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3tad

Crystal Structure of the Liprin-alpha/Liprin-beta complex

Method: X-RAY DIFFRACTION Dmax: 170.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Liprin-alpha-2

Homo sapiens

UniProt O75334

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 A； UniProt 866–1193 Fragment：UNP residues 866-975, 1113-1193 Liprin-beta-1 × 1 （Q8C8U0） GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；3-5% PEG8000, 0.15M NaCl, 0.1M Bis-Tris buffer, pH 6.0, vapor diffusion, hanging drop, temperature 289K Resolution 2.90 Å R-free 0.258
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 866–1193 Fragment：UNP residues 866-975, 1113-1193 Liprin-beta-1 × 1 （Q8C8U0） GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；3-5% PEG8000, 0.15M NaCl, 0.1M Bis-Tris buffer, pH 6.0, vapor diffusion, hanging drop, temperature 289K Resolution 2.90 Å R-free 0.258

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 3TAD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3TAC Crystal Structure of the Liprin-alpha/CASK complex Deposited 2011-08-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 866–1193（328 aa） Fragment：UNP residues 866-1193
Not recorded SO4 SULFATE ION × 7 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.4M ammonium sulfate, 0.2M NaCl, MES buffer, pH 6.5, vapor diffusion, hanging drop, temperature 289K
Resolution 2.20 Å R-free 0.236
6IUH Crystal structure of GIT1 PBD domain in complex with Liprin-alpha2 Deposited 2018-11-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 642–671（30 aa）
Not recorded IOD IODIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.2M Potassium iodide, 0.1M MES pH 6.5, 25% w/v PEG 4000
Resolution 1.80 Å R-free 0.267
6IUH Crystal structure of GIT1 PBD domain in complex with Liprin-alpha2 Deposited 2018-11-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 642–671（30 aa）
Not recorded IOD IODIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.2M Potassium iodide, 0.1M MES pH 6.5, 25% w/v PEG 4000
Resolution 1.80 Å R-free 0.267
7D2E Tetrameric coiled-coil structure of liprin-alpha2_H3 Deposited 2020-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 164–235（72 aa） Fragment：UNP residues 164-235
Chain B 164–235（72 aa） Fragment：UNP residues 164-235
Chain C 164–235（72 aa） Fragment：UNP residues 164-235
Chain D 164–235（72 aa） Fragment：UNP residues 164-235
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0, 10% w/v Polyethylene glycol 6,000
Resolution 1.70 Å R-free 0.269
7D2G Coiled-coil structure of liprin-alpha2_H2delC Deposited 2020-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 102–150（49 aa） Fragment：UNP residues 102-150
Chain B 102–150（49 aa） Fragment：UNP residues 102-150
Mutation：L106M, C143A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L106M, C143A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Sodium thiocyanate, 20% w/v Polyethylene glycol 3,350
Resolution 1.70 Å R-free 0.263
7D2G Coiled-coil structure of liprin-alpha2_H2delC Deposited 2020-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 102–150（49 aa） Fragment：UNP residues 102-150
Chain D 102–150（49 aa） Fragment：UNP residues 102-150
Mutation：L106M, C143A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L106M, C143A Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Sodium thiocyanate, 20% w/v Polyethylene glycol 3,350
Resolution 1.70 Å R-free 0.263
7D2H Tetrameric coiled-coil structure of liprin-alpha2_H2 Deposited 2020-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 102–163（62 aa） Fragment：UNP residues 102-163
Chain B 102–163（62 aa） Fragment：UNP residues 102-163
Chain C 102–163（62 aa） Fragment：UNP residues 102-163
Chain D 102–163（62 aa） Fragment：UNP residues 102-163
Mutation：C143A Mutation：C143A Mutation：C143A Mutation：C143A GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；20% v/v 2-Propanol, 0.1 M Tris pH 8.0, 5% w/v Polyethylene glycol 8,000
Resolution 2.20 Å R-free 0.281
8Z22 Crystal structure of the liprin-alpha2/RIM1 complex Deposited 2024-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 300–404（105 aa）
Chain D 300–404（105 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；28% V/V 2-Propanol; 0.1M BIS-TRIS pH 6.5; 3% V/V Polyethylene glycol 200
Resolution 2.75 Å R-free 0.234

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LIPA2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–297； UniProt 866–1193 Author chain B； PDBConstruct 7–297； UniProt 866–1193

