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1vfc

Solution Structure Of The DNA Complex Of Human Trf2

Method: SOLUTION NMR Dmax: 55.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Telomeric repeat binding factor 2

Homo sapiens

UniProt Q15554

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 Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts Chain A； UniProt 438–500 Fragment：DNA BINDING DOMAIN Short G-rich strand × 1 Short C-rich starnd × 1 SOLUTION NMR NMR measurement conditions：pH 6.9；303 K；Ionic strength (raw mmCIF value) 0.005M；Pressure ambient NMR sample composition：1.0-1.5mM TRF2 labeled with 15N and 13C, and DNA; 5mM potassium phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：1.0-1.5mM TRF2 labeled with 15N,and DNA; 5mM potassium phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O Resolution not provided

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 1VFC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1H6P Dimeristion domain from human TRF2 Deposited 2001-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 43–245（203 aa） Fragment：DIMERISATION DOMAIN RESIDUES 43-245
Chain B 43–245（203 aa） Fragment：DIMERISATION DOMAIN RESIDUES 43-245
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PH7.0, 15-20% PEG 8000, 100-200 MM MAGNESIUM ACETATE, pH 7.00
Resolution 2.20 Å R-free 0.268
1VF9 Solution Structure Of Human Trf2 Deposited 2004-04-12 Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 438–500（63 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) 0.020M；Pressure ambient
NMR sample composition 1.0-1.5mM TRF2 labeled with 15N and 13C; 20mM potassium phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0-1.5mM TRF2 labeled with 15N,and DNA; 20mM potassium phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
1W0U hTRF2 DNA-binding domain in complex with telomeric DNA. Deposited 2004-06-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 446–500（55 aa） Fragment：DNA-BINDING DOMAIN, RESIDUES 446-500
Chain B 446–500（55 aa） Fragment：DNA-BINDING DOMAIN, RESIDUES 446-500
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；CRYSTALS WERE GROWN FROM 50 MM MES, PH 6.0, 5MM MAGNESIUM ACETATE, 1 MM SPERMINE, AND 2M (NH4)2SO4 AND CRYOPROTECTED IN 15 % GLYCEROL
Resolution 1.80 Å R-free 0.242
1XG1 Solution structure of Myb-domain of human TRF2 Deposited 2004-09-16 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 438–500（63 aa） Fragment：C-terminal Myb domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.3；303 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient
NMR sample composition 2mM myb, 2mM phosphate buffer pH6, 50mM NaCl | 90% H2O/10% D2O
Resolution not provided
3BU8 Crystal Structure of TRF2 TRFH domain and TIN2 peptide complex Deposited 2008-01-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 42–276（235 aa） Fragment：TRFH domain, Dimerization domain
Chain B 42–276（235 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；289 K；PEG550 MME 14%, HEPES.Na 50 mM Tris.HCl 40 mM, MgCl2 5 mM, DTT 2 mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.15 Å R-free 0.256
3BU8 Crystal Structure of TRF2 TRFH domain and TIN2 peptide complex Deposited 2008-01-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 42–276（235 aa） Fragment：TRFH domain, Dimerization domain
Chain B 42–276（235 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；289 K；PEG550 MME 14%, HEPES.Na 50 mM Tris.HCl 40 mM, MgCl2 5 mM, DTT 2 mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.15 Å R-free 0.256
3BU8 Crystal Structure of TRF2 TRFH domain and TIN2 peptide complex Deposited 2008-01-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–276（235 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；289 K；PEG550 MME 14%, HEPES.Na 50 mM Tris.HCl 40 mM, MgCl2 5 mM, DTT 2 mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.15 Å R-free 0.256
3BU8 Crystal Structure of TRF2 TRFH domain and TIN2 peptide complex Deposited 2008-01-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 42–276（235 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；289 K；PEG550 MME 14%, HEPES.Na 50 mM Tris.HCl 40 mM, MgCl2 5 mM, DTT 2 mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.15 Å R-free 0.256
3BUA Crystal Structure of TRF2 TRFH domain and APOLLO peptide complex Deposited 2008-01-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 42–245（204 aa） Fragment：TRFH domain, dimerization domain
Chain B 42–245（204 aa） Fragment：TRFH domain, dimerization domain
Chain C 42–245（204 aa） Fragment：TRFH domain, dimerization domain
Chain D 42–245（204 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 5.6；289 K；(NH4)2SO4 2.6 M DTT 1 mM MES 0.05 M pH 5.6 MgAc2 10 mM, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.50 Å R-free 0.254
3BUA Crystal Structure of TRF2 TRFH domain and APOLLO peptide complex Deposited 2008-01-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–245（204 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 5.6；289 K；(NH4)2SO4 2.6 M DTT 1 mM MES 0.05 M pH 5.6 MgAc2 10 mM, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.50 Å R-free 0.254
3BUA Crystal Structure of TRF2 TRFH domain and APOLLO peptide complex Deposited 2008-01-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 42–245（204 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 5.6；289 K；(NH4)2SO4 2.6 M DTT 1 mM MES 0.05 M pH 5.6 MgAc2 10 mM, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.50 Å R-free 0.254
3BUA Crystal Structure of TRF2 TRFH domain and APOLLO peptide complex Deposited 2008-01-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 42–245（204 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 5.6；289 K；(NH4)2SO4 2.6 M DTT 1 mM MES 0.05 M pH 5.6 MgAc2 10 mM, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.50 Å R-free 0.254
3BUA Crystal Structure of TRF2 TRFH domain and APOLLO peptide complex Deposited 2008-01-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 42–245（204 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 5.6；289 K；(NH4)2SO4 2.6 M DTT 1 mM MES 0.05 M pH 5.6 MgAc2 10 mM, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.50 Å R-free 0.254
3K6G Crystal structure of Rap1 and TRF2 complex Deposited 2009-10-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 275–316（42 aa） Fragment：TRF2 (residues 275-316)
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, HANGING DROP；pH 5.2；277 K；20% PEG2K, 16% isopropanol, 0.1 M sodium Citrate, 10 mM DTT, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.236
3K6G Crystal structure of Rap1 and TRF2 complex Deposited 2009-10-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 275–316（42 aa） Fragment：TRF2 (residues 275-316)
