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9hcv

Crystal structure of human TRF1 TRFH domain in complex with compound 16

Method: X-RAY DIFFRACTION Dmax: 75.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Telomeric repeat-binding factor 1

Homo sapiens

UniProt P54274

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 48–268 Not recorded EDO 1,2-ETHANEDIOL × 2 A1ITZ 5-cyclobutyl-3-pyridin-2-yl-1,2,4-oxadiazole × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution. Resolution 2.08 Å R-free 0.268

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 9HCV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BA5 DNA-BINDING DOMAIN OF HUMAN TELOMERIC PROTEIN, HTRF1, NMR, 18 STRUCTURES Deposited 1998-04-22 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 378–430（53 aa） Fragment：DNA-BINDING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；300 K；Ionic strength (raw mmCIF value) 100 mM PHOSPHATE POTASSIU；Pressure 1
NMR sample composition H2O
Resolution not provided
1H6O Dimerisation domain from human TRF1 Deposited 2001-06-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 62–265（204 aa） Fragment：DIMERISATION DOMAIN RESIDUES 63-265
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；PH6, 5-15% GLYCEROL, 1-5 MM MAGNESIUM ACETATE, 1 % PEG 8000, pH 6.00
Resolution 2.90 Å R-free 0.303
1ITY Solution structure of the DNA binding domain of human TRF1 Deposited 2002-02-15 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 371–439（69 aa） Fragment：DNA binding domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；300 K；Pressure ambient
NMR sample composition 1.5-2.5mM TRF1 U-15N, 13C, 50mM phosphate buffer, 100mM NaCl | 90% H2O, 10% D2O, 100% D2O
Resolution not provided
1IV6 Solution Structure of the DNA Complex of Human TRF1 Deposited 2002-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 371–439（69 aa） Fragment：DNA-binding domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；305 K；Pressure ambient
NMR sample composition 1.5-2.5mM TRF1-DNA complex; 5mM Phosphate buffer with 10mM NaCl | 90% H2O, 10% D2O or 100% D2O
Resolution not provided
1W0T hTRF1 DNA-binding domain in complex with telomeric DNA. Deposited 2004-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 379–431（53 aa） Fragment：DNA-BINDING DOMAIN, RESIDUES 379-431
Chain B 379–431（53 aa） Fragment：DNA-BINDING DOMAIN, RESIDUES 379-431
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；PROTEIN WAS CRYSTALLISED IN 50 MM MES, PH 6.0, 0.1 M KCL, 2 MM MGCL2 AND 10 % PEG 400 AND CRYOPROTECTED IN 20 % GLYCEROL
Resolution 2.00 Å R-free 0.273
3BQO Crystal Structure of TRF1 TRFH domain and TIN2 peptide complex Deposited 2007-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 58–268（211 aa） Fragment：TRFH domain, Dimerization domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；289 K；NaCl 2.5 M MgCl2 0.35 M Tris 0.1 M pH 8.6 DTT 5 mM , VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.00 Å R-free 0.237
3BQO Crystal Structure of TRF1 TRFH domain and TIN2 peptide complex Deposited 2007-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 58–268（211 aa） Fragment：TRFH domain, Dimerization domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；289 K；NaCl 2.5 M MgCl2 0.35 M Tris 0.1 M pH 8.6 DTT 5 mM , VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.00 Å R-free 0.237
3L82 X-ray Crystal structure of TRF1 and Fbx4 complex Deposited 2009-12-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 58–268（211 aa） Fragment：Dimerization domain residues 58-268
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.2；289 K；300 mM NH4H2PO4, 100 mM sodium citrate pH 6.2, 10% n-propanol and 10 mM DTT, VAPOR DIFFUSION, temperature 289K
Resolution 2.40 Å R-free 0.263
3L82 X-ray Crystal structure of TRF1 and Fbx4 complex Deposited 2009-12-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 58–268（211 aa） Fragment：Dimerization domain residues 58-268
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.2；289 K；300 mM NH4H2PO4, 100 mM sodium citrate pH 6.2, 10% n-propanol and 10 mM DTT, VAPOR DIFFUSION, temperature 289K
Resolution 2.40 Å R-free 0.263
3L82 X-ray Crystal structure of TRF1 and Fbx4 complex Deposited 2009-12-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 58–268（211 aa） Fragment：Dimerization domain residues 58-268
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.2；289 K；300 mM NH4H2PO4, 100 mM sodium citrate pH 6.2, 10% n-propanol and 10 mM DTT, VAPOR DIFFUSION, temperature 289K
Resolution 2.40 Å R-free 0.263
5HKP Crystal structure of mouse Tankyrase/human TRF1 complex Deposited 2016-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–55（55 aa） Fragment：UNP residues 1-55
Chain D 1–55（55 aa） Fragment：UNP residues 1-55
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.035M Calcium Chloride dihydrate 0.07M MES monohydrate pH6.0 0.03M Tris pH8.5 31.5% v/v Polyethylene glycol 200 6% v/v Ethanol
Resolution 2.20 Å R-free 0.229
5WIR Structure of the TRF1-TERB1 interface Deposited 2017-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 62–265（204 aa）
Chain B 62–265（204 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；TRF1-TRFH and TERB1-TBM were mixed in a 1:5 molar ratio and crystal screens set up using 0.3 microliter protein solution and 0.3 microliter reservoir solution in a sitting drop format. Diffracting crystals were obtained in 0.1 M Tris-Cl (pH 8.5) and 30% PEG 300. Crystals were cryoprotected in the crystallization solution plus 10% PEG 400 and harvested in liquid nitrogen.
