SAXSdb — 8iw0

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

Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 256–315 Chain B； UniProt 256–315	Fragment：N-terminal,N-terminal	No other associated polymer	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
2	Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 256–315 Chain D； UniProt 256–315	Fragment：N-terminal,N-terminal	No other associated polymer	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

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 8IW0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5YBJ Structure of apo KANK1 ankyrin domain Deposited 2017-09-05	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 1080–1329（250 aa） Fragment：UNP residues 1080-1329	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1M HEPES, pH 7.5, 0.2M Lithium sulfate monohydrate, 25% PEG 3350	Resolution 2.34 Å R-free 0.242
5YBU Structure of the KANK1 ankyrin domain in complex with KIF21A peptide Deposited 2017-09-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1080–1329（250 aa） Fragment：UNP residues 1080-1329	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.05M magnesium formate, 21% PEG 3350	Resolution 1.89 Å R-free 0.253

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

View Construct and Data Evidence

UniProt name	KANK1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 28–87； UniProt 256–315 Author chain B； PDBConstruct 28–87； UniProt 256–315 Author chain C； PDBConstruct 28–87； UniProt 256–315 Author chain D； PDBConstruct 28–87； UniProt 256–315

Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1

Homo sapiens

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	Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–23 Chain B； UniProt 1–23	Fragment：N-terminal,N-terminal	No other associated polymer	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
2	Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–23 Chain D； UniProt 1–23	Fragment：N-terminal,N-terminal	No other associated polymer	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

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 8IW0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3TAD Crystal Structure of the Liprin-alpha/Liprin-beta complex Deposited 2011-08-04	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 C 593–853（261 aa） Fragment：UNP residues 593-853	Not recorded	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
3TAD Crystal Structure of the Liprin-alpha/Liprin-beta complex Deposited 2011-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 593–853（261 aa） Fragment：UNP residues 593-853	Not recorded	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
8IW5 Crystal structure of liprin-beta H2H3 dimer Deposited 2023-03-29	Different construct 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–23； UniProt 1–23 Author chain B； PDBConstruct 1–23； UniProt 1–23 Author chain C； PDBConstruct 1–23； UniProt 1–23 Author chain D； PDBConstruct 1–23； UniProt 1–23

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	8iw0
Deposition date deposition_date	2023-03-29
最后修订 last_revision	2023-11-08
Structure title title	Crystal structure of the KANK1/liprin-beta1 complex
Keywords keywords	Focal adhesion, Cortical microtubule stabilizing complex, PROTEIN BINDING; PROTEIN BINDING
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	30.73 Å
Radius of gyration Rg (electron density) rg_electron	30.37 Å
Forward intensity I(0) i0	21913300.00
Molecular weight molecular_weight	35476.0 kDa
Excluded volume excluded_volume	44297 Å³
Envelope volume envelope_volume	57771 Å³
Hydration-shell volume shell_volume	18363 Å³
Envelope diameter envelope_diameter	105.6 Å
Shell Rg shell_rg	32.33 Å
Envelope Rg envelope_rg	30.10 Å
Shape Rg shape_rg	30.38 Å
Total Rg total_rg	30.55 Å
Total atoms total_atoms	2472
Residues n_residues	324
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	109.2 Å
Rg (real space) rg_real	31.24 Å
Rg uncertainty (real space) rg_real_error	1.33 Å
I(0) (real space) i0_real	2.1910e+07
I(0) uncertainty (real space) i0_real_error	4.0540e+05
Rg (reciprocal space) rg_reciprocal	31.03 Å
I(0) (reciprocal space) i0_reciprocal	21910000.0000
Solution quality estimate total_estimate	0.4874
Solution quality rating solution_quality	SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	107.1 Å
Skewness Skewness skewness	0.548
Kurtosis Kurtosis kurtosis	-0.538
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1650000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.517; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.200; Smooth: 0.000

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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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Unit-cell length a length_a	48.151 Å
Unit-cell length b length_b	36.882 Å
Unit-cell length c length_c	93.011 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	47.920 Å
R factor r_factor	0.2306
R_work r_work	0.2274
R_free r_free	0.2587

Description description	Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1
Molecular weight formula_weight	10766.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,C
Atom count atom_count	2583

Crystal structure of the KANK1/liprin-beta1 complex

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

Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Liprin-beta-1,KN motif and ankyrin repeat domain-containing protein 1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	100

fit	/app/data/saxs_computation/iw/8iw0/8iw0.fit
pddf	/app/data/pr_computation/iw/8iw0/8iw0.pr.out
profile	/app/data/saxs_computation/iw/8iw0/8iw0.dat