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, HANGING DROP；pH 5.2；277 K；20% PEG2K, 16% isopropanol, 0.1 M sodium Citrate, 10 mM DTT, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.236
3K6G Crystal structure of Rap1 and TRF2 complex Deposited 2009-10-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 275–316（42 aa） Fragment：TRF2 (residues 275-316)
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, HANGING DROP；pH 5.2；277 K；20% PEG2K, 16% isopropanol, 0.1 M sodium Citrate, 10 mM DTT, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.236
3SJM Crystal Structure Analysis of TRF2-Dbd-DNA complex Deposited 2011-06-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 441–500（60 aa）
Chain B 441–500（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM HEPES, pH 7.5, 1 mM spermine, 2 M ammonium sulfate and 40 mM Mg(OAc)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.35 Å R-free 0.208
4M7C Crystal structure of the TRF2-binding motif of SLX4 in complex with the TRFH domain of TRF2 Deposited 2013-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 45–244（200 aa） Fragment：TRFH domain, UNP residues 45-244
Chain B 45–244（200 aa） Fragment：TRFH domain, UNP residues 45-244
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；10% PEG 4000, 0.1M HEPES, pH 7.4, 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.05 Å R-free 0.262
4RQI Structure of TRF2/RAP1 secondary interaction binding site Deposited 2014-11-03 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 × 4 PDB declaration: tetrameric
Chain A 85–287（203 aa） Fragment：TRFH: residues 43-245
Chain B 85–287（203 aa） Fragment：TRFH: residues 43-245
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEGmme 550, Hepes buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.44 Å R-free 0.241
4RQI Structure of TRF2/RAP1 secondary interaction binding site Deposited 2014-11-03 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 × 4 PDB declaration: tetrameric
Chain C 85–287（203 aa） Fragment：TRFH: residues 43-245
Chain D 85–287（203 aa） Fragment：TRFH: residues 43-245
Not recorded GOL GLYCEROL × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEGmme 550, Hepes buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.44 Å R-free 0.241
5WQD Crystal structure of TRF2 TRFH in complex with an NBS1 peptide Deposited 2016-11-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 84–287（204 aa） Fragment：UNP residues 84-287
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 20% PEG8000, 2mM DTT
Resolution 3.00 Å R-free 0.284
5WQD Crystal structure of TRF2 TRFH in complex with an NBS1 peptide Deposited 2016-11-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 84–287（204 aa） Fragment：UNP residues 84-287
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 20% PEG8000, 2mM DTT
Resolution 3.00 Å R-free 0.284
5WQD Crystal structure of TRF2 TRFH in complex with an NBS1 peptide Deposited 2016-11-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 84–287（204 aa） Fragment：UNP residues 84-287
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 20% PEG8000, 2mM DTT
Resolution 3.00 Å R-free 0.284
5WQD Crystal structure of TRF2 TRFH in complex with an NBS1 peptide Deposited 2016-11-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 84–287（204 aa） Fragment：UNP residues 84-287
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 20% PEG8000, 2mM DTT
Resolution 3.00 Å R-free 0.284
5WQD Crystal structure of TRF2 TRFH in complex with an NBS1 peptide Deposited 2016-11-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 84–287（204 aa） Fragment：UNP residues 84-287
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 20% PEG8000, 2mM DTT
Resolution 3.00 Å R-free 0.284
5WQD Crystal structure of TRF2 TRFH in complex with an NBS1 peptide Deposited 2016-11-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 84–287（204 aa） Fragment：UNP residues 84-287
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 20% PEG8000, 2mM DTT
Resolution 3.00 Å R-free 0.284
5WQD Crystal structure of TRF2 TRFH in complex with an NBS1 peptide Deposited 2016-11-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 84–287（204 aa） Fragment：UNP residues 84-287
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 20% PEG8000, 2mM DTT
Resolution 3.00 Å R-free 0.284
5XYF Crystal structure of the human TIN2-TPP1-TRF2 telomeric complex Deposited 2017-07-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 392–408（17 aa） Fragment：UNP RESIDUES 392-408
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl, pH 8.5, 0.2M Magnesium chloride, 25% PEG 3350, 2mM DTT
Resolution 2.20 Å R-free 0.227
6J67 Crystal structure of the compound 34 in a complex with TRF2 Deposited 2019-01-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 84–287（204 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；30% PEG3350, 100mM MgF, 100 mM Tris-HCl, PH 8.5
Resolution 2.05 Å R-free 0.222
7C5D Crystal structure of TRF2 TRFH domain in complex with a MCPH1 peptide Deposited 2020-05-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 84–287（204 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；30% PEG400, 100 mM CHES-NaOH, pH 9.5
Resolution 2.15 Å R-free 0.235
7C5D Crystal structure of TRF2 TRFH domain in complex with a MCPH1 peptide Deposited 2020-05-19 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 84–287（204 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；30% PEG400, 100 mM CHES-NaOH, pH 9.5
Resolution 2.15 Å R-free 0.235
9Q9J Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric factor TRF2 fragment (438-542) Deposited 2025-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain J 438–542（105 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 MN MANGANESE (II) ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25mM Hepes-NaOH, pH 7.5, 150 mM NaCl, 1 mM DTT, 1 mM ATP, 1mM BeF3, 5 mM MgCl2, 1 mM MnCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
9Q9K Cryo-EM structure of human Mre11-Rad50 (MR) complex bound to DNA and telomeric factor TRF2 fragment (438-542) Deposited 2025-02-26 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 × 6 PDB declaration: octameric
Chain J 438–542（105 aa）
Chain K 438–542（105 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 MN MANGANESE (II) ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25mM Hepes-NaOH, pH 7.5, 150 mM NaCl, 1 mM DTT, 1 mM ATP, 1mM BeF3, 5 mM MgCl2, 1 mM MnCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.59 Å
9Q9M Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric factor TRF2 Deposited 2025-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain J 1–542（542 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 MN MANGANESE (II) ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25mM Hepes-NaOH, pH 7.5, 150 mM NaCl, 1 mM DTT, 1 mM ATP, 1mM BeF3, 5 mM MgCl2, 1 mM MnCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å