Resolution 2.10 Å R-free 0.210
5XUP Crystal structure of TRF1 and TERB1 Deposited 2017-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 65–266（202 aa） Fragment：TRFH domain (UNP RESIDUES 65-266)
Chain B 65–266（202 aa） Fragment：TRFH domain (UNP RESIDUES 65-266)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；10% 2-propanol, 0.1M Tris-HCl
Resolution 2.10 Å R-free 0.221
8F0A Client-bound structure of a DegP trimer within a 12mer cage Deposited 2022-11-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Chain b 404–430（27 aa） Fragment：UNP residues 404-430
Chain c 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.60 Å
8F0U Structure of a 12mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
8F0U Structure of a 12mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
8F0U Structure of a 12mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
8F1T Structure of an 18mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Chain b 404–430（27 aa） Fragment：UNP residues 404-430
Chain c 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 12.10 Å
8F1T Structure of an 18mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Chain b 404–430（27 aa） Fragment：UNP residues 404-430
Chain c 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 12.10 Å
8F1T Structure of an 18mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Chain b 404–430（27 aa） Fragment：UNP residues 404-430
Chain c 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 12.10 Å
8F1U Structure of a 24mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 72 PDB declaration: 72-meric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Chain b 404–430（27 aa） Fragment：UNP residues 404-430
Chain c 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 13.80 Å
8F1U Structure of a 24mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Chain b 404–430（27 aa） Fragment：UNP residues 404-430
Chain c 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 13.80 Å
8F1U Structure of a 24mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Chain b 404–430（27 aa） Fragment：UNP residues 404-430
Chain c 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 13.80 Å
8F21 Structure of a 30mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 90 PDB declaration: 90-meric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Chain b 404–430（27 aa） Fragment：UNP residues 404-430
Chain c 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 14.10 Å
8F21 Structure of a 30mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Chain b 404–430（27 aa） Fragment：UNP residues 404-430
Chain c 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 14.10 Å
8F21 Structure of a 30mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Chain b 404–430（27 aa） Fragment：UNP residues 404-430
Chain c 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 14.10 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 180 PDB declaration: 180-meric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain a 404–430（27 aa） Fragment：UNP residues 404-430
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 9.70 Å
8OX1 Structure of TRF1core in complex with telomeric nucleosome Deposited 2023-04-28 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 × 10 PDB declaration: dodecameric
Chain L 1–439（439 aa）
Chain M 1–439（439 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Blot Force: -15 Blot Time: 2.5 s
Resolution 2.70 Å
8W8G Crystal structure of human TRF1 with PinX1 Deposited 2023-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 58–269（212 aa）
Chain B 58–269（212 aa）
Not recorded HEZ HEXANE-1,6-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；289 K；0.05 M HEPES, 4% PEG2000 MME, 3% 1.6-hexanediol and 0.04 M NaCl
Resolution 2.70 Å R-free 0.263
8W8G Crystal structure of human TRF1 with PinX1 Deposited 2023-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 58–269（212 aa）
Chain D 58–269（212 aa）
Not recorded HEZ HEXANE-1,6-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；289 K；0.05 M HEPES, 4% PEG2000 MME, 3% 1.6-hexanediol and 0.04 M NaCl
Resolution 2.70 Å R-free 0.263
9HCL Crystal structure of human TRF1 TRFH domain in complex with compound 12 Deposited 2024-11-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded TWC 2-ethyl-5-(trifluoromethyl)-2,4-dihydro-3H-pyrazol-3-one × 6 DMS DIMETHYL SULFOXIDE × 10 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 1.87 Å R-free 0.220
9HCM Crystal structure of human TRF1 TRFH domain in complex with compound 45 Deposited 2024-11-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded LX7 1-[4-(trifluoromethyloxy)phenyl]thiourea × 2 DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 2.32 Å R-free 0.314
9HCN Crystal structure of human TRF1 TRFH domain in complex with compound 46 Deposited 2024-11-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded UVA N-methyl-2-(methylsulfonyl)aniline × 2 EDO 1,2-ETHANEDIOL × 6 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 1.93 Å R-free 0.224
9HCP Crystal structure of human TRF1 TRFH domain in complex with compound 15 Deposited 2024-11-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded LL0 2-(difluoromethoxy)benzene-1-sulfonamide × 2 EDO 1,2-ETHANEDIOL × 8 1PE PENTAETHYLENE GLYCOL × 4 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 1.70 Å R-free 0.240
