9q9j

Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric factor TRF2 fragment (438-542)

Method: ELECTRON MICROSCOPY D_max: 163.2 Å Quality: GOOD

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

Telomeric repeat-binding factor 2

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts	Chain J； UniProt 438–542	Not recorded	DNA (64-MER) × 1 DNA (64-MER) × 1 Nibrin × 1 （O60934） DNA repair protein RAD50 × 2 （Q92878） Double-strand break repair protein MRE11 × 2 （P49959） 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

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 9Q9J	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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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） 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
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 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 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	1
Chains and sequence ranges	Author chain J； PDBConstruct 12–116； UniProt 438–542

Nibrin

Homo sapiens

UniProt O60934

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts	Chain F； UniProt 1–754	Not recorded	Telomeric repeat-binding factor 2 × 1 （Q15554） DNA (64-MER) × 1 DNA (64-MER) × 1 DNA repair protein RAD50 × 2 （Q92878） Double-strand break repair protein MRE11 × 2 （P49959） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9Q9J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5WQD Crystal structure of TRF2 TRFH in complex with an NBS1 peptide Deposited 2016-11-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 423–438（16 aa） Fragment：UNP residues 423-438	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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 423–438（16 aa） Fragment：UNP residues 423-438	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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 423–438（16 aa） Fragment：UNP residues 423-438	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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 423–438（16 aa） Fragment：UNP residues 423-438	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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 423–438（16 aa） Fragment：UNP residues 423-438	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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 423–438（16 aa） Fragment：UNP residues 423-438	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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 423–438（16 aa） Fragment：UNP residues 423-438	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
7SID Human ATM Dimer Bound to Nbs1 Deposited 2021-10-13	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 B 727–754（28 aa） Chain D 727–754（28 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
8BAH Human Mre11-Nbs1 complex Deposited 2022-10-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–754（754 aa）	Not recorded	MN MANGANESE (II) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7；20 mM HEPES (pH 7.0), 140 mM NaCl, 5 mM MgCl2, 1 mM MnCl2, 0.020 mM ZnCl2, 0.2 mM TCEP, 2 mM ATPgS, plus 0.05 percent beta-OG cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.13 Å
9Q9I Cryo-EM structure of human Mre11-Rad50-Nbs1 complex bound to DNA Deposited 2025-02-26	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain F 1–754（754 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 MN MANGANESE (II) ION × 2	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 2.79 Å
9Q9M Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric factor TRF2 Deposited 2025-02-26	Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain F 1–754（754 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
9ULO Cryo-EM structure of Human Mre11-Nbs1 complex Deposited 2025-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–754（754 aa）	Not recorded	MN MANGANESE (II) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.91 Å

6 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NBN_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–754； UniProt 1–754

DNA repair protein RAD50

Homo sapiens

UniProt Q92878

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts	Chain A； UniProt 1–1312 Chain B； UniProt 1–1312	Not recorded	Telomeric repeat-binding factor 2 × 1 （Q15554） DNA (64-MER) × 1 DNA (64-MER) × 1 Nibrin × 1 （O60934） Double-strand break repair protein MRE11 × 2 （P49959） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9Q9J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5GOX Eukaryotic Rad50 Functions as A Rod-shaped Dimer Deposited 2016-07-30	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 585–766（182 aa） Fragment：UNP residues 585-766 Chain B 585–766（182 aa） Fragment：UNP residues 585-766	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；291 K；28 - 30% PEG 600, 0.1 M bis-tris propane, 3% 1, 6-hexanediol, 5 mM DTT	Resolution 2.40 Å R-free 0.271
9Q9H Cryo-EM structure of human Mre11-Rad50 complex bound to DNA Deposited 2025-02-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 1–1312（1312 aa） Chain B 1–1312（1312 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 3.11 Å
9Q9I Cryo-EM structure of human Mre11-Rad50-Nbs1 complex bound to DNA Deposited 2025-02-26	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain A 1–1312（1312 aa） Chain B 1–1312（1312 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 MN MANGANESE (II) ION × 2	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 2.79 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–1312（1312 aa） Chain B 1–1312（1312 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–1312（1312 aa） Chain B 1–1312（1312 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

