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3saf

Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site

Method: X-RAY DIFFRACTION Dmax: 105.4 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Exosome component 10

Homo sapiens

UniProt Q01780

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 180–606 Fragment：UNP residues 180-606 Mutation：D313N MG MAGNESIUM ION × 1 YT3 YTTRIUM (III) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.50 Å R-free 0.240
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 180–606 Fragment：UNP residues 180-606 Mutation：D313N MG MAGNESIUM ION × 1 YT3 YTTRIUM (III) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.50 Å R-free 0.240

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 3SAF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2CPR Solution structure of the HRDC domain of human Exosome component 10 Deposited 2005-05-19 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 483–593（111 aa） Fragment：HRDC
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.45mM 13C/15N-PROTEIN; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3 | 90% H2O/10% D2O
Resolution not provided
3SAG Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site Deposited 2011-06-02 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 180–606（427 aa） Fragment：UNP residues 180-606
Mutation：D313N YT3 YTTRIUM (III) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.70 Å R-free 0.262
3SAG Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site Deposited 2011-06-02 Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 180–606（427 aa） Fragment：UNP residues 180-606
Mutation：D313N YT3 YTTRIUM (III) ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.70 Å R-free 0.262
3SAH Crystal structure of the human RRP6 catalytic domain with Y436A mutation in the catalytic site Deposited 2011-06-02 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 180–606（427 aa） Fragment：UNP residues 180-606
Mutation：Y436A YT3 YTTRIUM (III) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.65 Å R-free 0.265
3SAH Crystal structure of the human RRP6 catalytic domain with Y436A mutation in the catalytic site Deposited 2011-06-02 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 180–606（427 aa） Fragment：UNP residues 180-606
Mutation：Y436A YT3 YTTRIUM (III) ION × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.65 Å R-free 0.265
6D6Q Human nuclear exosome-MTR4 RNA complex - overall reconstruction Deposited 2018-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain J 1–648（648 aa）
Chain J 705–804（100 aa）
Mutation：D313N Mutation：D313N MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；30 sec wait time, 2.5 sec blot time
Resolution 3.45 Å
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain J 1–648（648 aa）
Chain J 705–804（100 aa）
Mutation：D313N Mutation：D313N ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；30 sec wait time, 2.5 sec blot time
Resolution 3.45 Å
7MQA Cryo-EM structure of the human SSU processome, state post-A1 Deposited 2021-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric
Chain NV 1–885（885 aa）
Not recorded MG MAGNESIUM ION × 64 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EXOSX_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–428； UniProt 180–606 Author chain B； PDBConstruct 2–428； UniProt 180–606

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 3saf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3saf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3saf
Deposition date deposition_date2011-06-02
Structure title titleCrystal structure of the human RRP6 catalytic domain with D313N mutation in the active site
Keywords keywordsexoribonuclease, RNA exosome, HYDROLASE; HYDROLASE
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_guinier32.44 Å
Radius of gyration Rg (electron density) rg_electron31.90 Å
Forward intensity I(0) i0124143000.00
Molecular weight molecular_weight89745.0 kDa
Excluded volume excluded_volume112850 ų
Envelope volume envelope_volume146690 ų
Hydration-shell volume shell_volume38844 ų
Envelope diameter envelope_diameter117.8 Å
Shell Rg shell_rg38.18 Å
Envelope Rg envelope_rg31.76 Å
Shape Rg shape_rg31.86 Å
Total Rg total_rg32.59 Å
Total atoms total_atoms6309
Residues n_residues761
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 dmax105.4 Å
Rg (real space) rg_real32.39 Å
Rg uncertainty (real space) rg_real_error0.85 Å
I(0) (real space) i0_real1.2410e+08
I(0) uncertainty (real space) i0_real_error2.0330e+06
Rg (reciprocal space) rg_reciprocal32.41 Å
I(0) (reciprocal space) i0_reciprocal124100000.0000
Solution quality estimate total_estimate0.9014
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.7 Å
Skewness Skewness skewness0.238
Kurtosis Kurtosis kurtosis-0.516
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23720000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.937
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3safA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id3safA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily80 — HRDC domain
Domain ID domain_id3safB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id3safB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily80 — HRDC domain
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8. Citations (1)

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9. Files and Curves (10)