SAXSdb — 5gvi

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

Ubiquitin carboxyl-terminal hydrolase 30

Danio rerio

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 61–501	Fragment：UNP residues 61-501 Mutation：C73A, D127V	ubiquitin × 1 （P62983） ubiquitin × 1 （P62983） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；90 mM Tris-HCl, 180 mM ammonium acetate, 23% PEG3350, 10 mM TCEP	Resolution 1.87 Å R-free 0.206

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A0R4ILB8_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–444； UniProt 61–501

ubiquitin

Mus musculus

UniProt P62983

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–76 Chain C； UniProt 1–72	Mutation：K6R	Ubiquitin carboxyl-terminal hydrolase 30 × 1 （A0A0R4ILB8） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；90 mM Tris-HCl, 180 mM ammonium acetate, 23% PEG3350, 10 mM TCEP	Resolution 1.87 Å R-free 0.206

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 5GVI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3VHT Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in complex with ubiquitin Deposited 2011-09-06	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2M DL-Malic acid, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 2.40 Å R-free 0.238
5XIS Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I Deposited 2017-04-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–76（76 aa） Chain C 1–76（76 aa）	Mutation：K63R	XYZ beta-D-xylofuranose × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；15% PEG3350, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2	Resolution 1.78 Å R-free 0.245
5XIS Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I Deposited 2017-04-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–76（76 aa） Chain F 1–76（76 aa）	Mutation：K63R	XYZ beta-D-xylofuranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；15% PEG3350, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2	Resolution 1.78 Å R-free 0.245
5XIT Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II Deposited 2017-04-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–76（76 aa） Chain D 1–76（76 aa）	Mutation：K63R	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG MME 2000, 0.1 M Bis-Tris (pH 6.5), 10 mM Pr acetate	Resolution 2.25 Å R-free 0.239
5XIT Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II Deposited 2017-04-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–76（76 aa） Chain H 1–76（76 aa）	Mutation：K63R	GOL GLYCEROL × 1 PR PRASEODYMIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG MME 2000, 0.1 M Bis-Tris (pH 6.5), 10 mM Pr acetate	Resolution 2.25 Å R-free 0.239
5XIU Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin Deposited 2017-04-27	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 1–76（76 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；25% PEG3350, 0.1 M Tris-HCl (pH8.5), 0.2 M Ammonium Acetate	Resolution 1.80 Å R-free 0.207
7E62 Mouse TAB2 NZF in complex with Lys6-linked diubiquitin Deposited 2021-02-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–77（77 aa）	Mutation：K6R Mutation：A77D	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100 mM HEPES-NaOH (pH 7.5), 1.44 M sodium citrate	Resolution 1.99 Å R-free 0.264
7E62 Mouse TAB2 NZF in complex with Lys6-linked diubiquitin Deposited 2021-02-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–76（76 aa） Chain I 1–77（77 aa）	Mutation：K6R Mutation：A77D	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100 mM HEPES-NaOH (pH 7.5), 1.44 M sodium citrate	Resolution 1.99 Å R-free 0.264
7LS1 80S ribosome from mouse bound to eEF2 (Class II) Deposited 2021-02-17	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 × 80 PDB declaration: 85-meric	Chain U3 1–156（156 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；3 second blotting, force 3	Resolution 3.30 Å
7LS2 80S ribosome from mouse bound to eEF2 (Class I) Deposited 2021-02-17	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 × 80 PDB declaration: 85-meric	Chain U3 1–156（156 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；3 second blotting, force 3	Resolution 3.10 Å
9QOH Mouse Ribosome POST translocation state Deposited 2025-03-26	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 × 77 PDB declaration: 83-meric	Chain U3 1–156（156 aa）	Not recorded	MG MAGNESIUM ION × 122 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes pH 7.5, 150 mM NaCl, 10 mM MgCl2, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å
9QQL Mouse RPS15 P131 Mutant Ribosome POST translocation state Deposited 2025-04-01	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 × 76 PDB declaration: 83-meric	Chain U3 1–156（156 aa）	Not recorded	MG MAGNESIUM ION × 122 UNK UNKNOWN × 22 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes pH 7.5, 150 mM NaCl, 10 mM MgCl2, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
9QZP Mouse Ribosome Classical Pre translocation state Deposited 2025-04-23	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 × 77 PDB declaration: 85-meric	Chain U3 1–156（156 aa）	Not recorded	MG MAGNESIUM ION × 118 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes pH 7.5, 150 mM NaCl, 10 mM MgCl2, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å