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

View Construct and Data Evidence

UniProt name	RAD50_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain A； PDBConstruct 1–1312； UniProt 1–1312 Author chain B； PDBConstruct 1–1312； UniProt 1–1312

Double-strand break repair protein MRE11

Homo sapiens

UniProt P49959

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts	Chain D； UniProt 1–708 Chain E； UniProt 1–708	Not recorded	Telomeric repeat-binding factor 2 × 1 （Q15554） DNA (64-MER) × 1 DNA (64-MER) × 1 Nibrin × 1 （O60934） DNA repair protein RAD50 × 2 （Q92878） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9Q9J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3T1I Crystal Structure of Human Mre11: Understanding Tumorigenic Mutations Deposited 2011-07-22	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 1–411（411 aa） Fragment：UNP residues 1-411 Chain B 1–411（411 aa） Fragment：UNP residues 1-411	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 4 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；14% PEG 3350, 0.1M Bicne, 0.5mM manganese chloride, 2mM Dithiothreitol, 4mM Glutathione, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.00 Å R-free 0.250
3T1I Crystal Structure of Human Mre11: Understanding Tumorigenic Mutations Deposited 2011-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–411（411 aa） Fragment：UNP residues 1-411 Chain D 1–411（411 aa） Fragment：UNP residues 1-411	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 4 GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；14% PEG 3350, 0.1M Bicne, 0.5mM manganese chloride, 2mM Dithiothreitol, 4mM Glutathione, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.00 Å R-free 0.250
8BAH Human Mre11-Nbs1 complex Deposited 2022-10-11	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–708（708 aa） Chain B 1–708（708 aa）	Mutation：H129N Mutation：H129N	MN MANGANESE (II) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7；20 mM HEPES (pH 7.0), 140 mM NaCl, 5 mM MgCl2, 1 mM MnCl2, 0.020 mM ZnCl2, 0.2 mM TCEP, 2 mM ATPgS, plus 0.05 percent beta-OG cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.13 Å
8K00 RPA70N-MRE11 fusion Deposited 2023-07-07	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 × 2 PDB declaration: dimeric	Chain B 538–563（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Ammonium sulate	Resolution 1.40 Å R-free 0.199
9Q9H Cryo-EM structure of human Mre11-Rad50 complex bound to DNA Deposited 2025-02-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain D 1–708（708 aa） Chain E 1–708（708 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 3.11 Å
9Q9I Cryo-EM structure of human Mre11-Rad50-Nbs1 complex bound to DNA Deposited 2025-02-26	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain D 1–708（708 aa） Chain E 1–708（708 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 MN MANGANESE (II) ION × 2	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 2.79 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain D 1–708（708 aa） Chain E 1–708（708 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 structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain D 1–708（708 aa） Chain E 1–708（708 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
9ULO Cryo-EM structure of Human Mre11-Nbs1 complex Deposited 2025-04-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–708（708 aa） Chain B 1–708（708 aa）	Not recorded	MN MANGANESE (II) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.91 Å

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MRE11_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain D； PDBConstruct 1–708； UniProt 1–708 Author chain E； PDBConstruct 1–708； UniProt 1–708

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	9q9j
Deposition date deposition_date	2025-02-26
最后修订 last_revision	2025-10-01
Structure title title	Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric factor TRF2 fragment (438-542)
Keywords keywords	Mre11-Rad50-Nbs1 complex, double-strand DNA break repair protein, nuclease, HYDROLASE; HYDROLASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	43.80 Å
Radius of gyration Rg (electron density) rg_electron	44.07 Å
Forward intensity I(0) i0	997932000.00
Molecular weight molecular_weight	249190.0 kDa
Excluded volume excluded_volume	307400 Å³
Envelope volume envelope_volume	413570 Å³
Hydration-shell volume shell_volume	78851 Å³
Envelope diameter envelope_diameter	173.9 Å
Shell Rg shell_rg	48.05 Å
Envelope Rg envelope_rg	44.58 Å
Shape Rg shape_rg	44.10 Å
Total Rg total_rg	44.13 Å
Total atoms total_atoms	17435
Residues n_residues	2056
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	163.2 Å
Rg (real space) rg_real	44.01 Å
Rg uncertainty (real space) rg_real_error	1.87 Å
I(0) (real space) i0_real	9.9790e+08
I(0) uncertainty (real space) i0_real_error	1.9960e+07
Rg (reciprocal space) rg_reciprocal	43.80 Å
I(0) (reciprocal space) i0_reciprocal	997700000.0000
Solution quality estimate total_estimate	0.8073
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	49.9 Å
Skewness Skewness skewness	0.654
Kurtosis Kurtosis kurtosis	0.490
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	151800000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.536; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.917

