← Back to search
4k17

Crystal Structure of mouse CARMIL residues 1-668

Method: X-RAY DIFFRACTION Dmax: 218.8 Å Quality: GOOD
▼

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

Leucine-rich repeat-containing protein 16A

Mus musculus

UniProt Q6EDY6

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–668 Fragment：PH and LRR domains (UNP residues 1-668) Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.7；293 K；16 % PEG3350, 130 mM lithium sulfate, 0.25 % w/v salicylamide, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.259
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–668 Fragment：PH and LRR domains (UNP residues 1-668) Non-standard monomer：Yes (specific site not provided by mmCIF) OHB salicylamide × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.7；293 K；16 % PEG3350, 130 mM lithium sulfate, 0.25 % w/v salicylamide, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.259
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 1–668 Fragment：PH and LRR domains (UNP residues 1-668) Non-standard monomer：Yes (specific site not provided by mmCIF) ABU GAMMA-AMINO-BUTANOIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.7；293 K；16 % PEG3350, 130 mM lithium sulfate, 0.25 % w/v salicylamide, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.259
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 1–668 Fragment：PH and LRR domains (UNP residues 1-668) Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.7；293 K；16 % PEG3350, 130 mM lithium sulfate, 0.25 % w/v salicylamide, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 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 4K17 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KZ7 Solution structure of the CARMIL CAH3a/b domain bound to capping protein (CP) Deposited 2010-06-12 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 965–1039（75 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；305 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 0.35 mM [U-99% 15N; U-80% 2H] CPalpha subunit, 0.35 mM [U-99% 15N; U-80% 2H] CPbeta subunit, 0.39 mM [U-2H] CARMIL CAH3a/b domain, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.35 mM [U-99% 15N; U-80% 2H] CARMIL CAH3a/b domain, 0.39 mM [U-2H] CPalpha subunit, 0.39 mM [U-2H] CPbeta subunit, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.35 mM [U-99% 15N; U-80% 2H] CPalpha subunit, 0.35 mM [U-99% 15N; U-80% 2H] CPbeta subunit, 0.39 mM [U-2H; spin labeled at 1 or 5 postions] CARMIL CAH3a/b domain, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
3AA0 Crystal structure of Actin Capping Protein in complex with the Cp-binding motif derived from CARMIL Deposited 2009-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 985–1005（21 aa） Fragment：CP-BINDING MOTIF, recidues 985-1005
Not recorded CO3 CARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；18% PEG 400, 40MM BACL2, 100MM MES-NAOH, PH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 1.70 Å R-free 0.239
3AAE Crystal structure of Actin capping protein in complex with CARMIL fragment Deposited 2009-11-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain X 971–1002（32 aa） Fragment：CP-BINDING MOTIF, residues 971-1002
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；14% PEG 3350, 180MM TRI-AMMONIUM CITRATE, 100MM MES-NAOH, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.30 Å R-free 0.271
3AAE Crystal structure of Actin capping protein in complex with CARMIL fragment Deposited 2009-11-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Y 971–1002（32 aa） Fragment：CP-BINDING MOTIF, residues 971-1002
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；14% PEG 3350, 180MM TRI-AMMONIUM CITRATE, 100MM MES-NAOH, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.30 Å R-free 0.271
3AAE Crystal structure of Actin capping protein in complex with CARMIL fragment Deposited 2009-11-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Z 971–1002（32 aa） Fragment：CP-BINDING MOTIF, residues 971-1002
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；14% PEG 3350, 180MM TRI-AMMONIUM CITRATE, 100MM MES-NAOH, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.30 Å R-free 0.271
3AAE Crystal structure of Actin capping protein in complex with CARMIL fragment Deposited 2009-11-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain W 971–1002（32 aa） Fragment：CP-BINDING MOTIF, residues 971-1002
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；14% PEG 3350, 180MM TRI-AMMONIUM CITRATE, 100MM MES-NAOH, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.30 Å R-free 0.271
3AAE Crystal structure of Actin capping protein in complex with CARMIL fragment Deposited 2009-11-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain V 971–1002（32 aa） Fragment：CP-BINDING MOTIF, residues 971-1002
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；14% PEG 3350, 180MM TRI-AMMONIUM CITRATE, 100MM MES-NAOH, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.30 Å R-free 0.271

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LR16A_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–669； UniProt 1–668 Author chain B； PDBConstruct 2–669； UniProt 1–668 Author chain C； PDBConstruct 2–669； UniProt 1–668 Author chain D； PDBConstruct 2–669； UniProt 1–668

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 4k17

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4k17
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id4k17
Deposition date deposition_date2013-04-04
Structure title titleCrystal Structure of mouse CARMIL residues 1-668
Keywords keywords;PH domain, LRR domain, lipid binding, protein-protein interaction, phosphatidylserine, phosphatidylinositol, phosphatidylinositol-5-phosphate, plasma membrane, LIPID BINDING PROTEIN ;; LIPID BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier66.22 Å
Radius of gyration Rg (electron density) rg_electron67.58 Å
Forward intensity I(0) i01254600000.00
Molecular weight molecular_weight294330.0 kDa
Excluded volume excluded_volume366730 ų
Envelope volume envelope_volume568810 ų
Hydration-shell volume shell_volume75769 ų
Envelope diameter envelope_diameter251.4 Å
Shell Rg shell_rg60.01 Å
Envelope Rg envelope_rg66.35 Å
Shape Rg shape_rg67.53 Å
Total Rg total_rg67.60 Å
Total atoms total_atoms20357
Residues n_residues2559
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
▼

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

Maximum dimension Dmax dmax218.8 Å
Rg (real space) rg_real66.94 Å
Rg uncertainty (real space) rg_real_error1.88 Å
I(0) (real space) i0_real1.2520e+09
I(0) uncertainty (real space) i0_real_error2.5860e+07
Rg (reciprocal space) rg_reciprocal65.20 Å
I(0) (reciprocal space) i0_reciprocal1250000000.0000
Solution quality estimate total_estimate0.8181
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary63.8 Å
Skewness Skewness skewness0.541
Kurtosis Kurtosis kurtosis-0.329
Angular range angular_range— – 0.1200 Å−1
Current regularization parameter α current_alpha0.0040
Highest regularization parameter α highest_alpha42920000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.861; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.908; Smooth: 0.145
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▼

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id4k17A01
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_id4k17A02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1850 —
Domain ID domain_id4k17A03
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id4k17B01
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_id4k17B02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1850 —
Domain ID domain_id4k17B03
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id4k17C01
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_id4k17C02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1850 —
Domain ID domain_id4k17C03
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id4k17D01
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_id4k17D02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1850 —
Domain ID domain_id4k17D03
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
▶

8. Citations (1)

▶

9. Files and Curves (10)