1y19

Structural basis for phosphatidylinositol phosphate kinase type I-gamma binding to talin at focal adhesions

Method: X-RAY DIFFRACTION Dmax: 153.0 Å Quality: GOOD

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

Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma

Mus musculus

UniProt O70161

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 638–651 Fragment:C-TERMINAL REGION Talin 1 × 1 (P26039) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K Resolution 2.60 Å R-free 0.286
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 638–651 Fragment:C-TERMINAL REGION Talin 1 × 1 (P26039) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K Resolution 2.60 Å R-free 0.286
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 638–651 Fragment:C-TERMINAL REGION Talin 1 × 1 (P26039) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K Resolution 2.60 Å R-free 0.286
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 638–651 Fragment:C-TERMINAL REGION Talin 1 × 1 (P26039) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K Resolution 2.60 Å R-free 0.286
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain I; UniProt 638–651 Fragment:C-TERMINAL REGION Talin 1 × 1 (P26039) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K Resolution 2.60 Å R-free 0.286
6 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain K; UniProt 638–651 Fragment:C-TERMINAL REGION Talin 1 × 1 (P26039) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K Resolution 2.60 Å R-free 0.286

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.

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

View Construct and Data Evidence
UniProt name PI51C_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–14; UniProt 638–651 Author chain C; PDBConstruct 1–14; UniProt 638–651 Author chain E; PDBConstruct 1–14; UniProt 638–651 Author chain G; PDBConstruct 1–14; UniProt 638–651 Author chain I; PDBConstruct 1–14; UniProt 638–651 Author chain K; PDBConstruct 1–14; UniProt 638–651

Talin 1

Mus musculus

UniProt P26039

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 B; UniProt 209–410 Fragment:F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma × 1 (O70161) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K Resolution 2.60 Å R-free 0.286
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 209–410 Fragment:F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma × 1 (O70161) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K Resolution 2.60 Å R-free 0.286
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 209–410 Fragment:F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma × 1 (O70161) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K Resolution 2.60 Å R-free 0.286
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 209–410 Fragment:F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma × 1 (O70161) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K Resolution 2.60 Å R-free 0.286
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain J; UniProt 209–410 Fragment:F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma × 1 (O70161) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K Resolution 2.60 Å R-free 0.286
6 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain L; UniProt 209–410 Fragment:F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma × 1 (O70161) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K Resolution 2.60 Å R-free 0.286

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.

50 other PDB entries and 65 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TLN1_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–202; UniProt 209–410 Author chain D; PDBConstruct 1–202; UniProt 209–410 Author chain F; PDBConstruct 1–202; UniProt 209–410 Author chain H; PDBConstruct 1–202; UniProt 209–410 Author chain J; PDBConstruct 1–202; UniProt 209–410 Author chain L; PDBConstruct 1–202; UniProt 209–410

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 1y19

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1y19
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1y19
Deposition date deposition_date2004-11-17
Structure title titleStructural basis for phosphatidylinositol phosphate kinase type I-gamma binding to talin at focal adhesions
Keywords keywordsFOCAL ADHESION; FERM DOMAIN; CYTOSKELETON; NPXY MOTIF; PTB DOMAIN, STRUCTURAL PROTEIN, SIGNALING PROTEIN; STRUCTURAL PROTEIN, SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier47.42
Radius of gyration Rg (electron density) rg_electron47.04
Forward intensity I(0) i0270681000.00
Molecular weight molecular_weight140040.0 kDa
Excluded volume excluded_volume177530 ų
Envelope volume envelope_volume281490 ų
Hydration-shell volume shell_volume52784 ų
Envelope diameter envelope_diameter157.5
Shell Rg shell_rg48.33
Envelope Rg envelope_rg45.03
Shape Rg shape_rg47.02
Total Rg total_rg47.19
Total atoms total_atoms9882
Residues n_residues1218
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax153.0
Rg (real space) rg_real47.37
Rg uncertainty (real space) rg_real_error1.61
I(0) (real space) i0_real2.7070e+08
I(0) uncertainty (real space) i0_real_error5.5820e+06
Rg (reciprocal space) rg_reciprocal47.42
I(0) (reciprocal space) i0_reciprocal270700000.0000
Solution quality estimate total_estimate0.8927
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary55.6
Skewness Skewness skewness0.183
Kurtosis Kurtosis kurtosis-0.542
Angular range angular_range— – 0.1650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10370000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.951; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.749

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1y19b1
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.1 — Second domain of FERM
Domain ID domain_idd1y19b2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.5 — Third domain of FERM
Domain ID domain_idd1y19d1
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.1 — Second domain of FERM
Domain ID domain_idd1y19d2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.5 — Third domain of FERM
Domain ID domain_idd1y19f1
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.1 — Second domain of FERM
Domain ID domain_idd1y19f2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.5 — Third domain of FERM
Domain ID domain_idd1y19h1
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.1 — Second domain of FERM
Domain ID domain_idd1y19h2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.5 — Third domain of FERM
Domain ID domain_idd1y19j1
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.1 — Second domain of FERM
Domain ID domain_idd1y19j2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.5 — Third domain of FERM
Domain ID domain_idd1y19l1
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.1 — Second domain of FERM
Domain ID domain_idd1y19l2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.5 — Third domain of FERM

CATH v4.4 (12 domains)

Domain ID domain_id1y19B01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10
Domain ID domain_id1y19B02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id1y19D01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10
Domain ID domain_id1y19D02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id1y19F01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10
Domain ID domain_id1y19F02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id1y19H01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10
Domain ID domain_id1y19H02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id1y19J01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10
Domain ID domain_id1y19J02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id1y19L01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10
Domain ID domain_id1y19L02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

8. Citations (1)

9. Files and Curves (10)