SAXSdb — 7afs

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

Protein artemis

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–361	Mutation：D37A	NI NICKEL (II) ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M Bis-TRIS pH 5.5, 25% PEG 3350	Resolution 1.70 Å R-free 0.216

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 7AFS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3W1B Crystal Structure of Human DNA ligase IV-Artemis Complex (Mercury Derivative) Deposited 2012-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 485–495（11 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1 SO4 SULFATE ION × 10 HG MERCURY (II) ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；2M ammonium sulfate, 10mM YCl, 100mM MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.40 Å R-free 0.225
3W1G Crystal Structure of Human DNA ligase IV-Artemis Complex (Native) Deposited 2012-11-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 485–495（11 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO4 SULFATE ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；2M ammonium sulfate, 10mM YCl, 100mM MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.55 Å R-free 0.234
4HTP Crystal structure of the DBD domain of human DNA ligase IV bound to Artemis peptide Deposited 2012-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 485–495（11 aa） Fragment：C-terminal	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；18% PEG 1000, 200 mM Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 2.25 Å R-free 0.249
4HTP Crystal structure of the DBD domain of human DNA ligase IV bound to Artemis peptide Deposited 2012-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 485–495（11 aa） Fragment：C-terminal	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；18% PEG 1000, 200 mM Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 2.25 Å R-free 0.249
6TT5 Crystal structure of DCLRE1C/Artemis Deposited 2019-12-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–361（361 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 2 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；20% PEG 3350 0.3 M Ammonium Chloride	Resolution 1.50 Å R-free 0.192
6WNL human Artemis/SNM1C catalytic domain, crystal form 2 Deposited 2020-04-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–368（367 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；50 mM MES pH 6.5, 0.1 M LiCl, 0.01 M MgCl2, 12% PEG 4000 (w/v)	Resolution 2.37 Å R-free 0.280
6WNL human Artemis/SNM1C catalytic domain, crystal form 2 Deposited 2020-04-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–368（367 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；50 mM MES pH 6.5, 0.1 M LiCl, 0.01 M MgCl2, 12% PEG 4000 (w/v)	Resolution 2.37 Å R-free 0.280
6WO0 human Artemis/SNM1C catalytic domain, crystal form 1 Deposited 2020-04-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–368（367 aa）	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；50 mM MES pH 6.5, 0.1 M LiCl, 0.01 M MgCl2, 12% PEG 4000 (w/v)	Resolution 1.97 Å R-free 0.270
7ABS Structure of human DCLRE1C/Artemis in complex with DNA - re-evaluation of 6WO0 Deposited 2020-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 2–368（367 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；50 mM MES pH 6.5, 0.1 M LiCl, 0.01 M MgCl2, 12% PEG 4000 (w/v)	Resolution 1.97 Å R-free 0.276
7AF1 The structure of Artemis/SNM1C/DCLRE1C with 2 Zinc ions Deposited 2020-09-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–361（361 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 8 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；20% PEG 3350 0.3 M Ammonium Chloride	Resolution 1.70 Å R-free 0.212
7AFU The structure of Artemis variant H33A Deposited 2020-09-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–361（361 aa）	Mutation：H33A	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；0.1 M Sodium Citrate pH 5.5, 20% PEG 3350	Resolution 1.56 Å R-free 0.212
7AGI The structure of Artemis variant H35D Deposited 2020-09-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–361（361 aa）	Mutation：H35D	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；0.1M Sodium Citrate pH 5.5, 20% PEG 3350	Resolution 1.70 Å R-free 0.210
7APV Structure of Artemis/DCLRE1C/SNM1C in complex with Ceftriaxone Deposited 2020-10-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–361（361 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5 9F2 Ceftriaxone × 1 ZN ZINC ION × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；15% PEG3350 and 0.2 M Ammonium chloride	Resolution 1.95 Å R-free 0.227
7SGL DNA-PK complex of DNA end processing Deposited 2021-10-06	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 D 1–692（692 aa）	Not recorded	MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7TYR Cryo-EM structure of the basal state of the Artemis:DNA-PKcs complex (see COMPND 13/14) Deposited 2022-02-14	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 1–692（692 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Plunge-freeze was performed using a home-made manual plunger at typical indoor humidity (Los Angeles, CA) and at room temperature.	Resolution 3.33 Å

13 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DCR1C_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–362； UniProt 1–361

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	7afs
Deposition date deposition_date	2020-09-20
Structure title title	The structure of Artemis variant D37A
Keywords keywords	Artemis, SNM1C, DCLRE1C, Nuclease, HYDROLASE; HYDROLASE
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	23.22 Å
Radius of gyration Rg (electron density) rg_electron	22.19 Å
Forward intensity I(0) i0	27325400.00
Molecular weight molecular_weight	40192.0 kDa
Excluded volume excluded_volume	50265 Å³
Envelope volume envelope_volume	59732 Å³
Hydration-shell volume shell_volume	22615 Å³
Envelope diameter envelope_diameter	81.7 Å
Shell Rg shell_rg	28.84 Å
Envelope Rg envelope_rg	22.43 Å
Shape Rg shape_rg	22.21 Å
Total Rg total_rg	22.95 Å
Total atoms total_atoms	2823
Residues n_residues	359
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	78.9 Å
Rg (real space) rg_real	23.21 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	2.7330e+07
I(0) uncertainty (real space) i0_real_error	3.6800e+05
Rg (reciprocal space) rg_reciprocal	23.22 Å
I(0) (reciprocal space) i0_reciprocal	27330000.0000
Solution quality estimate total_estimate	0.8744
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.344
Kurtosis Kurtosis kurtosis	-0.336
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6810000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.928

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Protein artemis
Molecular weight formula_weight	41729.1 kDa
EC 编号 ec_number	3.1.-.-
Mutation mutation	D37A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3134

SMSSFEGQMAEYPTISIDRFDRENLRARAYFLSHCHKAHMKGLRAPTLKRRLECSLKVYLYCSPVTKELLLTSPKYRFWKKRIISIEIETPTQISLVDEASGEKEEIVVTLLPAGHCPGSVMFLFQGNNGTVLYTGDFRLAQGEAARMELLHSGGRVKDIQSVYLDTTFCDPRFYQIPSREECLSGVLELVRSWITRSPYHVVWLNCKAAYGYEYLFTNLSEELGVQVHVNKLDMFRNMPEILHHLTTDRNTQIHACRHPKAEEYFQWSKLPCGITSRNRIPLHIISIKPSTMWFGERSRKTNVIVRTGESSYRACFSFHSSYSEIKDFLSYLCPVNAYPNVIPVGTTMDKVVEILKPLCRS

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	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	163

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8. Citations (1)

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Unit-cell length a length_a	35.909 Å
Unit-cell length b length_b	48.062 Å
Unit-cell length c length_c	48.207 Å
Unit-cell angle α angle_alpha	82.89 °
Unit-cell angle β angle_beta	76.43 °
Unit-cell angle γ angle_gamma	86.38 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	47.660 Å
R factor r_factor	0.1874
R_work r_work	0.1859
R_free r_free	0.2161

fit	/app/data/saxs_computation/af/7afs/7afs.fit
pddf	/app/data/pr_computation/af/7afs/7afs.pr.out
profile	/app/data/saxs_computation/af/7afs/7afs.dat

The structure of Artemis variant D37A

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

Protein artemis

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