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6f8d

Crystal structure of Human ARS2 residues 171-270 + 408-763 (P65 form)

Method: X-RAY DIFFRACTION Dmax: 143.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serrate RNA effector molecule homolog

Homo sapiens

UniProt Q9BXP5

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 171–270 Chain C； UniProt 408–763 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 10.5；277 K；Crystals of ARS2 were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution (6 mg/ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to crystallisation solution. The crystallisation solution was 1.2 M sodium dihydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.2 M lithium sulphate, 0.1 M CAPS pH 10.5 Resolution 3.48 Å R-free 0.292
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 171–270 Chain D； UniProt 408–763 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 10.5；277 K；Crystals of ARS2 were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution (6 mg/ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to crystallisation solution. The crystallisation solution was 1.2 M sodium dihydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.2 M lithium sulphate, 0.1 M CAPS pH 10.5 Resolution 3.48 Å R-free 0.292

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 6F8D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 827–871（45 aa）
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.
Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 827–871（45 aa）
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.
Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 827–871（45 aa）
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.
Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 827–871（45 aa）
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.
Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain O 827–871（45 aa）
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.
Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 827–871（45 aa）
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.
Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain U 827–871（45 aa）
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.
Resolution 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide Deposited 2017-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain X 827–871（45 aa）
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.
Resolution 2.80 Å R-free 0.268
6F7J Crystal structure of Human ARS2 residues 171-270 + 408-763 Deposited 2017-12-10 Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 171–270（100 aa）
Chain B 408–763（356 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；281 K；Protein solution at 6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8, mixed 1:1 with reservoir solution containing 1.2 M sodium dihydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.2 M lithium sulphate and 0.1 M CAPS pH 10.5.
Resolution 3.22 Å R-free 0.322
6F7P Crystal structure of Human ARS2 residues 147-270 + 408-763 Deposited 2017-12-11 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 147–270（124 aa）
Chain C 408–763（356 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；281 K；Crystals were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution at 6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to crystallisation solution. The crystallisation solution was 0.2 M lithium sulphate and 20% (w/v) PEG 3550.
Resolution 3.70 Å R-free 0.309
6F7P Crystal structure of Human ARS2 residues 147-270 + 408-763 Deposited 2017-12-11 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 147–270（124 aa）
Chain D 408–763（356 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；281 K；Crystals were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution at 6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to crystallisation solution. The crystallisation solution was 0.2 M lithium sulphate and 20% (w/v) PEG 3550.
Resolution 3.70 Å R-free 0.309
6F7S Crystal structure of Human ARS2 residues 147-270 + 408-763 with deletion of loop B Deposited 2017-12-11 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 147–270（124 aa） Fragment：UNP residues 147-270
Chain C 408–567（160 aa） Fragment：UNP residues 408-567,UNP residues 599-763
Chain C 599–763（165 aa） Fragment：UNP residues 408-567,UNP residues 599-763
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；281 K；Crystals of human ARS2 were obtained at 4 C in 2 microliter hanging drops with a 1:1 ratio of protein solution (6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine, pH 7.8) to crystallisation solution. The crystallisation solution was 0.2 M potassium citrate tribasic monohydrate, 20 % (w/v) PEG 3350.
Resolution 3.37 Å R-free 0.303
6F7S Crystal structure of Human ARS2 residues 147-270 + 408-763 with deletion of loop B Deposited 2017-12-11 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 147–270（124 aa） Fragment：UNP residues 147-270
Chain D 408–567（160 aa） Fragment：UNP residues 408-567,UNP residues 599-763
Chain D 599–763（165 aa） Fragment：UNP residues 408-567,UNP residues 599-763
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；281 K；Crystals of human ARS2 were obtained at 4 C in 2 microliter hanging drops with a 1:1 ratio of protein solution (6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine, pH 7.8) to crystallisation solution. The crystallisation solution was 0.2 M potassium citrate tribasic monohydrate, 20 % (w/v) PEG 3350.
Resolution 3.37 Å R-free 0.303
8PMP Structure of the human nuclear cap-binding complex bound to ARS2[147-871] and m7GTP Deposited 2023-06-29 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 × 3 PDB declaration: trimeric
Chain D 148–876（729 aa）
Not recorded MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å

5 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SRRT_HUMAN
Isoform Q9BXP5-4
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 1–100； UniProt 171–270 Author chain B； PDBConstruct 1–100； UniProt 171–270 Author chain C； PDBConstruct 1–356； UniProt 408–763 Author chain D； PDBConstruct 1–356； UniProt 408–763

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 6f8d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6f8d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6f8d
Deposition date deposition_date2017-12-13
Structure title titleCrystal structure of Human ARS2 residues 171-270 + 408-763 (P65 form)
Keywords keywordsRNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.11 Å
Radius of gyration Rg (electron density) rg_electron33.83 Å
Forward intensity I(0) i0136905000.00
Molecular weight molecular_weight92434.0 kDa
Excluded volume excluded_volume115750 ų
Envelope volume envelope_volume165610 ų
Hydration-shell volume shell_volume41714 ų
Envelope diameter envelope_diameter150.1 Å
Shell Rg shell_rg39.13 Å
Envelope Rg envelope_rg34.21 Å
Shape Rg shape_rg33.83 Å
Total Rg total_rg34.27 Å
Total atoms total_atoms6504
Residues n_residues782
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 dmax143.7 Å
Rg (real space) rg_real34.19 Å
Rg uncertainty (real space) rg_real_error2.07 Å
I(0) (real space) i0_real1.3690e+08
I(0) uncertainty (real space) i0_real_error2.4680e+06
Rg (reciprocal space) rg_reciprocal34.14 Å
I(0) (reciprocal space) i0_reciprocal136900000.0000
Solution quality estimate total_estimate0.7612
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.7 Å
Skewness Skewness skewness0.516
Kurtosis Kurtosis kurtosis0.376
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha24360000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.359; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.816; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)