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	Telomeric repeat-binding factor 2
Molecular weight formula_weight	12931.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J
Atom count atom_count	17465

GPGGSSGGSSGQPLPGEKNPKVPKGKWNSSNGVEEKETWVEEDELFQVQAAPDEDSTTNITKKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKRLGMN

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	DNA (64-MER)
Molecular weight formula_weight	19423.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	P

TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Entity 3 Entity 3 polymer

Description description	DNA (64-MER)
Molecular weight formula_weight	20000.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Entity 4 Entity 4 polymer

Description description	Nibrin
Molecular weight formula_weight	85073.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MWKLLPAAGPAGGEPYRLLTGVEYVVGRKNCAILIENDQSISRNHAVLTANFSVTNLSQTDEIPVLTLKDNSKYGTFVNEEKMQNGFSRTLKSGDGITFGVFGSKFRIEYEPLVACSSCLDVSGKTALNQAILQLGGFTVNNWTEECTHLVMVSVKVTIKTICALICGRPIVKPEYFTEFLKAVESKKQPPQIESFYPPLDEPSIGSKNVDLSGRQERKQIFKGKTFIFLNAKQHKKLSSAVVFGGGEARLITEENEEEHNFFLAPGTCVVDTGITNSQTLIPDCQKKWIQSIMDMLQRQGLRPIPEAEIGLAVIFMTTKNYCDPQGHPSTGLKTTTPGPSLSQGVSVDEKLMPSAPVNTTTYVADTESEQADTWDLSERPKEIKVSKMEQKFRMLSQDAPTVKESCKTSSNNNSMVSNTLAKMRIPNYQLSPTKLPSINKSKDRASQQQQTNSIRNYFQPSTKKRERDEENQEMSSCKSARIETSCSLLEQTQPATPSLWKNKEQHLSENEPVDTNSDNNLFTDTDLKSIVKNSASKSHAAEKLRSNKKREMDDVAIEDEVLEQLFKDTKPELEIDVKVQKQEEDVNVRKRPRMDIETNDTFSDEAVPESSKISQENEIGKKRELKEDSLWSAKEISNNDKLQDDSEMLPKKLLLTEFRSLVIKNSTSRNPSGINDDYGQLKNFKKFKKVTYPGAGKLPHIIGGSDLIAHHARKNTELEEWLRQEMEVQNQHAKEESLADDLFRYNPYLKRRR