17 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TERF2_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–63； UniProt 438–500

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 1vfc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1vfc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1vfc
Deposition date deposition_date2004-04-12
Structure title titleSolution Structure Of The DNA Complex Of Human Trf2
Keywords keywordsMyb, helix-turn-helix, telomere, protein-DNA complex, STRUCTURAL PROTEIN-DNA COMPLEX; STRUCTURAL PROTEIN/DNA
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.81 Å
Radius of gyration Rg (electron density) rg_electron15.74 Å
Forward intensity I(0) i02397460000.00
Molecular weight molecular_weight306900.0 kDa
Excluded volume excluded_volume338900 ų
Envelope volume envelope_volume41133 ų
Hydration-shell volume shell_volume18418 ų
Envelope diameter envelope_diameter63.5 Å
Shell Rg shell_rg25.27 Å
Envelope Rg envelope_rg19.76 Å
Shape Rg shape_rg15.69 Å
Total Rg total_rg15.98 Å
Total atoms total_atoms36180
Residues n_residues1780
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 dmax55.6 Å
Rg (real space) rg_real15.80 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real2.3970e+09
I(0) uncertainty (real space) i0_real_error3.0410e+07
Rg (reciprocal space) rg_reciprocal15.80 Å
I(0) (reciprocal space) i0_reciprocal2397000000.0000
Solution quality estimate total_estimate0.6374
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary18.3 Å
Skewness Skewness skewness0.317
Kurtosis Kurtosis kurtosis-0.278
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha565400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.920; Smooth: 0.000
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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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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1vfca1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.1 — Homeodomain-like
Family Family familya.4.1.4 — DNA-binding domain of telomeric protein

CATH v4.4 (1 domains)

Domain ID domain_id1vfcA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
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8. Citations (1)

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9. Files and Curves (10)