7en4

Multi-state structure determination and dynamics analysis elucidate a new ubiquitin-recognition mechanism of yeast ubiquitin C-terminal hydrolase.

Method: SOLUTION NMR D_max: 60.0 Å Quality: GOOD

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

Ubiquitin carboxyl-terminal hydrolase YUH1

Saccharomyces cerevisiae

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 1–236	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；303 K；Ionic strength (raw mmCIF value) 100；Pressure AMBIENT NMR sample composition：2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：2 mM [U-100% 15N] ubiquitin hydrolase, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：2 mM Ile/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled ubiquitin hydrolase, 90% H2O/10% D2O \| 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 7EN4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CMX STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDROLASES Deposited 1999-05-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–235（235 aa） Fragment：ALL Chain C 1–235（235 aa） Fragment：ALL	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；16% PEG 6000 0.1 M SODIUM ACETATE PH 4.4, pH 4.5	Resolution 2.25 Å R-free 0.285

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBL1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–236； UniProt 1–236

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7en4
Deposition date deposition_date	2021-04-15
Structure title title	Multi-state structure determination and dynamics analysis elucidate a new ubiquitin-recognition mechanism of yeast ubiquitin C-terminal hydrolase.
Keywords keywords	PROTEIN solution NMR, HYDROLASE; HYDROLASE
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	18.46 Å
Radius of gyration Rg (electron density) rg_electron	17.81 Å
Forward intensity I(0) i0	3852920000.00
Molecular weight molecular_weight	527030.0 kDa
Excluded volume excluded_volume	657630 Å³
Envelope volume envelope_volume	71846 Å³
Hydration-shell volume shell_volume	27404 Å³
Envelope diameter envelope_diameter	71.2 Å
Shell Rg shell_rg	28.98 Å
Envelope Rg envelope_rg	21.32 Å
Shape Rg shape_rg	17.78 Å
Total Rg total_rg	18.07 Å
Total atoms total_atoms	73080
Residues n_residues	4720
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	60.0 Å
Rg (real space) rg_real	18.31 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	3.8530e+09
I(0) uncertainty (real space) i0_real_error	4.8300e+07
Rg (reciprocal space) rg_reciprocal	18.33 Å
I(0) (reciprocal space) i0_reciprocal	3853000000.0000
Solution quality estimate total_estimate	0.7964
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.036
Kurtosis Kurtosis kurtosis	-0.458
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2406000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; 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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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Description description	Ubiquitin carboxyl-terminal hydrolase YUH1
Molecular weight formula_weight	26405.2 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	73080

来源生物 organism	Saccharomyces cerevisiae
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Multi-state structure determination and dynamics analysis elucidate a new ubiquitin-recognition mechanism of yeast ubiquitin C-terminal hydrolase.

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

Ubiquitin carboxyl-terminal hydrolase YUH1

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/en/7en4/7en4.fit
pddf	/app/data/pr_computation/en/7en4/7en4.pr.out
profile	/app/data/saxs_computation/en/7en4/7en4.dat