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	Trichoplusia ni

Entity 5 Entity 5 polymer

Description description	DNA repair protein RAD50
Molecular weight formula_weight	154150.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MSRIEKMSILGVRSFGIEDKDKQIITFFSPLTILVGPNGAGKTTIIECLKYICTGDFPPGTKGNTFVHDPKVAQETDVRAQIRLQFRDVNGELIAVQRSMVCTQKSKKTEFKTLEGVITRTKHGEKVSLSSKCAEIDREMISSLGVSKAVLNNVIFCHQEDSNWPLSEGKALKQKFDEIFSATRYIKALETLRQVRQTQGQKVKEYQMELKYLKQYKEKACEIRDQITSKEAQLTSSKEIVKSYENELDPLKNRLKEIEHNLSKIMKLDNEIKALDSRKKQMEKDNSELEEKMEKVFQGTDEQLNDLYHNHQRTVREKERKLVDCHRELEKLNKESRLLNQEKSELLVEQGRLQLQADRHQEHIRARDSLIQSLATQLELDGFERGPFSERQIKNFHKLVRERQEGEAKTANQLMNDFAEKETLKQKQIDEIRDKKTGLGRIIELKSEILSKKQNELKNVKYELQQLEGSSDRILELDQELIKAERELSKAEKNSNVETLKMEVISLQNEKADLDRTLRKLDQEMEQLNHHTTTRTQMEMLTKDKADKDEQIRKIKSRHSDELTSLLGYFPNKKQLEDWLHSKSKEINQTRDRLAKLNKELASSEQNKNHINNELKRKEEQLSSYEDKLFDVCGSQDFESDLDRLKEEIEKSSKQRAMLAGATAVYSQFITQLTDENQSCCPVCQRVFQTEAELQEVISDLQSKLRLAPDKLKSTESELKKKEKRRDEMLGLVPMRQSIIDLKEKEIPELRNKLQNVNRDIQRLKNDIEEQETLLGTIMPEEESAKVCLTDVTIMERFQMELKDVERKIAQQAAKLQGIDLDRTVQQVNQEKQEKQHKLDTVSSKIELNRKLIQDQQEQIQHLKSTTNELKSEKLQISTNLQRRQQLEEQTVELSTEVQSLYREIKDAKEQVSPLETTLEKFQQEKEELINKKNTSNKIAQDKLNDIKEKVKNIHGYMKDIENYIQDGKDDYKKQKETELNKVIAQLSECEKHKEKINEDMRLMRQDIDTQKIQERWLQDNLTLRKRNEELKEVEEERKQHLKEMGQMQVLQMKSEHQKLEENIDNIKRNHNLALGRQKGYEEEIIHFKKELREPQFRDAEEKYREMMIVMRTTELVNKDLDIYYKTLDQAIMKFHSMKMEEINKIIRDLWRSTYRGQDIEYIEIRSDADENVSASDKRRNYNYRVVMLKGDTALDMRGRCSAGQKVLASLIIRLALAETFCLNCGIIALDEPTTNLDRENIESLAHALVEIIKSRSQQRNFQLLVITHDEDFVELLGRSEYVEKFYRIKKNIDQCSEIVKCSVSSLGFNVH

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	Trichoplusia ni

Entity 6 Entity 6 polymer

Description description	Double-strand break repair protein MRE11
Molecular weight formula_weight	84032.7 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSTADALDDENTFKILVATDIHLGFMEKDAVRGNDTFVTLDEILRLAQENEVDFILLGGDLFHENKPSRKTLHTCLELLRKYCMGDRPVQFEILSDQSVNFGFSKFPWVNYQDGNLNISIPVFSIHGNHDDPTGADALCALDILSCAGFVNHFGRSMSVEKIDISPVLLQKGSTKIALYGLGSIPDERLYRMFVNKKVTMLRPKEDENSWFNLFVIHQNRSKHGSTNFIPEQFLDDFIDLVIWGHEHECKIAPTKNEQQLFYISQPGSSVVTSLSPGEAVKKHVGLLRIKGRKMNMHKIPLHTVRQFFMEDIVLANHPDIFNPDNPKVTQAIQSFCLEKIEEMLENAERERLGNSHQPEKPLVRLRVDYSGGFEPFSVLRFSQKFVDRVANPKDIIHFFRHREQKEKTGEEINFGKLITKPSEGTTLRVEDLVKQYFQTAEKNVQLSLLTERGMGEAVQEFVDKEEKDAIEELVKYQLEKTQRFLKERHIDALEDKIDEEVRRFRETRQKNTNEEDDEVREAMTRARALRSQSEESASAFSADDLMSIDLAEQMANDSDDSISAATNKGRGRGRGRRGGRGQNSASRGGSQRGRADTGLETSTRSRNSKTAVSASRNMSIIDAFKSTRQQPSRNVTTKNYSEVIEVDESDVEEDIFPTTSKTDQRWSSTSSSKIMSQSQVSKGVDFESSEDDDDDPFMNTSSLRRNRRSGGSLEVLFQGPDYKDDDDKGTDYKDDDDK

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	Trichoplusia ni

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.71 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	129300

fit	/app/data/saxs_computation/q9/9q9j/9q9j.fit
pddf	/app/data/pr_computation/q9/9q9j/9q9j.pr.out
profile	/app/data/saxs_computation/q9/9q9j/9q9j.dat

Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric factor TRF2 fragment (438-542)

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

Telomeric repeat-binding factor 2

State in the Current Structure

Other States of the Same Protein in the Database

Nibrin

State in the Current Structure

Other States of the Same Protein in the Database

DNA repair protein RAD50

State in the Current Structure

Other States of the Same Protein in the Database

Double-strand break repair protein MRE11

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)