDa
Excluded volume excluded_volume39464 ų
Envelope volume envelope_volume48379 ų
Hydration-shell volume shell_volume19502 ų
Envelope diameter envelope_diameter68.3 Å
Shell Rg shell_rg27.18 Å
Envelope Rg envelope_rg21.36 Å
Shape Rg shape_rg20.95 Å
Total Rg total_rg22.39 Å
Total atoms total_atoms2200
Residues n_residues279
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 dmax67.5 Å
Rg (real space) rg_real22.47 Å
Rg uncertainty (real space) rg_real_error0.36 Å
I(0) (real space) i0_real1.9550e+07
I(0) uncertainty (real space) i0_real_error2.2770e+05
Rg (reciprocal space) rg_reciprocal22.49 Å
I(0) (reciprocal space) i0_reciprocal19550000.0000
Solution quality estimate total_estimate0.9173
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.5 Å
Skewness Skewness skewness0.151
Kurtosis Kurtosis kurtosis-0.655
Angular range angular_range— – 0.3550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1985000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.985; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.968
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)