SAXSdb — 6k3f

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

Beta-arrestin-2

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1–356 Chain B； UniProt 1–356 Chain C； UniProt 1–356 Chain D； UniProt 1–356 Chain E； UniProt 1–356 Chain F； UniProt 1–356	Not recorded	Peptide from Atypical chemokine receptor 3 × 6 （P25106）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；0.2M Ammonium acetate, 0.1M Bis-Tris pH5.5, 25% (w/v) PEG 3350	Resolution 2.30 Å R-free 0.246

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 6K3F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8J9K Structure of basal beta-arrestin2 Deposited 2023-05-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 6–398（393 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

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

View Construct and Data Evidence

UniProt name	ARRB2_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–377； UniProt 1–356 Author chain B； PDBConstruct 22–377； UniProt 1–356 Author chain C； PDBConstruct 22–377； UniProt 1–356 Author chain D； PDBConstruct 22–377； UniProt 1–356 Author chain E； PDBConstruct 22–377； UniProt 1–356 Author chain F； PDBConstruct 22–377； UniProt 1–356

Peptide from Atypical chemokine receptor 3

OrganismNot specified

UniProt P25106

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain U； UniProt 331–345 Chain V； UniProt 331–345 Chain W； UniProt 331–345 Chain X； UniProt 331–345 Chain Y； UniProt 331–345 Chain Z； UniProt 331–345	Non-standard monomer：Yes (specific site not provided by mmCIF)	Beta-arrestin-2 × 6 （P29067）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；0.2M Ammonium acetate, 0.1M Bis-Tris pH5.5, 25% (w/v) PEG 3350	Resolution 2.30 Å R-free 0.246

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 6K3F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7SK3 Cryo-EM structure of ACKR3 in complex with CXCL12, an intracellular Fab, and an extracellular Fab Deposited 2021-10-19	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 A 2–362（361 aa）	Not recorded	CLR CHOLESTEROL × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7SK4 Cryo-EM structure of ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ, an intracellular Fab, and an extracellular Fab Deposited 2021-10-19	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 A 2–362（361 aa）	Not recorded	CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7SK5 Cryo-EM structure of ACKR3 in complex with CXCL12 and an intracellular Fab Deposited 2021-10-19	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 2–362（361 aa）	Not recorded	CLR CHOLESTEROL × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7SK6 Cryo-EM structure of human ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ and an intracellular Fab Deposited 2021-10-19	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 2–362（361 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7SK7 Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, and an extracellular Fab Deposited 2021-10-19	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 2–362（361 aa）	Not recorded	GJ9 (1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7SK8 Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, an extracellular Fab, and an intracellular Fab Deposited 2021-10-19	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 A 2–362（361 aa）	Not recorded	CLR CHOLESTEROL × 6 LMN Lauryl Maltose Neopentyl Glycol × 1 GJ9 (1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7SK9 Cryo-EM structure of human ACKR3 in complex with a small molecule partial agonist CCX662, and an intracellular Fab Deposited 2021-10-19	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 × 3 PDB declaration: trimeric	Chain A 2–362（361 aa）	Not recorded	GJ9 (1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium × 1 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8TII Human ACKR3 phosphorylated by GRK2 in complex with Arrestin2 in nanodisc Deposited 2023-07-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–362（361 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8TIL Human ACKR3 phosphorylated by GRK5 in complex with Arrestin3 reconstructed without receptor/micelle Deposited 2023-07-19	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 R 2–362（361 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8TIN Human ACKR3 phosphorylated by GRK2 in complex with Arrestin3 reconstructed without receptor/micelle Deposited 2023-07-19	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 R 2–362（361 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8TIO Human ACKR3 with C tail extended by 12 glycines phosphorylated by GRK5 in complex with Arrestin2 reconstructed without receptor/micelle Deposited 2023-07-19	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 R 2–362（361 aa） Fragment：C-tail extended by 12 glycines	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8VJ9 CryoEM structure of human ACKR3 phosphorylated by GRK5 in complex with Arrestin3 variant with the C edge loop from Arrestin2 inserted Deposited 2024-01-06	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 R 2–362（361 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9E82 ACKR3 phosphorylated by GRK5 in complex with arrestin2 and Fab7 Deposited 2024-11-04	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 R 2–362（361 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

