3aae

Crystal structure of Actin capping protein in complex with CARMIL fragment

Method: X-RAY DIFFRACTION Dmax: 156.8 Å Quality: GOOD

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

F-actin-capping protein subunit alpha-1

Gallus gallus

UniProt P13127

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–286 Not recorded F-actin-capping protein subunit beta isoforms 1 and 2 × 1 (P14315) 32mer peptide from Leucine-rich repeat-containing protein 16A × 1 (Q6EDY6) 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 1–286 Not recorded F-actin-capping protein subunit beta isoforms 1 and 2 × 1 (P14315) 32mer peptide from Leucine-rich repeat-containing protein 16A × 1 (Q6EDY6) 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 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 1–286 Not recorded F-actin-capping protein subunit beta isoforms 1 and 2 × 1 (P14315) 32mer peptide from Leucine-rich repeat-containing protein 16A × 1 (Q6EDY6) 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
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain G; UniProt 1–286 Not recorded F-actin-capping protein subunit beta isoforms 1 and 2 × 1 (P14315) 32mer peptide from Leucine-rich repeat-containing protein 16A × 1 (Q6EDY6) 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
5 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain I; UniProt 1–286 Not recorded F-actin-capping protein subunit beta isoforms 1 and 2 × 1 (P14315) 32mer peptide from Leucine-rich repeat-containing protein 16A × 1 (Q6EDY6) 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

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.

19 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAZA1_CHICK
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–286; UniProt 1–286 Author chain C; PDBConstruct 1–286; UniProt 1–286 Author chain E; PDBConstruct 1–286; UniProt 1–286 Author chain G; PDBConstruct 1–286; UniProt 1–286 Author chain I; PDBConstruct 1–286; UniProt 1–286

F-actin-capping protein subunit beta isoforms 1 and 2

Gallus gallus

UniProt P14315

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–277 Not recorded F-actin-capping protein subunit alpha-1 × 1 (P13127) 32mer peptide from Leucine-rich repeat-containing protein 16A × 1 (Q6EDY6) 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 1–277 Not recorded F-actin-capping protein subunit alpha-1 × 1 (P13127) 32mer peptide from Leucine-rich repeat-containing protein 16A × 1 (Q6EDY6) 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 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 1–277 Not recorded F-actin-capping protein subunit alpha-1 × 1 (P13127) 32mer peptide from Leucine-rich repeat-containing protein 16A × 1 (Q6EDY6) 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
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain H; UniProt 1–277 Not recorded F-actin-capping protein subunit alpha-1 × 1 (P13127) 32mer peptide from Leucine-rich repeat-containing protein 16A × 1 (Q6EDY6) 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
5 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain J; UniProt 1–277 Not recorded F-actin-capping protein subunit alpha-1 × 1 (P13127) 32mer peptide from Leucine-rich repeat-containing protein 16A × 1 (Q6EDY6) 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

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.

19 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAPZB_CHICK
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–277; UniProt 1–277 Author chain D; PDBConstruct 1–277; UniProt 1–277 Author chain F; PDBConstruct 1–277; UniProt 1–277 Author chain H; PDBConstruct 1–277; UniProt 1–277 Author chain J; PDBConstruct 1–277; UniProt 1–277

32mer peptide from 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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain X; UniProt 971–1002 Fragment:CP-BINDING MOTIF, residues 971-1002 F-actin-capping protein subunit alpha-1 × 1 (P13127) F-actin-capping protein subunit beta isoforms 1 and 2 × 1 (P14315) 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain Y; UniProt 971–1002 Fragment:CP-BINDING MOTIF, residues 971-1002 F-actin-capping protein subunit alpha-1 × 1 (P13127) F-actin-capping protein subunit beta isoforms 1 and 2 × 1 (P14315) 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 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain Z; UniProt 971–1002 Fragment:CP-BINDING MOTIF, residues 971-1002 F-actin-capping protein subunit alpha-1 × 1 (P13127) F-actin-capping protein subunit beta isoforms 1 and 2 × 1 (P14315) 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
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain W; UniProt 971–1002 Fragment:CP-BINDING MOTIF, residues 971-1002 F-actin-capping protein subunit alpha-1 × 1 (P13127) F-actin-capping protein subunit beta isoforms 1 and 2 × 1 (P14315) 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
5 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain V; UniProt 971–1002 Fragment:CP-BINDING MOTIF, residues 971-1002 F-actin-capping protein subunit alpha-1 × 1 (P13127) F-actin-capping protein subunit beta isoforms 1 and 2 × 1 (P14315) 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

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.

