5eay

Crystal structure of a Dna2 peptide in complex with Rpa 70N

Method: X-RAY DIFFRACTION D_max: 86.7 Å Quality: GOOD

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

Replication protein A 70 kDa DNA-binding subunit

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 3–120 Chain B； UniProt 3–120 Chain C； UniProt 3–120 Chain D； UniProt 3–120	Fragment：UNP residues 3-120	DNA replication ATP-dependent helicase/nuclease DNA2 × 4 （P51530）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；50 mM Tris-HCl, 35 % PEG 1500, 2 mM TCEP, pH 8.0	Resolution 1.55 Å R-free 0.267

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 5EAY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EWI HUMAN REPLICATION PROTEIN A: GLOBAL FOLD OF THE N-TERMINAL RPA-70 DOMAIN REVEALS A BASIC CLEFT AND FLEXIBLE C-TERMINAL LINKER Deposited 2000-04-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–114（114 aa） Fragment：N-TERMINAL FRAGMENT (RESIDUES 1-114)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.6；298 K；Ionic strength (raw mmCIF value) 50 mM；Pressure ambient NMR sample composition 1mM d169, 100 mM Tris, 100 mM Tris-HCL, 0.25 mM EDTA, 50 mM NaCl, 0.2% NaN3 and 1mM DTT, pH 7.6 \| 90% H20, 10% D20	Resolution not provided
1FGU SSDNA-BINDING DOMAIN OF THE LARGE SUBUNIT OF REPLICATION PROTEIN A Deposited 2000-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 182–432（251 aa） Fragment：CENTRAL DOMAIN Chain B 182–432（251 aa） Fragment：CENTRAL DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.1 M K,NaH2PO4 0.1 M Tris 3.8 M NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.50 Å R-free 0.281
1JMC SINGLE STRANDED DNA-BINDING DOMAIN OF HUMAN REPLICATION PROTEIN A BOUND TO SINGLE STRANDED DNA, RPA70 SUBUNIT, RESIDUES 183-420 Deposited 1996-11-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 181–422（242 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；24-27% PEG2000 MME, 20MM NA_CL, 20MM MGCL2, 5MM DTT, 100MM MES PH 6.8, VAPOR DIFFUSION, SITTING DROP	Resolution 2.40 Å R-free 0.330
1L1O Structure of the human Replication Protein A (RPA) trimerization core Deposited 2002-02-19	Different construct Different mutation/modification 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 436–616（181 aa） Fragment：RPA70 C-terminal domain (residues 436-616) Chain F 436–616（181 aa） Fragment：RPA70 C-terminal domain (residues 436-616)	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；300 K；0.1 M Hepes, 9% glycerol, and 1.6 M ammonium sulfate, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 300K	Resolution 2.80 Å R-free 0.282
2B29 N-terminal domain of the RPA70 subunit of human replication protein A. Deposited 2005-09-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：N-terminal domain (Residues 1-120)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ammonium Sulphate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.261
2B3G p53N (fragment 33-60) bound to RPA70N Deposited 2005-09-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–120（120 aa） Fragment：N-terminal domain (Residues 1-120)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.9；298 K；Na3 Citrate, Hepes, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.90	Resolution 1.60 Å R-free 0.239
4IJH Fragment-based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A Deposited 2012-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：N-terminal domain (UNP residues 1-120)	Mutation：E7R	1EJ 3-chloro-6-[3-(4-fluorophenyl)-5-sulfanyl-4H-1,2,4-triazol-4-yl]-1-benzothiophene-2-carboxylic acid × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；100 mM MES, 200 mM calcium acetate, 15% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.50 Å R-free 0.189
4IJL Fragment-based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A Deposited 2012-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：N-terminal domain (UNP residues 1-120)	Mutation：E7R	1EK {[5-(3-chloro-1-benzothiophen-2-yl)-4-phenyl-4H-1,2,4-triazol-3-yl]sulfanyl}acetic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；100 mM MES, 200 calcium acetate, 15% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.70 Å R-free 0.233
4IPC Structure of the N-terminal domain of RPA70, E7R mutant Deposited 2013-01-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：E7R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；100 mM MES, 200 mM Calcium Acetate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.22 Å R-free 0.175
4IPD Structure of the N-terminal domain of RPA70, E100R mutant Deposited 2013-01-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：E100R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；100 mM BIS-TRIS, 2M ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.51 Å R-free 0.166
4IPG Structure of the N-terminal domain of RPA70, E7R, E100R mutant Deposited 2013-01-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：E7R, E100R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；294 K；100 mM Citrate, 200 mM NaCl, 30% PEG 8000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.58 Å R-free 0.201