9HCQ Crystal structure of human TRF1 TRFH domain in complex with compound 47 Deposited 2024-11-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 JHJ N-(4-methoxyphenyl)-N'-pyridin-4-ylurea × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 1.96 Å R-free 0.245
9HCR Crystal structure of human TRF1 TRFH domain in complex with compound 48 Deposited 2024-11-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded W1P 5-methyl-2-phenyl-2,4-dihydro-3H-pyrazol-3-one × 2 EDO 1,2-ETHANEDIOL × 6 DMS DIMETHYL SULFOXIDE × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 1.93 Å R-free 0.217
9HCS Crystal structure of human TRF1 TRFH domain in complex with compound 49 Deposited 2024-11-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded JGA N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea × 2 EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 2.20 Å R-free 0.242
9HCT Crystal structure of human TRF1 TRFH domain in complex with compound 50 Deposited 2024-11-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded B0V 2-methoxy-~{N}-(2,4,6-trimethylphenyl)ethanamide × 2 EDO 1,2-ETHANEDIOL × 10 CA CALCIUM ION × 2 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 1.70 Å R-free 0.240
9HCU Crystal structure of human TRF1 TRFH domain in complex with compound 51 Deposited 2024-11-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded ZU7 N-(4-fluorophenyl)-2-(piperazin-1-yl)acetamide × 2 EDO 1,2-ETHANEDIOL × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 2.07 Å R-free 0.260
9HCW Crystal structure of human TRF1 TRFH domain in complex with compound 52 Deposited 2024-11-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded A1IT0 1-(methylsulfonylamino)cyclohexane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 2.08 Å R-free 0.255
9HCX Crystal structure of human TRF1 TRFH domain in complex with compound 53 Deposited 2024-11-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded W0S 1-(3,4,5-trimethoxyphenyl)methanamine × 2 EDO 1,2-ETHANEDIOL × 10 DMS DIMETHYL SULFOXIDE × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 1.69 Å R-free 0.247
9HCY Crystal structure of human TRF1 TRFH domain in complex with compound 54 Deposited 2024-11-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded A9E 2-(4-ethylphenoxy)-1-piperidin-1-yl-ethanone × 2 EDO 1,2-ETHANEDIOL × 8 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 1.93 Å R-free 0.223
9HCZ Crystal structure of human TRF1 TRFH domain in complex with compound 6 Deposited 2024-11-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded TT3 2-(3-fluorophenoxy)-N,N-dimethylacetamide × 2 EDO 1,2-ETHANEDIOL × 8 DMS DIMETHYL SULFOXIDE × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 1.55 Å R-free 0.214
9HD0 Crystal structure of human TRF1 TRFH domain in complex with compound 55 Deposited 2024-11-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded A9E 2-(4-ethylphenoxy)-1-piperidin-1-yl-ethanone × 2 EDO 1,2-ETHANEDIOL × 8 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；SNAQVQVGAPEEEEEEEEDAGLVAEAEAVAAGWMLDFLCLSLCRAFRDGRSEDFRRTRNSAEAIIHGLSSLTACQLRTIYICQFLTRIAAGKTLDAQFENDERITPLESALMIWGSIEKEHDKLHEEIQNLIKIQAIAVCMENGNFKEAEEVFERIFGDPNSHMPFKSKLLMIISQKDTFHSFFQHFSYNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVVESKR
Resolution 1.93 Å R-free 0.223
9HD1 Crystal structure of human TRF1 TRFH domain in complex with compound 59 Deposited 2024-11-11 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded XH1 N-propan-2-ylurea × 2 EDO 1,2-ETHANEDIOL × 6 1PE PENTAETHYLENE GLYCOL × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 1.73 Å R-free 0.227
9HD2 Crystal structure of human TRF1 TRFH domain in complex with compound 40 Deposited 2024-11-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded A1ITY 4-[(3,5-dimethoxyphenyl)methoxy]naphthalene-1-sulfonic acid × 2 EDO 1,2-ETHANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution
Resolution 2.07 Å R-free 0.268
9HD3 Crystal structure of human TRF1 TRFH domain in complex with compound 27 Deposited 2024-11-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded A1ITX 4-ethoxynaphthalene-1-sulfonic acid × 2 EDO 1,2-ETHANEDIOL × 4 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 2.19 Å R-free 0.274
9HD9 Crystal structure of human TRF1 TRFH domain in complex with compound 1 Deposited 2024-11-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded UUP N-cyclopropylpyrazolo[1,5-a]pyrimidine-3-carboxamide × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 1.87 Å R-free 0.266
9HDA Crystal structure of human TRF1 TRFH domain in complex with compound 58 Deposited 2024-11-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded PYZ 4-IODOPYRAZOLE × 4 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 2.10 Å R-free 0.283
9HF4 Crystal structure of human TRF1 TRFH domain in complex with compound 32 Deposited 2024-11-15 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded A1IUC 4-phenylmethoxynaphthalene-1-sulfonic acid × 2 DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 2.17 Å R-free 0.258
9HF6 Crystal structure of human TRF1 TRFH domain in complex with compound 1 Deposited 2024-11-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded GOL GLYCEROL × 2 UUP N-cyclopropylpyrazolo[1,5-a]pyrimidine-3-carboxamide × 2 DMS DIMETHYL SULFOXIDE × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.23 Å R-free 0.248