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

View Construct and Data Evidence

UniProt name	ACKR3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain U； PDBConstruct 1–15； UniProt 331–345 Author chain V； PDBConstruct 1–15； UniProt 331–345 Author chain W； PDBConstruct 1–15； UniProt 331–345 Author chain X； PDBConstruct 1–15； UniProt 331–345 Author chain Y； PDBConstruct 1–15； UniProt 331–345 Author chain Z； PDBConstruct 1–15； UniProt 331–345

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	6k3f
Deposition date deposition_date	2019-05-18
Structure title title	Crystal Structure of beta-Arrestin 2 in Complex with CXCR7 Phosphopeptide
Keywords keywords	Complex, SIGNALING PROTEIN; 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	45.63 Å
Radius of gyration Rg (electron density) rg_electron	45.60 Å
Forward intensity I(0) i0	817282000.00
Molecular weight molecular_weight	238230.0 kDa
Excluded volume excluded_volume	300130 Å³
Envelope volume envelope_volume	437060 Å³
Hydration-shell volume shell_volume	80783 Å³
Envelope diameter envelope_diameter	164.9 Å
Shell Rg shell_rg	49.02 Å
Envelope Rg envelope_rg	45.63 Å
Shape Rg shape_rg	45.59 Å
Total Rg total_rg	45.82 Å
Total atoms total_atoms	16746
Residues n_residues	2089
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	155.0 Å
Rg (real space) rg_real	45.65 Å
Rg uncertainty (real space) rg_real_error	1.85 Å
I(0) (real space) i0_real	8.1730e+08
I(0) uncertainty (real space) i0_real_error	1.4130e+07
Rg (reciprocal space) rg_reciprocal	45.63 Å
I(0) (reciprocal space) i0_reciprocal	817300000.0000
Solution quality estimate total_estimate	0.8585
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	53.1 Å
Skewness Skewness skewness	0.414
Kurtosis Kurtosis kurtosis	-0.079
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	72500000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.790; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.792

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Beta-arrestin-2
Molecular weight formula_weight	42442.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	17270

MGSSHHHHHHSSGLVPRGSHMMGEKPGTRVFKKSSPNCKLTVYLGKRDFVDHLDKVDPVDGVVLVDPDYLKDRKVFVTLTCAFRYGREDLDVLGLSFRKDLFIATYQAFPPMPNPPRPPTRLQDRLLKKLGQHAHPFFFTIPQNLPCSVTLQPGPEDTGKACGVDFEIRAFCAKSIEEKSHKRNSVRLIIRKVQFAPETPGPQPSAETTRHFLMSDRRSLHLEASLDKELYYHGEPLNVNVHVTNNSAKTVKKIRVSVRQYADICLFSTAQYKCPVAQLEQDDQVSPSSTFCKVYTITPLLSDNREKRGLALDGQLKHEDTNLASSTIVKEGANKEVLGILVSYRVKVKLVVSRGGDVSVELPFVLMHPKPHDHITL

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli K-12

Entity 2 Entity 2 polymer

Description description	Peptide from Atypical chemokine receptor 3
Molecular weight formula_weight	1941.0 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,V,W,X,Y,Z

IFKYSAKTGLTKLID

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	524

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8. Citations (1)

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Unit-cell length a length_a	91.170 Å
Unit-cell length b length_b	127.910 Å
Unit-cell length c length_c	206.040 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.04 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	46.804 Å
R factor r_factor	0.2358
R_work r_work	0.2332
R_free r_free	0.2461

fit	/app/data/saxs_computation/k3/6k3f/6k3f.fit
pddf	/app/data/pr_computation/k3/6k3f/6k3f.pr.out
profile	/app/data/saxs_computation/k3/6k3f/6k3f.dat

Crystal Structure of beta-Arrestin 2 in Complex with CXCR7 Phosphopeptide

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

Beta-arrestin-2

State in the Current Structure

Other States of the Same Protein in the Database

Peptide from Atypical chemokine receptor 3

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)