4IPH Structure of N-terminal domain of RPA70 in complex with VU079104 inhibitor Deposited 2013-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Mutation：E7R	1FJ ~{N}-(2,3-dimethylphenyl)-7-oxidanylidene-12-sulfanylidene-5,11-dithia-1,8-diazatricyclo[7.3.0.0^{2,6}]dodeca-2(6),3,9-triene-10-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；100 mM MES, 200 mM Calcium Acetate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.94 Å R-free 0.274
4LUO Fragment-Based Discovery of a Potent Inhibitor of Replication Protein A Protein-Protein Interactions Deposited 2013-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：RPA70N (unp residues 1-120)	Mutation：E7R	1DZ 1-(3-methylphenyl)-5-phenyl-1H-pyrazole-3-carboxylic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；100 MM MES, 200 MM CALCIUM ACETATE, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.54 Å R-free 0.189
4LUV Fragment-Based Discovery of a Potent Inhibitor of Replication Protein A Protein-Protein Interactions Deposited 2013-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：RPA70N (unp residues 1-120)	Mutation：E7R	1XS 5-(3-chloro-4-fluorophenyl)furan-2-carboxylic acid × 1 1DZ 1-(3-methylphenyl)-5-phenyl-1H-pyrazole-3-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；100 MM MES, 200 MM CALCIUM ACETATE, 20% PEG 8000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.40 Å R-free 0.170
4LUZ Fragment-Based Discovery of a Potent Inhibitor of Replication Protein A Protein-Protein Interactions Deposited 2013-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：RPA70N (unp residues 1-120)	Mutation：E7R	1XT 5-(4-{[4-(5-carboxyfuran-2-yl)benzyl]oxy}phenyl)-1-(3-methylphenyl)-1H-pyrazole-3-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；100 MM MES, 200 MM CALCIUM ACETATE, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.90 Å R-free 0.237
4LW1 Fragment-Based Discovery of a Potent Inhibitor of Replication Protein A Protein-Protein Interactions Deposited 2013-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：RPA70N (unp residues 1-120)	Mutation：E7R	1XS 5-(3-chloro-4-fluorophenyl)furan-2-carboxylic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；100 MM MES, 200 MM CALCIUM ACETATE, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.63 Å R-free 0.210
4LWC Fragment-Based Discovery of a Potent Inhibitor of Replication Protein A Protein-Protein Interactions Deposited 2013-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：RPA70N (unp residues 1-120)	Mutation：E7R	1XU 5-[3-chloro-4-({4-[1-(3,4-dichlorophenyl)-1H-pyrazol-5-yl]benzyl}carbamothioyl)phenyl]furan-2-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；100 MM MES, 200 MM CALCIUM ACETATE, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.61 Å R-free 0.215
4NB3 Crystal structure of RPA70N in complex with a 3,4 dichlorophenylalanine ATRIP derived peptide Deposited 2013-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–120（120 aa）	Mutation：E7R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；100 mM Bis-Tris, 200 mM ammonium acetate, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.35 Å R-free 0.175
4NB3 Crystal structure of RPA70N in complex with a 3,4 dichlorophenylalanine ATRIP derived peptide Deposited 2013-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–120（120 aa）	Mutation：E7R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；100 mM Bis-Tris, 200 mM ammonium acetate, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.35 Å R-free 0.175
4O0A Fragment-Based Discovery of a Potent Inhibitor of Replication Protein A Protein-Protein Interactions Deposited 2013-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：N-terminal domain of Replication Protein A	Mutation：E7R	2P9 5-{4-[({[4-(5-carboxyfuran-2-yl)-2-chlorophenyl]carbonothioyl}amino)methyl]phenyl}-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；100 MM MES, 200 MM CALCIUM ACETATE, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.20 Å R-free 0.176
4R4C Structure of RPA70N in complex with 5-(4-((4-(5-carboxyfuran-2-yl)-2-chlorobenzamido)methyl)phenyl)-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid Deposited 2014-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：N-terminal domain (UNP residues 1-120)	Mutation：E7R	3HS 5-[4-({[4-(5-carboxyfuran-2-yl)-2-chlorobenzoyl]amino}methyl)phenyl]-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；100 MM MES, 200 MM CALCIUM ACETATE, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.40 Å R-free 0.189
4R4I Structure of RPA70N in complex with 5-(4-((6-(5-carboxyfuran-2-yl)-1-thioxo-3,4-dihydroisoquinolin-2(1H)-yl)methyl)phenyl)-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid Deposited 2014-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：N-terminal domain (UNP residues 1-120)	Mutation：E7R	3HV 5-(4-{[6-(5-carboxyfuran-2-yl)-1-thioxo-3,4-dihydroisoquinolin-2(1H)-yl]methyl}phenyl)-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；100 MM MES, 200 MM CALCIUM ACETATE, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.40 Å R-free 0.191
