9dhk

RMI1-RMI2 bound to cyclic peptide L3

Method: X-RAY DIFFRACTION Dmax: 122.9 Å Quality: EXCELLENT

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

RecQ-mediated genome instability protein 1

Homo sapiens

UniProt Q9H9A7

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 475–625 Not recorded RecQ-mediated genome instability protein 2 × 1 (Q96E14) L3 peptide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0 Resolution 2.35 Å R-free 0.247
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 475–625 Not recorded RecQ-mediated genome instability protein 2 × 1 (Q96E14) L3 peptide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0 Resolution 2.35 Å R-free 0.247
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain G; UniProt 482–625 Not recorded RecQ-mediated genome instability protein 2 × 1 (Q96E14) L3 peptide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0 Resolution 2.35 Å R-free 0.247
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain J; UniProt 475–625 Not recorded RecQ-mediated genome instability protein 2 × 1 (Q96E14) L3 peptide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0 Resolution 2.35 Å R-free 0.247

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.

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

View Construct and Data Evidence
UniProt name RMI1_HUMAN
Isoform
PDB entities 1, 4
Chains and sequence ranges Author chain A; PDBConstruct 2–152; UniProt 475–625 Author chain D; PDBConstruct 2–152; UniProt 475–625 Author chain J; PDBConstruct 2–152; UniProt 475–625 Author chain G; PDBConstruct 2–145; UniProt 482–625

RecQ-mediated genome instability protein 2

Homo sapiens

UniProt Q96E14

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 B; UniProt 1–147 Not recorded RecQ-mediated genome instability protein 1 × 1 (Q9H9A7) L3 peptide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0 Resolution 2.35 Å R-free 0.247
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 14–147 Not recorded RecQ-mediated genome instability protein 1 × 1 (Q9H9A7) L3 peptide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0 Resolution 2.35 Å R-free 0.247
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain H; UniProt 15–147 Not recorded RecQ-mediated genome instability protein 1 × 1 (Q9H9A7) L3 peptide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0 Resolution 2.35 Å R-free 0.247
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain K; UniProt 1–147 Not recorded RecQ-mediated genome instability protein 1 × 1 (Q9H9A7) L3 peptide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0 Resolution 2.35 Å R-free 0.247

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.

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

View Construct and Data Evidence
UniProt name RMI2_HUMAN
Isoform
PDB entities 2, 3, 5
Chains and sequence ranges Author chain B; PDBConstruct 1–147; UniProt 1–147 Author chain K; PDBConstruct 1–147; UniProt 1–147 Author chain E; PDBConstruct 2–135; UniProt 14–147 Author chain H; PDBConstruct 7–139; UniProt 15–147

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 9dhk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9dhk
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id9dhk
Deposition date deposition_date2024-09-03
Structure title titleRMI1-RMI2 bound to cyclic peptide L3
Keywords keywordsDNA damage repair, complex, cyclic peptide, competitive inhibitor, NUCLEAR PROTEIN; NUCLEAR PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier38.46
Radius of gyration Rg (electron density) rg_electron37.80
Forward intensity I(0) i0252659000.00
Molecular weight molecular_weight130760.0 kDa
Excluded volume excluded_volume164810 ų
Envelope volume envelope_volume217110 ų
Hydration-shell volume shell_volume48644 ų
Envelope diameter envelope_diameter128.2
Shell Rg shell_rg43.07
Envelope Rg envelope_rg37.11
Shape Rg shape_rg37.79
Total Rg total_rg38.15
Total atoms total_atoms18525
Residues n_residues1172
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax122.9
Rg (real space) rg_real38.33
Rg uncertainty (real space) rg_real_error1.02
I(0) (real space) i0_real2.5270e+08
I(0) uncertainty (real space) i0_real_error4.2010e+06
Rg (reciprocal space) rg_reciprocal38.41
I(0) (reciprocal space) i0_reciprocal252700000.0000
Solution quality estimate total_estimate0.9002
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.0
Skewness Skewness skewness0.136
Kurtosis Kurtosis kurtosis-0.627
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha43210000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.900

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)