SAXSdb — 8u61

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

RPA-related protein RADX

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 Homooligomer Protein × 4 DNA 1 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 1–855 Chain B； UniProt 1–855 Chain C； UniProt 1–855 Chain D； UniProt 1–855	Not recorded	dT25 DNA (25-MER) × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.00 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 8U61	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7SRK Single chain trimer HLA-A*24:02 (Y108C, A163C) with 8mer peptide YPPVPETF Deposited 2021-11-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM MES, pH 6.0, 200 mM KSCN, 18% Peg 3350	Resolution 2.50 Å R-free 0.260
7SRK Single chain trimer HLA-A*24:02 (Y108C, A163C) with 8mer peptide YPPVPETF Deposited 2021-11-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM MES, pH 6.0, 200 mM KSCN, 18% Peg 3350	Resolution 2.50 Å R-free 0.260
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 10 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 11 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain U 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 12 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain W 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 13 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 14 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain a 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 15 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain c 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 16 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain e 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 7 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 8 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
7STG Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 9 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 509–516（8 aa）	Mutation：Y108C, A163C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 8.0, 200 mM Li2SO4, 1.1 M AmSO4	Resolution 2.70 Å R-free 0.276
8U5Y human RADX trimer bound to ssDNA Deposited 2023-09-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: tetrameric	Chain A 1–855（855 aa） Chain B 1–855（855 aa） Chain C 1–855（855 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen HELIUM	Resolution 3.01 Å

3 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RADX_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–855； UniProt 1–855 Author chain B； PDBConstruct 1–855； UniProt 1–855 Author chain C； PDBConstruct 1–855； UniProt 1–855 Author chain D； PDBConstruct 1–855； UniProt 1–855

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8u61
Deposition date deposition_date	2023-09-13
Structure title title	Human RADX tetramer bound to ssDNA
Keywords keywords	oligomer OB-fold, RAD51 regulator, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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	51.60 Å
Radius of gyration Rg (electron density) rg_electron	51.34 Å
Forward intensity I(0) i0	1496980000.00
Molecular weight molecular_weight	327410.0 kDa
Excluded volume excluded_volume	411570 Å³
Envelope volume envelope_volume	574860 Å³
Hydration-shell volume shell_volume	93195 Å³
Envelope diameter envelope_diameter	185.3 Å
Shell Rg shell_rg	55.29 Å
Envelope Rg envelope_rg	49.94 Å
Shape Rg shape_rg	51.35 Å
Total Rg total_rg	51.44 Å
Total atoms total_atoms	45918
Residues n_residues	2805
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	175.4 Å
Rg (real space) rg_real	51.50 Å
Rg uncertainty (real space) rg_real_error	2.20 Å
I(0) (real space) i0_real	1.4970e+09
I(0) uncertainty (real space) i0_real_error	2.9710e+07
Rg (reciprocal space) rg_reciprocal	51.68 Å
I(0) (reciprocal space) i0_reciprocal	1497000000.0000
Solution quality estimate total_estimate	0.8839
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	62.2 Å
Skewness Skewness skewness	0.204
Kurtosis Kurtosis kurtosis	-0.423
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	115500000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.918

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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	RPA-related protein RADX
Molecular weight formula_weight	97680.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,B,A,C
Atom count atom_count	45921

MSGESGQPEAGPSHAGLDWPNPERNRAGVPGGVIRRAGSQGPRSWIQKVLEQIMDSPRQCVTPSEVVPVTVLAVQRYLLEDEPRDTVPKPPLYCYDVTISDGVYQEKCYLDPSLNSLVYQNILKVGIQMRISRVSCLYNEKRIGQGILCIDNVHCGETSDSISLETPFRNRAHQEKPERPLRGGKSHYLALWNNEDPYGDIWLTDKQPEEHNFSDTKIISLSHLEMTWTNRRNFPALLVRILHKSKLRYYGKPDKKMIEPYQTFLEVADSSGTVSVIMWNALCPEWYKSLRVGLVLLLQDYSVKKSYPFRIQPVPVDPQIKLISTMEICLNLRDPPTNIIIIPEKQVKPEWRLPKLNHRFTTRSELDDMPENCICDVIGLLVFVGRVQRSKKKENREDFWSYRWIHIADGTSEQPFIVELFSTSQPEIFENIYPMAYFVCTQLKVVRNDNQVPKLLYLTTTNESGVFITGHRGQPYTYDAKVKNFIQWIRTKSDSGEQKNMVIGGYYPYPPVPETFSKYSSSIKVESLLTAISEVRKEIEDLQYREQKRIAIQGIITAIKYIPHSSATESASASETLRNANRPSTSQAARVEIQERNGKRHQDDEPVNSQYFQTTSTNLSLSNKIRILQGPHANPVAVPQPGASVQTKGIKPGMPSIFNRRANINANLQGKARKTISDRWESQLWREKKFGLIDHLHYSRVYPESIPRKFMFEHRKFLSDQYNSQPAKYVPPEGRPPKLDDFKSARSLGHFEVTILGLNHEIAIDVAFLPMYCPEDIRTSQIDTLLTSMNYSCAYPQDTTGNDRLPGPRAVAGDIIKAATELDRVHIVGILDICNLGNNKVEVYLHKIYSPENTS

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	dT25 DNA (25-MER)
Molecular weight formula_weight	7559.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

TTTTTTTTTTTTTTTTTTTTTTTTT

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8. Citations (1)

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Resolution resolution	4.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	58000

fit	/app/data/saxs_computation/u6/8u61/8u61.fit
pddf	/app/data/pr_computation/u6/8u61/8u61.pr.out
profile	/app/data/saxs_computation/u6/8u61/8u61.dat

Human RADX tetramer bound to ssDNA

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

RPA-related protein RADX

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)