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8bah

Human Mre11-Nbs1 complex

Method: ELECTRON MICROSCOPY Dmax: 109.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–708 Chain B； UniProt 1–708 Mutation：H129N Nibrin × 1 （O60934） 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

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 8BAH 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
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 2.71 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 mutation/modification 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 1
Chains and sequence ranges Author chain A； PDBConstruct 1–708； UniProt 1–708 Author chain B； PDBConstruct 1–708； UniProt 1–708

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 1–754 Not recorded Double-strand break repair protein MRE11 × 2 （P49959） 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

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 8BAH 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
9Q9I Cryo-EM structure of human Mre11-Rad50-Nbs1 complex bound to DNA Deposited 2025-02-26 Different oligomeric state Different ligand/ion Different experimental conditions 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
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 oligomeric state Different ligand/ion Different experimental conditions 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 2.71 Å
9Q9M Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric factor TRF2 Deposited 2025-02-26 Different oligomeric state Different ligand/ion Different experimental conditions 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 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 2
Chains and sequence ranges Author chain C； PDBConstruct 1–754； UniProt 1–754

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8bah

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8bah
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8bah
Deposition date deposition_date2022-10-11
Structure title titleHuman Mre11-Nbs1 complex
Keywords keywordsDNA repair, complex, HYDROLASE; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.39 Å
Radius of gyration Rg (electron density) rg_electron32.87 Å
Forward intensity I(0) i0147757000.00
Molecular weight molecular_weight97624.0 kDa
Excluded volume excluded_volume122440 ų
Envelope volume envelope_volume155930 ų
Hydration-shell volume shell_volume40158 ų
Envelope diameter envelope_diameter116.2 Å
Shell Rg shell_rg38.95 Å
Envelope Rg envelope_rg33.11 Å
Shape Rg shape_rg32.91 Å
Total Rg total_rg33.26 Å
Total atoms total_atoms13675
Residues n_residues855
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax109.3 Å
Rg (real space) rg_real33.39 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real1.4780e+08
I(0) uncertainty (real space) i0_real_error2.1330e+06
Rg (reciprocal space) rg_reciprocal33.39 Å
I(0) (reciprocal space) i0_reciprocal147800000.0000
Solution quality estimate total_estimate0.8912
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.9 Å
Skewness Skewness skewness0.299
Kurtosis Kurtosis kurtosis-0.510
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29740000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.889
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)