4R4O Crystal structure of RPA70N in complex with 5-(4-((4-(5-carboxyfuran-2-yl)benzyl)carbamothioyl)phenyl)-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid Deposited 2014-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：N-terminal domain (UNP residues 1-120)	Mutation：E7R	3HW 5-(4-{[4-(5-carboxyfuran-2-yl)benzyl]carbamothioyl}phenyl)-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；100 mM MES, 200 mM Calcium Acetate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.33 Å R-free 0.195
4R4Q Crystal structure of RPA70N in complex with 5-(3-((N-(4-(5-carboxyfuran-2-yl)benzyl)acetamido)methyl)phenyl)-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid Deposited 2014-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：N-terminal domain (UNP residues 1-120)	Mutation：E7R	3HZ 5-[4-({acetyl[4-(5-carboxyfuran-2-yl)benzyl]amino}methyl)phenyl]-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；100 mM MES, 200 mM Calcium Acetate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.35 Å R-free 0.188
4R4T Crystal Structure of RPA70N in complex with 5-(4-((4-(5-carboxyfuran-2-yl)phenylthioamido)methyl)phenyl)-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid Deposited 2014-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：N-terminal domain (UNP residues 1-120)	Mutation：E7R	3J0 5-{4-[({[4-(5-carboxyfuran-2-yl)phenyl]carbonothioyl}amino)methyl]phenyl}-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；100 mM MES, 200 mM Calcium Acetate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.28 Å R-free 0.175
5E7N Crystal Structure of RPA70N in complex with VU0085636 Deposited 2015-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：residues 1-120	Mutation：E7R	5KR 2-({3-[(4-bromophenyl)sulfamoyl]-4-methylbenzoyl}amino)benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；100 mM MES, 200 mM Calcium Acetate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.21 Å R-free 0.215
5N85 Structure of RPA70N in complex with PrimPol (fragment 514-525) Deposited 2017-02-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–120（120 aa）	Mutation：E7R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293.15 K；0.2 M Ammonium acetate 0.1 M Sodium acetate 4.5 20 % w/v PEG 3350	Resolution 2.00 Å R-free 0.228
5N8A Structure of RPA70N in complex with PrimPol (fragment 480-560) Deposited 2017-02-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–120（120 aa）	Mutation：E7R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；0.2M imidazole malate, 30% w/v PEG 4000	Resolution 1.28 Å R-free 0.178
7XUT Crystal structure of RPA70N-WRN fusion Deposited 2022-05-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；20% PEG3350, 200 mM ammonium sulfate	Resolution 1.60 Å R-free 0.214
7XUV Crystal structure of RPA70N-RMI1 fusion Deposited 2022-05-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–120（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；278 K；30% PEG 2000 MME	Resolution 1.60 Å R-free 0.220
7XUW Crystal structure of RPA70N-BLMp2 fusion Deposited 2022-05-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；278 K；8% PEG 4000	Resolution 1.80 Å R-free 0.217
7XV0 Crystal structure of RPA70N-BLMp1 fusion Deposited 2022-05-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；278 K；2000 mM Ammonium sulfate	Resolution 1.50 Å R-free 0.200
7XV1 Crystal structure of RPA70N-HelB fusion Deposited 2022-05-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–120（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；20% PEG3350 200 mM Ammonium Acetate	Resolution 1.80 Å R-free 0.216
7XV4 Crystal structure of RPA70N-ATRIP fusion Deposited 2022-05-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–120（120 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
8JZV RPA70N-ETAA1 fusion Deposited 2023-07-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–120（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, Ammonium chloride	Resolution 1.50 Å R-free 0.200
8JZY RPA70N-RAD9 fusion Deposited 2023-07-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–120（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, sodium phosphate	Resolution 1.50 Å R-free 0.200
8K00 RPA70N-MRE11 fusion Deposited 2023-07-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–120（120 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
8RK2 Human Replication protein A (RPA; trimeric core) - ssDNA complex Deposited 2023-12-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–616（616 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9J1S Human replication protein A: RPA70 subunit N-terminal domain Deposited 2024-08-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa） Fragment：N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2 M Ammonium sulfate, 0.1 M Bis-Tris, pH 7.0, 25% PEG 3350	Resolution 1.55 Å R-free 0.230
9MJ5 Catalytic domain of human DNA polymerase alpha in complex with DNA and RPA Deposited 2024-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain C 438–616（179 aa）	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9PD3 NER dual incision complex - DuIS Deposited 2025-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric	Chain N 1–616（616 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9PD4 NER dual incision complex - DuIM Deposited 2025-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain N 1–616（616 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