Liprin-beta-1

Mus musculus

UniProt Q8C8U0

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 C； UniProt 593–853 Fragment：UNP residues 593-853 Liprin-alpha-2 × 1 （O75334） GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；3-5% PEG8000, 0.15M NaCl, 0.1M Bis-Tris buffer, pH 6.0, vapor diffusion, hanging drop, temperature 289K Resolution 2.90 Å R-free 0.258
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 593–853 Fragment：UNP residues 593-853 Liprin-alpha-2 × 1 （O75334） GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；3-5% PEG8000, 0.15M NaCl, 0.1M Bis-Tris buffer, pH 6.0, vapor diffusion, hanging drop, temperature 289K Resolution 2.90 Å R-free 0.258

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 3TAD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8IW0 Crystal structure of the KANK1/liprin-beta1 complex Deposited 2023-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–23（23 aa） Fragment：N-terminal,N-terminal
Chain B 1–23（23 aa） Fragment：N-terminal,N-terminal
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 3,350
Resolution 2.10 Å R-free 0.259
8IW0 Crystal structure of the KANK1/liprin-beta1 complex Deposited 2023-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–23（23 aa） Fragment：N-terminal,N-terminal
Chain D 1–23（23 aa） Fragment：N-terminal,N-terminal
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 3,350
Resolution 2.10 Å R-free 0.259
8IW5 Crystal structure of liprin-beta H2H3 dimer Deposited 2023-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 43–89（47 aa）
Chain B 43–89（47 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.05 M Calcium acetate, 0.1 M Sodium cacodylate pH 6.0 and 25% v/v MPD
Resolution 1.70 Å R-free 0.272

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LIPB1_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 5–265； UniProt 593–853 Author chain D； PDBConstruct 5–265； UniProt 593–853

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 3tad

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3tad
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3tad
Deposition date deposition_date2011-08-04
Structure title titleCrystal Structure of the Liprin-alpha/Liprin-beta complex
Keywords keywordsPROTEIN BINDING; PROTEIN BINDING
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_guinier47.41 Å
Radius of gyration Rg (electron density) rg_electron48.37 Å
Forward intensity I(0) i0201889000.00
Molecular weight molecular_weight115590.0 kDa
Excluded volume excluded_volume144570 ų
Envelope volume envelope_volume213160 ų
Hydration-shell volume shell_volume41263 ų
Envelope diameter envelope_diameter181.2 Å
Shell Rg shell_rg45.12 Å
Envelope Rg envelope_rg48.16 Å
Shape Rg shape_rg48.41 Å
Total Rg total_rg48.06 Å
Total atoms total_atoms8143
Residues n_residues1031
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 dmax170.7 Å
Rg (real space) rg_real48.30 Å
Rg uncertainty (real space) rg_real_error2.49 Å
I(0) (real space) i0_real2.0190e+08
I(0) uncertainty (real space) i0_real_error4.5960e+06
Rg (reciprocal space) rg_reciprocal47.41 Å
I(0) (reciprocal space) i0_reciprocal201700000.0000
Solution quality estimate total_estimate0.7649
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.2 Å
Skewness Skewness skewness0.627
Kurtosis Kurtosis kurtosis-0.170
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10070000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.644; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.565; Smooth: 0.442
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id3tadA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily50 — Transcription Factor, Ets-1
Domain ID domain_id3tadA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily50 — Transcription Factor, Ets-1
Domain ID domain_id3tadA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily50 — Transcription Factor, Ets-1
Domain ID domain_id3tadB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily50 — Transcription Factor, Ets-1
Domain ID domain_id3tadB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily50 — Transcription Factor, Ets-1
Domain ID domain_id3tadB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily50 — Transcription Factor, Ets-1
Domain ID domain_id3tadC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily50 — Transcription Factor, Ets-1
Domain ID domain_id3tadC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily50 — Transcription Factor, Ets-1
Domain ID domain_id3tadC03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily50 — Transcription Factor, Ets-1
Domain ID domain_id3tadD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily50 — Transcription Factor, Ets-1
Domain ID domain_id3tadD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily50 — Transcription Factor, Ets-1
Domain ID domain_id3tadD03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily50 — Transcription Factor, Ets-1
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8. Citations (1)

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9. Files and Curves (10)