SAXSdb — 2cpr

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

Exosome component 10

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 483–593	Fragment：HRDC	No other associated polymer	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

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 2CPR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3SAF Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site Deposited 2011-06-02	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 180–606（427 aa） 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
3SAF Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site Deposited 2011-06-02	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions 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	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
3SAG Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site Deposited 2011-06-02	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 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 construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions 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 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 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 construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions 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 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 9 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 8–118； UniProt 483–593

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	2cpr
Deposition date deposition_date	2005-05-19
Structure title title	Solution structure of the HRDC domain of human Exosome component 10
Keywords keywords	;HRDC, helix-bundle, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, GENE REGULATION ;; GENE REGULATION
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	17.56 Å
Radius of gyration Rg (electron density) rg_electron	16.93 Å
Forward intensity I(0) i0	1086700000.00
Molecular weight molecular_weight	278240.0 kDa
Excluded volume excluded_volume	348950 Å³
Envelope volume envelope_volume	85040 Å³
Hydration-shell volume shell_volume	27525 Å³
Envelope diameter envelope_diameter	98.8 Å
Shell Rg shell_rg	32.78 Å
Envelope Rg envelope_rg	28.06 Å
Shape Rg shape_rg	16.92 Å
Total Rg total_rg	17.42 Å
Total atoms total_atoms	39340
Residues n_residues	2480
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	47.0 Å
Rg (real space) rg_real	16.14 Å
Rg uncertainty (real space) rg_real_error	0.08 Å
I(0) (real space) i0_real	1.0320e+09
I(0) uncertainty (real space) i0_real_error	9.1090e+06
Rg (reciprocal space) rg_reciprocal	17.87 Å
I(0) (reciprocal space) i0_reciprocal	1087000000.0000
Solution quality estimate total_estimate	0.6823
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	18.2 Å
Skewness Skewness skewness	0.391
Kurtosis Kurtosis kurtosis	-0.228
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	2.2450
Highest regularization parameter α highest_alpha	711400.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.018; Oscil: 0.962; Stabil: 0.995; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2cpra1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.8 — HRDC-like
Family Family family	a.60.8.4 — EXOSC10 HRDC domain-like

Domain ID domain_id	d2cpra2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2cpra3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2cprA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	80 — HRDC domain

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8. Citations (1)

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Description description	Exosome component 10
Molecular weight formula_weight	13945.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	39340

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

fit	/app/data/saxs_computation/cp/2cpr/2cpr.fit
pddf	/app/data/pr_computation/cp/2cpr/2cpr.pr.out
profile	/app/data/saxs_computation/cp/2cpr/2cpr.dat

Solution structure of the HRDC domain of human Exosome component 10

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

Exosome component 10

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)