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6m3r

Crystal structure of AnkG/beta4-spectrin complex

Method: X-RAY DIFFRACTION Dmax: 136.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ankyrin-3

Rattus norvegicus

UniProt O70511

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 975–1465 Not recorded Spectrin beta chain × 1 （Q8VIE5） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8.5；289 K；0.8 M potassium sodium tartrate tetrahydrate, 0.1 M Tris, pH 8.5 and 0.5% w/v polyethylene glycol monomethyl ether 5,000 Resolution 4.31 Å R-free 0.295

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 6M3R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5YIP Crystal Structure of AnkG LIR/GABARAPL1 complex Deposited 2017-10-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1985–2010（26 aa） Fragment：UNP RESIDUES 1985-2010
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；289 K；35% w/v Pentaerythritol ethoxylate 797 (15/4 EO/OH), 0.2 M ammonium sulfate, 0.1 M sodium acetate (pH 4.6)
Resolution 1.85 Å R-free 0.222
5YIQ Crystal structure of AnkG LIR/LC3B complex Deposited 2017-10-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1985–2010（26 aa） Fragment：UNP RESIDUES 1985-2010
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；289 K；10% v/v 2-propanol, 0.2 M zinc acetate, 0.1 M MES buffer (pH 6.5)
Resolution 2.60 Å R-free 0.259
6A9X Crystal Structure of AnkG/GABARAP Complex Deposited 2018-07-16 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1987–2010（24 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；289 K；2.0 M ammonium citrate tribasic, 0.1 M BIS-TRIS propane buffer
Resolution 2.20 Å R-free 0.249
6M3P Crystal structure of AnkG/beta2-spectrin complex Deposited 2020-03-04 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 975–1465（491 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10% w/v polyethylene glycol 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol and 0.1 M HEPES pH 7.5
Resolution 3.31 Å R-free 0.295
6M3P Crystal structure of AnkG/beta2-spectrin complex Deposited 2020-03-04 Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 975–1465（491 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10% w/v polyethylene glycol 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol and 0.1 M HEPES pH 7.5
Resolution 3.31 Å R-free 0.295
7XCE Crystal structure of Ankyrin G in complex with neurofascin Deposited 2022-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 275–500（226 aa）
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289.2 K；0.1 M ammonium acetate, 0.1 M Bis-Tris (pH 5.5), 17% w/v polyethylene glycol 10000
Resolution 2.50 Å R-free 0.233

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ANK3_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain E； PDBConstruct 1–491； UniProt 975–1465

Spectrin beta chain

Mus musculus

UniProt Q8VIE5

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain F； UniProt 1616–1937 Not recorded Ankyrin-3 × 1 （O70511） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8.5；289 K；0.8 M potassium sodium tartrate tetrahydrate, 0.1 M Tris, pH 8.5 and 0.5% w/v polyethylene glycol monomethyl ether 5,000 Resolution 4.31 Å R-free 0.295

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 6M3R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6M3Q Crystal structure of AnkB/beta4-spectrin complex Deposited 2020-03-04 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1616–1937（322 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；25% w/v pentaerythritol propoxylate 629 (17/8 PO/OH), 50 mM magnesium chloride and 0.1 M HEPES, pH 7.5
Resolution 3.44 Å R-free 0.307

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

View Construct and Data Evidence
UniProt name Q8VIE5_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain F； PDBConstruct 1–322； UniProt 1616–1937

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

SAXS profile for 6m3r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6m3r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6m3r
Deposition date deposition_date2020-03-04
Structure title titleCrystal structure of AnkG/beta4-spectrin complex
Keywords keywordsPROTEIN BINDING, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.57 Å
Radius of gyration Rg (electron density) rg_electron36.93 Å
Forward intensity I(0) i080941700.00
Molecular weight molecular_weight70945.0 kDa
Excluded volume excluded_volume88499 ų
Envelope volume envelope_volume128860 ų
Hydration-shell volume shell_volume32636 ų
Envelope diameter envelope_diameter143.8 Å
Shell Rg shell_rg37.60 Å
Envelope Rg envelope_rg37.90 Å
Shape Rg shape_rg36.95 Å
Total Rg total_rg36.89 Å
Total atoms total_atoms4999
Residues n_residues711
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax136.3 Å
Rg (real space) rg_real36.93 Å
Rg uncertainty (real space) rg_real_error2.03 Å
I(0) (real space) i0_real8.0940e+07
I(0) uncertainty (real space) i0_real_error1.5170e+06
Rg (reciprocal space) rg_reciprocal36.70 Å
I(0) (reciprocal space) i0_reciprocal80920000.0000
Solution quality estimate total_estimate0.8161
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.0 Å
Skewness Skewness skewness0.546
Kurtosis Kurtosis kurtosis-0.100
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6432000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.696; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.568; Smooth: 0.951
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)