SAXSdb — 8hsv

▼

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

Beta-arrestin-1

Rattus norvegicus

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–394 Chain B； UniProt 1–394	Mutation：C59V,C125S,C140S,C150V,C242V,C251V,C269S	peptide from E3 ubiquitin-protein ligase Mdm2 × 2 （D3ZVH5） SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；1M ammonium sulfate, 0.1M HEPES pH 9.5, 5mM n-dodecyl-b-iminodipropionic acid, monosodium salt	Resolution 3.00 Å R-free 0.208

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 8HSV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4JQI Structure of active beta-arrestin1 bound to a G protein-coupled receptor phosphopeptide Deposited 2013-03-20	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 A 2–393（392 aa）	Not recorded	CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；17% PEG 3350, 0.1 M HEPES, 0.2 M L-proline , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.247
4JQI Structure of active beta-arrestin1 bound to a G protein-coupled receptor phosphopeptide Deposited 2013-03-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–393（392 aa）	Not recorded	CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 6 PRO PROLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；17% PEG 3350, 0.1 M HEPES, 0.2 M L-proline , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.247
6KL7 Beta-arrestin 1 mutant S13D/T275D Deposited 2019-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–418（418 aa）	Mutation：S13D, T275D	BA BARIUM ION × 3 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.05 M HEPES 7.5, 70 mM BaCl2, 9% PEG 3550	Resolution 2.79 Å R-free 0.274
6KL7 Beta-arrestin 1 mutant S13D/T275D Deposited 2019-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–418（418 aa）	Mutation：S13D, T275D	BA BARIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.05 M HEPES 7.5, 70 mM BaCl2, 9% PEG 3550	Resolution 2.79 Å R-free 0.274
6U1N GPCR-Beta arrestin structure in lipid bilayer Deposited 2019-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 2–393（392 aa）	Not recorded	2CU 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8GO8 Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1 Deposited 2022-08-24	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 × 8 PDB declaration: octameric	Chain A 1–418（418 aa） Chain B 1–418（418 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 3 seconds before plunging.	Resolution 3.41 Å
8GP3 Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C-X-C chemokine receptor type 4, CXCR4 Deposited 2022-08-25	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 × 8 PDB declaration: octameric	Chain A 1–418（418 aa） Chain B 1–418（418 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 3 seconds before plunging.	Resolution 4.80 Å
8HST The structure of rat beta-arrestin1 Deposited 2022-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–394（394 aa）	Mutation：C59V,C125S,C140S,C150V,C242V,C251V,C269S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；5% (w/v) PEG 8000, 100mM Imidazole/ Hydrochloric acid pH 8.0, 100mM Calcium acetate	Resolution 2.66 Å R-free 0.248
8HST The structure of rat beta-arrestin1 Deposited 2022-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–394（394 aa）	Mutation：C59V,C125S,C140S,C150V,C242V,C251V,C269S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；5% (w/v) PEG 8000, 100mM Imidazole/ Hydrochloric acid pH 8.0, 100mM Calcium acetate	Resolution 2.66 Å R-free 0.248
8I0N Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1 (Local refine) Deposited 2023-01-11	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 × 8 PDB declaration: octameric	Chain A 1–418（418 aa） Chain B 1–418（418 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 3 seconds before plunging.	Resolution 3.26 Å
8I0Q Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C-X-C chemokine receptor type 4, CXCR4 (Local refine) Deposited 2023-01-11	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 × 8 PDB declaration: octameric	Chain A 1–418（418 aa） Chain B 1–418（418 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 3 seconds before plunging.	Resolution 4.45 Å
8J8Z Structure of beta-arrestin1 in complex with D6Rpp Deposited 2023-05-02	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 × 8 PDB declaration: octameric	Chain A 1–418（418 aa） Chain B 1–418（418 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8JA3 Structure of beta-arrestin1 in complex with C3aRpp Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–357（357 aa） Chain B 1–357（357 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.94 Å
9BT8 Structure of Src in complex with beta-arrestin 1 revealing SH3 binding sites Deposited 2024-05-14	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 × 6 PDB declaration: hexameric	Chain B 2–393（392 aa）	Mutation：C59V, P120C, C125S, C140L, C150V, C242V, C251V, C269S	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.34 Å
9CX3 Structure of SH3 domain of Src in complex with beta-arrestin 1 Deposited 2024-07-30	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 × 6 PDB declaration: hexameric	Chain B 2–393（392 aa）	Mutation：C59V, P120C, C125S, C140L, C150V, C242V, C251V, C269S	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
9CX9 Structure of SH3 domain of Src in complex with beta-arrestin 1 Deposited 2024-07-31	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 × 5 PDB declaration: pentameric	Chain A 2–393（392 aa）	Mutation：C59V, E92C, C125S, C140L, C150V, C242V, C251V, C269S	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.34 Å
9DNG Structure of rat beta-arrestin 1 by fiducial-assisted cryo-EM Deposited 2024-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–176（175 aa） Chain A 182–393（212 aa）	Mutation：M29W, H124I, R128L Mutation：M29W, H124I, R128L	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.52 Å
9DNM Structure of rat beta-arrestin 1 bound to allosteric inhibitor Deposited 2024-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–176（175 aa） Chain A 182–393（212 aa）	Mutation：M29W, H124I, R128L Mutation：M29W, H124I, R128L	ODN (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
9KYU Structure of beta-arrestin1 in complex with mouse C5aR1pp Deposited 2024-12-09	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 × 8 PDB declaration: octameric	Chain A 1–418（418 aa） Chain D 1–418（418 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.72 Å

