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9l4c

ATR Spiral -ATRIP bound with RP-3500

Method: ELECTRON MICROSCOPY Dmax: 170.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein kinase ATR

Homo sapiens

UniProt Q13535

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–2644 Chain B； UniProt 1–2644 Not recorded ATR-interacting protein × 2 （Q8WXE1） ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.06 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 9L4C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
23FC Cryo-EM structure of human ATR-ATRIP complex with ATPgammaS and Chk1 Deposited 2026-02-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–2644（2644 aa）
Chain B 1–2644（2644 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
5YZ0 Cryo-EM Structure of human ATR-ATRIP complex Deposited 2017-12-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–2644（2644 aa）
Chain B 1–2644（2644 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
9L40 kinase of ATR bound VE-822 state Deposited 2024-12-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–2644（2644 aa）
Chain B 1–2644（2644 aa）
Not recorded A1EIE VE-822 × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
9L43 ATR Spiral -ATRIP bound with VE-822 Deposited 2024-12-19 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–2644（2644 aa）
Chain B 1–2644（2644 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
9L45 ATR-ATRIP bound with VE-822 Deposited 2024-12-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–2644（2644 aa）
Chain B 1–2644（2644 aa）
Not recorded A1EIE VE-822 × 4 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
9L46 ATR-ATRIP-bound with AMP-PNP Deposited 2024-12-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–2644（2644 aa）
Chain B 1–2644（2644 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.29 Å
9L4B Kinase domain of ATR bound with RP-3500 Deposited 2024-12-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–2644（2644 aa）
Chain B 1–2644（2644 aa）
Not recorded A1EIK Camonsertib × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9L4D ATR-ATRIP bound with RP-3500 Deposited 2024-12-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 8–2644（2637 aa）
Chain B 8–2644（2637 aa）
Not recorded A1EIK Camonsertib × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
9L4F ATR-ATRIP bound with ATPgammaS Deposited 2024-12-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–2644（2644 aa）
Chain B 1–2644（2644 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.22 Å

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

View Construct and Data Evidence
UniProt name ATR_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–2644； UniProt 1–2644 Author chain B； PDBConstruct 1–2644； UniProt 1–2644

ATR-interacting protein

Homo sapiens

UniProt Q8WXE1

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 1–791 Chain D； UniProt 1–791 Not recorded Serine/threonine-protein kinase ATR × 2 （Q13535） ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.06 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 9L4C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
23FC Cryo-EM structure of human ATR-ATRIP complex with ATPgammaS and Chk1 Deposited 2026-02-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–791（791 aa）
Chain D 1–791（791 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
4IGK Structure of human BRCA1 BRCT in complex with ATRIP peptide Deposited 2012-12-17 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 C 237–243（7 aa） Fragment：UNP residues 237-243
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG3350, 0.2 M ammonium acetate, 8% glycerol, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.75 Å R-free 0.204
4IGK Structure of human BRCA1 BRCT in complex with ATRIP peptide Deposited 2012-12-17 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 D 237–243（7 aa） Fragment：UNP residues 237-243
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG3350, 0.2 M ammonium acetate, 8% glycerol, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.75 Å R-free 0.204
5YZ0 Cryo-EM Structure of human ATR-ATRIP complex Deposited 2017-12-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–791（791 aa）
Chain D 1–791（791 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
7XV4 Crystal structure of RPA70N-ATRIP fusion Deposited 2022-05-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 53–69（17 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；278 K；2400 mM ammonium sulfate
Resolution 1.60 Å R-free 0.224
9L43 ATR Spiral -ATRIP bound with VE-822 Deposited 2024-12-19 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–791（791 aa）
Chain D 1–791（791 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
9L45 ATR-ATRIP bound with VE-822 Deposited 2024-12-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–791（791 aa）
Chain D 1–791（791 aa）
Not recorded A1EIE VE-822 × 4 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
9L46 ATR-ATRIP-bound with AMP-PNP Deposited 2024-12-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–791（791 aa）
Chain D 1–791（791 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.29 Å
9L4D ATR-ATRIP bound with RP-3500 Deposited 2024-12-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 301–791（491 aa）
Chain D 301–791（491 aa）
Not recorded A1EIK Camonsertib × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
9L4F ATR-ATRIP bound with ATPgammaS Deposited 2024-12-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–791（791 aa）
Chain D 1–791（791 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.22 Å

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ATRIP_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–791； UniProt 1–791 Author chain D； PDBConstruct 1–791； UniProt 1–791

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 9l4c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9l4c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9l4c
Deposition date deposition_date2024-12-20
Structure title titleATR Spiral -ATRIP bound with RP-3500
Keywords keywordsATR spiral ATRIP RP-3500, CELL CYCLE; CELL CYCLE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier48.94 Å
Radius of gyration Rg (electron density) rg_electron48.62 Å
Forward intensity I(0) i0735595000.00
Molecular weight molecular_weight191890.0 kDa
Excluded volume excluded_volume225810 ų
Envelope volume envelope_volume410590 ų
Hydration-shell volume shell_volume72040 ų
Envelope diameter envelope_diameter172.2 Å
Shell Rg shell_rg50.06 Å
Envelope Rg envelope_rg48.37 Å
Shape Rg shape_rg48.70 Å
Total Rg total_rg48.46 Å
Total atoms total_atoms21507
Residues n_residues2468
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 dmax170.1 Å
Rg (real space) rg_real49.15 Å
Rg uncertainty (real space) rg_real_error1.68 Å
I(0) (real space) i0_real7.3560e+08
I(0) uncertainty (real space) i0_real_error1.4200e+07
Rg (reciprocal space) rg_reciprocal48.94 Å
I(0) (reciprocal space) i0_reciprocal735400000.0000
Solution quality estimate total_estimate0.8525
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary58.5 Å
Skewness Skewness skewness0.445
Kurtosis Kurtosis kurtosis-0.253
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha52540000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.770; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.785
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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)