9HF7 Crystal structure of human TRF1 TRFH domain in complex with compound 3 Deposited 2024-11-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded GOL GLYCEROL × 2 JFP N-(4-methyl-1,3-thiazol-2-yl)propanamide × 2 DMS DIMETHYL SULFOXIDE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.38 Å R-free 0.255
9HF8 Crystal structure of human TRF1 TRFH domain in complex with compound 4 Deposited 2024-11-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded GOL GLYCEROL × 2 T9Q N-Benzyl-2-methoxyacetamide × 2 DMS DIMETHYL SULFOXIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.19 Å R-free 0.255
9HF9 Crystal structure of human TRF1 TRFH domain in complex with compound 5 Deposited 2024-11-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded NZ1 5-methoxy-1,3-benzothiazol-2-amine × 4 GOL GLYCEROL × 8 DMS DIMETHYL SULFOXIDE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 1.90 Å R-free 0.228
9HFA Crystal structure of human TRF1 TRFH domain in complex with compound 6 Deposited 2024-11-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded TT3 2-(3-fluorophenoxy)-N,N-dimethylacetamide × 4 GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.05 Å R-free 0.246
9HFB Crystal structure of human TRF1 TRFH domain in complex with compound 7 Deposited 2024-11-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded GOL GLYCEROL × 2 JP4 [2-(morpholin-4-yl)phenyl]methanol × 2 DMS DIMETHYL SULFOXIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.29 Å R-free 0.265
9HFC Crystal structure of human TRF1 TRFH domain in complex with compound 8 Deposited 2024-11-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded GOL GLYCEROL × 2 WHM 2-[(3-fluorophenyl)methyl]-1lambda~6~,2-thiazolidine-1,1-dione × 2 DMS DIMETHYL SULFOXIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.17 Å R-free 0.243
9HFD Crystal structure of human TRF1 TRFH domain in complex with compound 9 Deposited 2024-11-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded GOL GLYCEROL × 2 VW4 (2S)-2-phenylpropane-1-sulfonamide × 2 DMS DIMETHYL SULFOXIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.15 Å R-free 0.245
9HFE Crystal structure of human TRF1 TRFH domain in complex with compound 10 Deposited 2024-11-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded PK4 2-fluoro-N,3-dimethylbenzene-1-sulfonamide × 4 GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.04 Å R-free 0.247
9HFF Crystal structure of human TRF1 TRFH domain in complex with compound 11 Deposited 2024-11-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded GOL GLYCEROL × 2 A1IUE (2~{S})-2-[(5-chloranylpyrimidin-2-yl)-methyl-amino]propan-1-ol × 2 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.06 Å R-free 0.261
9HFG Crystal structure of human TRF1 TRFH domain in complex with compound 14 Deposited 2024-11-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded GOL GLYCEROL × 2 A1A34 2-methoxy-N-[(4-methylphenyl)methyl]acetamide × 2 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.02 Å R-free 0.253
9HFH Crystal structure of human TRF1 TRFH domain in complex with compound 16 Deposited 2024-11-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded A1ITZ 5-cyclobutyl-3-pyridin-2-yl-1,2,4-oxadiazole × 4 DMS DIMETHYL SULFOXIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.12 Å R-free 0.263
9HFI Crystal structure of human TRF1 TRFH domain in complex with compound 17 Deposited 2024-11-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded GOL GLYCEROL × 2 A1BGH (3R)-3-[1-methyl-4-(trifluoromethyl)-1H-imidazol-2-yl]piperidine × 2 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.44 Å R-free 0.276
9HHK Crystal structure of human TRF1 TRFH domain in complex with compound 2 Deposited 2024-11-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded GOL GLYCEROL × 2 A1IU1 ~{N}-(furan-2-ylmethyl)-2-methyl-furan-3-carboxamide × 2 DMS DIMETHYL SULFOXIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.23 Å R-free 0.246
9HLP Crystal structure of human TRF1 TRFH domain in complex with compound 18 Deposited 2024-12-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded GOL GLYCEROL × 2 A1IV7 1-piperidin-4-ylindole × 2 DMS DIMETHYL SULFOXIDE × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.24 Å R-free 0.255
9HLQ Crystal structure of human TRF1 TRFH domain in complex with compound 57 Deposited 2024-12-05 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded HHQ 4-iodanyl-3~{H}-pyridin-2-one × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 50 mM CaCl2 and 35-45 % PEG 200, against 35 microliter of crystallisation solution.
Resolution 2.50 Å R-free 0.297
9HLR Crystal structure of human TRF1 TRFH domain in complex with compound 15 Deposited 2024-12-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded GOL GLYCEROL × 2 LL0 2-(difluoromethoxy)benzene-1-sulfonamide × 2 DMS DIMETHYL SULFOXIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.48 Å R-free 0.269
9HLT Crystal structure of human TRF1 TRFH domain in complex with compound 13 Deposited 2024-12-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded GOL GLYCEROL × 2 UJK 1-(2-methylphenyl)-1,2,3-triazole-4-carboxylic acid × 4 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.16 Å R-free 0.261
9HLU Crystal structure of human TRF1 TRFH domain in complex with compound 19 Deposited 2024-12-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 48–268（221 aa）
Not recorded UUG (4-bromo-2-methoxyphenyl)methanol × 4 DMS DIMETHYL SULFOXIDE × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.
Resolution 2.23 Å R-free 0.279