16 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARRB1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–414； UniProt 1–394 Author chain B； PDBConstruct 21–414； UniProt 1–394

peptide from E3 ubiquitin-protein ligase Mdm2

OrganismNot specified

UniProt D3ZVH5

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 191–208 Chain F； UniProt 191–208	Not recorded	Beta-arrestin-1 × 2 （P29066） SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；1M ammonium sulfate, 0.1M HEPES pH 9.5, 5mM n-dodecyl-b-iminodipropionic acid, monosodium salt	Resolution 3.00 Å R-free 0.208

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	D3ZVH5_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–18； UniProt 191–208 Author chain F； PDBConstruct 1–18； UniProt 191–208

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8hsv
Deposition date deposition_date	2022-12-20
Structure title title	The structure of rat beta-arrestin1 in complex with a rat Mdm2 peptide
Keywords keywords	Arrestin, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	35.52 Å
Radius of gyration Rg (electron density) rg_electron	35.37 Å
Forward intensity I(0) i0	108038000.00
Molecular weight molecular_weight	84427.0 kDa
Excluded volume excluded_volume	106300 Å³
Envelope volume envelope_volume	145770 Å³
Hydration-shell volume shell_volume	35982 Å³
Envelope diameter envelope_diameter	124.9 Å
Shell Rg shell_rg	39.66 Å
Envelope Rg envelope_rg	35.48 Å
Shape Rg shape_rg	35.36 Å
Total Rg total_rg	35.70 Å
Total atoms total_atoms	5954
Residues n_residues	751
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	119.6 Å
Rg (real space) rg_real	35.75 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	1.0800e+08
I(0) uncertainty (real space) i0_real_error	1.9540e+06
Rg (reciprocal space) rg_reciprocal	35.61 Å
I(0) (reciprocal space) i0_reciprocal	108000000.0000
Solution quality estimate total_estimate	0.8412
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	31.9 Å
Skewness Skewness skewness	0.447
Kurtosis Kurtosis kurtosis	-0.464
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20890000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.828; Smooth: 0.638

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Beta-arrestin-1
Molecular weight formula_weight	46505.8 kDa
Mutation mutation	C59V,C125S,C140S,C150V,C242V,C251V,C269S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6042

MGSSHHHHHHSSGLVPRGSHMGDKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVDPVDGVVLVDPEYLKERRVYVTLTVAFRYGREDLDVLGLTFRKDLFVANVQSFPPAPEDKKPLTRLQERLIKKLGEHAYPFTFEIPPNLPSSVTLQPGPEDTGKALGVDYEVKAFVAENLEEKIHKRNSVRLVIRKVQYAPERPGPQPTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYADIVLFNTAQYKVPVAMEEADDTVAPSSTFSKVYTLTPFLANNREKRGLALDGKLKHEDTNLASSTLLREGANREILGIIVSYKVKVKLVVSRGGLLGDLASSDVAVELPFTLMHPKPKEEPPHREVPESETPVDTNLIELDTNDDDIVFEDFARQ

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	peptide from E3 ubiquitin-protein ligase Mdm2
Molecular weight formula_weight	1907.9 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

DLDDGVSDHSADCLDQDS

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	88

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8hsvA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	640 —

Domain ID domain_id	8hsvB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	640 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	80.673 Å
Unit-cell length b length_b	80.673 Å
Unit-cell length c length_c	173.555 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 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	40.340 Å
R factor r_factor	0.1786
R_work r_work	0.1760
R_free r_free	0.2085

fit	/app/data/saxs_computation/hs/8hsv/8hsv.fit
pddf	/app/data/pr_computation/hs/8hsv/8hsv.pr.out
profile	/app/data/saxs_computation/hs/8hsv/8hsv.dat

The structure of rat beta-arrestin1 in complex with a rat Mdm2 peptide

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

Beta-arrestin-1

State in the Current Structure

Other States of the Same Protein in the Database

peptide from E3 ubiquitin-protein ligase Mdm2

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)