41 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RFA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–118； UniProt 3–120 Author chain B； PDBConstruct 1–118； UniProt 3–120 Author chain C； PDBConstruct 1–118； UniProt 3–120 Author chain D； PDBConstruct 1–118； UniProt 3–120

DNA replication ATP-dependent helicase/nuclease DNA2

OrganismNot specified

UniProt P51530

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain E； UniProt 5–17 Chain F； UniProt 5–17 Chain G； UniProt 5–17 Chain H； UniProt 5–17	Fragment：UNP residues 1-17	Replication protein A 70 kDa DNA-binding subunit × 4 （P27694）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；50 mM Tris-HCl, 35 % PEG 1500, 2 mM TCEP, pH 8.0	Resolution 1.55 Å R-free 0.267

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	DNA2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–13； UniProt 5–17 Author chain F； PDBConstruct 1–13； UniProt 5–17 Author chain G； PDBConstruct 1–13； UniProt 5–17 Author chain H； PDBConstruct 1–13； UniProt 5–17

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	5eay
Deposition date deposition_date	2015-10-17
Structure title title	Crystal structure of a Dna2 peptide in complex with Rpa 70N
Keywords keywords	DNA binding protein; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	26.86 Å
Radius of gyration Rg (electron density) rg_electron	25.82 Å
Forward intensity I(0) i0	49646000.00
Molecular weight molecular_weight	56200.0 kDa
Excluded volume excluded_volume	71257 Å³
Envelope volume envelope_volume	91738 Å³
Hydration-shell volume shell_volume	29517 Å³
Envelope diameter envelope_diameter	90.0 Å
Shell Rg shell_rg	33.26 Å
Envelope Rg envelope_rg	25.53 Å
Shape Rg shape_rg	25.81 Å
Total Rg total_rg	26.70 Å
Total atoms total_atoms	3933
Residues n_residues	502
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	86.7 Å
Rg (real space) rg_real	26.75 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	4.9650e+07
I(0) uncertainty (real space) i0_real_error	6.6480e+05
Rg (reciprocal space) rg_reciprocal	26.79 Å
I(0) (reciprocal space) i0_reciprocal	49650000.0000
Solution quality estimate total_estimate	0.8994
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.2 Å
Skewness Skewness skewness	0.173
Kurtosis Kurtosis kurtosis	-0.502
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	22500000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Replication protein A 70 kDa DNA-binding subunit
Molecular weight formula_weight	12957.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3933

GQLSEGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQLSSNCVCQIHRFIVNTLKDGRRVVILMELEVLKSAEAVGVKIGNPVPYNE

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 replication ATP-dependent helicase/nuclease DNA2
Molecular weight formula_weight	1668.9 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

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

NELELLMEKSFWE

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5eayA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	5eayB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	5eayC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	5eayD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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8. Citations (1)

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Unit-cell length a length_a	134.303 Å
Unit-cell length b length_b	50.882 Å
Unit-cell length c length_c	76.528 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.94 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2327
R_work r_work	0.2316
R_free r_free	0.2667

fit	/app/data/saxs_computation/ea/5eay/5eay.fit
pddf	/app/data/pr_computation/ea/5eay/5eay.pr.out
profile	/app/data/saxs_computation/ea/5eay/5eay.dat

Crystal structure of a Dna2 peptide in complex with Rpa 70N

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

Replication protein A 70 kDa DNA-binding subunit

State in the Current Structure

Other States of the Same Protein in the Database

DNA replication ATP-dependent helicase/nuclease DNA2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)