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View Construct and Data Evidence
UniProt name TERF1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–224； UniProt 48–268

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 9hcv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9hcv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9hcv
Deposition date deposition_date2024-11-11
Structure title titleCrystal structure of human TRF1 TRFH domain in complex with compound 16
Keywords keywordsTelomere, Shelterin, Inhibitor, PROTEIN BINDING; PROTEIN BINDING
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_guinier19.77 Å
Radius of gyration Rg (electron density) rg_electron19.38 Å
Forward intensity I(0) i017262400.00
Molecular weight molecular_weight21097.0 kDa
Excluded volume excluded_volume20466 ų
Envelope volume envelope_volume34462 ų
Hydration-shell volume shell_volume16070 ų
Envelope diameter envelope_diameter78.1 Å
Shell Rg shell_rg24.23 Å
Envelope Rg envelope_rg20.05 Å
Shape Rg shape_rg19.33 Å
Total Rg total_rg20.05 Å
Total atoms total_atoms1582
Residues n_residues203
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 dmax75.2 Å
Rg (real space) rg_real19.94 Å
Rg uncertainty (real space) rg_real_error0.66 Å
I(0) (real space) i0_real1.7260e+07
I(0) uncertainty (real space) i0_real_error2.3210e+05
Rg (reciprocal space) rg_reciprocal19.91 Å
I(0) (reciprocal space) i0_reciprocal17260000.0000
Solution quality estimate total_estimate0.7785
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.2 Å
Skewness Skewness skewness0.651
Kurtosis Kurtosis kurtosis0.317
Angular range angular_range— – 0.4000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2506000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.520; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.634; Smooth: 0.922
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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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8. Citations (1)

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9. Files and Curves (10)