3k6g

Crystal structure of Rap1 and TRF2 complex

Method: X-RAY DIFFRACTION D_max: 85.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Telomeric repeat-binding factor 2-interacting protein 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 303–399	Fragment：Rap1 C-terminal domain (residues 303-399) Non-standard monomer：Yes (specific site not provided by mmCIF)	Telomeric repeat-binding factor 2 × 1 （Q15554）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 303–399	Fragment：Rap1 C-terminal domain (residues 303-399) Non-standard monomer：Yes (specific site not provided by mmCIF)	Telomeric repeat-binding factor 2 × 1 （Q15554）	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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 303–399	Fragment：Rap1 C-terminal domain (residues 303-399) Non-standard monomer：Yes (specific site not provided by mmCIF)	Telomeric repeat-binding factor 2 × 1 （Q15554）	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

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 3K6G	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FEX SOLUTION STRUCTURE OF MYB-DOMAIN OF HUMAN RAP1 Deposited 2000-07-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 132–190（59 aa） Fragment：MYB-DOMAIN	Mutation：25MDR	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；300 K；Pressure 1 NMR sample composition 1.0mM protein concentration in 100mM potassium phosphate buffer pH5.5, 1mM NaN3 ; 90%H2O, 10%D2O \| 90% H2O/10% D2O	Resolution not provided
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 conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 89–106（18 aa） Fragment：YXLXP interaction motif: residues 89-106 Chain F 89–106（18 aa） Fragment：YXLXP interaction motif: residues 89-106	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 conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 89–106（18 aa） Fragment：YXLXP interaction motif: residues 89-106 Chain H 89–106（18 aa） Fragment：YXLXP interaction motif: residues 89-106	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
7OZ0 Solution structure of the N-terminal domain of human telomeric Repeat-binding factor 2-interacting protein 1 (hRap1): implication for Rap1-TRF2 interaction in Human. Deposited 2021-06-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–114（114 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure 1 NMR sample composition 100 uM [U-100% 13C; U-100% 15N] human Telomeric Repeat-binding factor 2-interacting protein 1 (hRAP1), 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8RD4 Telomeric RAP1:DNA-PK complex Deposited 2023-12-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain D 1–399（399 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TE2IP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–98； UniProt 303–399 Author chain B； PDBConstruct 2–98； UniProt 303–399 Author chain C； PDBConstruct 2–98； UniProt 303–399

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 275–316	Fragment：TRF2 (residues 275-316) Non-standard monomer：Yes (specific site not provided by mmCIF)	Telomeric repeat-binding factor 2-interacting protein 1 × 1 （Q9NYB0）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 275–316	Fragment：TRF2 (residues 275-316) Non-standard monomer：Yes (specific site not provided by mmCIF)	Telomeric repeat-binding factor 2-interacting protein 1 × 1 （Q9NYB0）	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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 275–316	Fragment：TRF2 (residues 275-316) Non-standard monomer：Yes (specific site not provided by mmCIF)	Telomeric repeat-binding factor 2-interacting protein 1 × 1 （Q9NYB0）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3K6G	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 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 construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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
1VFC Solution Structure Of The DNA Complex Of Human Trf2 Deposited 2004-04-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 438–500（63 aa） Fragment：DNA BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.9；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
1W0U hTRF2 DNA-binding domain in complex with telomeric DNA. Deposited 2004-06-11	Different construct Different mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 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 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 mutation/modification 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 mutation/modification 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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
3SJM Crystal Structure Analysis of TRF2-Dbd-DNA complex Deposited 2011-06-21	Different construct Different mutation/modification Different oligomeric state 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 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 mutation/modification Different ligand/ion 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 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）	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 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 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 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TERF2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–42； UniProt 275–316 Author chain E； PDBConstruct 1–42； UniProt 275–316 Author chain F； PDBConstruct 1–42； UniProt 275–316

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3k6g
Deposition date deposition_date	2009-10-08
Structure title title	Crystal structure of Rap1 and TRF2 complex
Keywords keywords	helix, Chromosomal protein, Nucleus, Phosphoprotein, Telomere, Cell cycle, DNA-binding, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.43 Å
Radius of gyration Rg (electron density) rg_electron	26.02 Å
Forward intensity I(0) i0	31950300.00
Molecular weight molecular_weight	42518.0 kDa
Excluded volume excluded_volume	52839 Å³
Envelope volume envelope_volume	68137 Å³
Hydration-shell volume shell_volume	23201 Å³
Envelope diameter envelope_diameter	89.5 Å
Shell Rg shell_rg	31.48 Å
Envelope Rg envelope_rg	25.84 Å
Shape Rg shape_rg	26.04 Å
Total Rg total_rg	26.60 Å
Total atoms total_atoms	2959
Residues n_residues	371
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	85.8 Å
Rg (real space) rg_real	26.54 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	3.1950e+07
I(0) uncertainty (real space) i0_real_error	4.8820e+05
Rg (reciprocal space) rg_reciprocal	26.51 Å
I(0) (reciprocal space) i0_reciprocal	31950000.0000
Solution quality estimate total_estimate	0.8915
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.2 Å
Skewness Skewness skewness	0.411
Kurtosis Kurtosis kurtosis	-0.368
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6097000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.926

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Telomeric repeat-binding factor 2-interacting protein 1
Molecular weight formula_weight	12110.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3184

SEEKVSQPEVGAAIKIIRQLMEKFNLDLSTVTQAFLKNSGELEATSAFLASGQRADGYPIWSRQDDIDLQKDDEDTREALVKKFGAQNVARRIEFRKKGGSGGSGGSGGKL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Telomeric repeat-binding factor 2
Molecular weight formula_weight	4617.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

QLRNPPTTIGMMTLKAAFKTLSGAQDSEAAFAKLDQKDLVLP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	225

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8. Citations (1)

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Unit-cell length a length_a	42.568 Å
Unit-cell length b length_b	72.105 Å
Unit-cell length c length_c	150.993 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2242
R_free r_free	0.2356

fit	/app/data/saxs_computation/k6/3k6g/3k6g.fit
pddf	/app/data/pr_computation/k6/3k6g/3k6g.pr.out
profile	/app/data/saxs_computation/k6/3k6g/3k6g.dat

Crystal structure of Rap1 and TRF2 complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Telomeric repeat-binding factor 2-interacting protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Telomeric repeat-binding factor 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)