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

View Construct and Data Evidence

UniProt name	RS27A_MOUSE
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain C； PDBConstruct 1–72； UniProt 1–72

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	5gvi
Deposition date deposition_date	2016-09-05
Structure title title	Zebrafish USP30 in complex with Lys6-linked diubiquitin
Keywords keywords	Complex, mitophagy, Hydrolase-SIGNALING PROTEIN complex; Hydrolase/SIGNALING PROTEIN
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	25.27 Å
Radius of gyration Rg (electron density) rg_electron	24.16 Å
Forward intensity I(0) i0	49430100.00
Molecular weight molecular_weight	53842.0 kDa
Excluded volume excluded_volume	67117 Å³
Envelope volume envelope_volume	81275 Å³
Hydration-shell volume shell_volume	28424 Å³
Envelope diameter envelope_diameter	95.0 Å
Shell Rg shell_rg	31.08 Å
Envelope Rg envelope_rg	24.75 Å
Shape Rg shape_rg	24.09 Å
Total Rg total_rg	25.11 Å
Total atoms total_atoms	3781
Residues n_residues	474
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	89.0 Å
Rg (real space) rg_real	25.31 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	4.9430e+07
I(0) uncertainty (real space) i0_real_error	6.5350e+05
Rg (reciprocal space) rg_reciprocal	25.30 Å
I(0) (reciprocal space) i0_reciprocal	49430000.0000
Solution quality estimate total_estimate	0.8469
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.7 Å
Skewness Skewness skewness	0.500
Kurtosis Kurtosis kurtosis	0.084
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9846000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.696; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.988

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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	Ubiquitin carboxyl-terminal hydrolase 30
Molecular weight formula_weight	50492.8 kDa
Mutation mutation	C73A, D127V
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	3904

SHMGMVPGLLNLGNTAFMNSLLQGLAACPSFIRWLEDFTSQNSADRERTERETQLSRSLMQLLKALSSHVPGEDDVLDAGGLLEALRLYRWHISSFEEQDAHELFHVLTSSLEEEQERQPRVAHLFDMQTLEKSVESKEKNISCRSGGPLHPIPSLWRTRHPFHGRLTSYMACKRCEQQSPVHYDSFDSLSLSIPSIQWGRPVTLDQCLQHFISSETIKEVECENCTKQQAGELVNGEVLESQRTTFVKQLKLGKLPQCLCIHLQRLTWSKEGSPIKRQEHVQFTEYLSLDRYKHCSAAQSQQKTSRTNKAKASADPKDKAIANGVDSEHCNNNKPQSNGTFPSVFLHSPGLSSQLNLTYDYSTSEYLFRLTAVLVHHGDMHSGHFITYRRCPAAPRGTSPFSSQWLWVSDDSVRKASLQEVLSSSAYLLFYERMQRPGLRVEE

来源 Source

来源生物 organism	Danio rerio
通用名 common_name	Zebrafish
NCBI Class编号 ncbi_taxonomy_id	7955
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	ubiquitin
Molecular weight formula_weight	8604.8 kDa
Mutation mutation	K6R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MQIFVRTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	ubiquitin
Molecular weight formula_weight	8192.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	123

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5gvib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d5gvic_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (1 domains)

Domain ID domain_id	5gviA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

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8. Citations (1)

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Unit-cell length a length_a	130.270 Å
Unit-cell length b length_b	130.270 Å
Unit-cell length c length_c	59.881 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.870 Å
Low-resolution limit resolution_low	44.083 Å
R factor r_factor	0.1779
R_work r_work	0.1764
R_free r_free	0.2060

fit	/app/data/saxs_computation/gv/5gvi/5gvi.fit
pddf	/app/data/pr_computation/gv/5gvi/5gvi.pr.out
profile	/app/data/saxs_computation/gv/5gvi/5gvi.dat

Zebrafish USP30 in complex with Lys6-linked diubiquitin

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

Ubiquitin carboxyl-terminal hydrolase 30

State in the Current Structure

Other States of the Same Protein in the Database

ubiquitin

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)