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

View Construct and Data Evidence
UniProt name LR16A_MOUSE
Isoform
PDB entities 3
Chains and sequence ranges Author chain V; PDBConstruct 6–37; UniProt 971–1002 Author chain W; PDBConstruct 6–37; UniProt 971–1002 Author chain X; PDBConstruct 6–37; UniProt 971–1002 Author chain Y; PDBConstruct 6–37; UniProt 971–1002 Author chain Z; PDBConstruct 6–37; UniProt 971–1002

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 3aae

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3aae
Deposition date deposition_date2009-11-16
Structure title titleCrystal structure of Actin capping protein in complex with CARMIL fragment
Keywords keywords;ACTIN CAPPING PROTEIN, BARBED END REGULATION, CARMIL FAMILY PROTEIN, CONFORMATIONAL CHANGE, CELL MOTILITY, Actin capping, Actin-binding, Cytoskeleton, Isopeptide bond, Leucine-rich repeat, PROTEIN BINDING ;; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier50.19
Radius of gyration Rg (electron density) rg_electron49.47
Forward intensity I(0) i01485000000.00
Molecular weight molecular_weight314740.0 kDa
Excluded volume excluded_volume391360 ų
Envelope volume envelope_volume593380 ų
Hydration-shell volume shell_volume97436 ų
Envelope diameter envelope_diameter159.5
Shell Rg shell_rg56.99
Envelope Rg envelope_rg47.19
Shape Rg shape_rg49.47
Total Rg total_rg49.74
Total atoms total_atoms22177
Residues n_residues2758
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 dmax156.8
Rg (real space) rg_real49.92
Rg uncertainty (real space) rg_real_error1.14
I(0) (real space) i0_real1.4850e+09
I(0) uncertainty (real space) i0_real_error2.8590e+07
Rg (reciprocal space) rg_reciprocal50.40
I(0) (reciprocal space) i0_reciprocal1486000000.0000
Solution quality estimate total_estimate0.8836
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary65.8
Skewness Skewness skewness-0.003
Kurtosis Kurtosis kurtosis-0.491
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha56670000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.890

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

Domain ID domain_id3aaeA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1140 — Ribosomal protein S3 C-terminal domain
Homologous superfamily homologous superfamily60 — F-actin capping protein, alpha subunit
Domain ID domain_id3aaeA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily210 — F-actin capping protein, beta subunit
Domain ID domain_id3aaeB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily570 — F-actin capping protein, alpha/beta subunit, N-terminal domain
Domain ID domain_id3aaeB02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily210 — F-actin capping protein, beta subunit
Domain ID domain_id3aaeC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1140 — Ribosomal protein S3 C-terminal domain
Homologous superfamily homologous superfamily60 — F-actin capping protein, alpha subunit
Domain ID domain_id3aaeC02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily210 — F-actin capping protein, beta subunit
Domain ID domain_id3aaeD01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily570 — F-actin capping protein, alpha/beta subunit, N-terminal domain
Domain ID domain_id3aaeD02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily210 — F-actin capping protein, beta subunit
Domain ID domain_id3aaeE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1140 — Ribosomal protein S3 C-terminal domain
Homologous superfamily homologous superfamily60 — F-actin capping protein, alpha subunit
Domain ID domain_id3aaeE02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily210 — F-actin capping protein, beta subunit
Domain ID domain_id3aaeF01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily570 — F-actin capping protein, alpha/beta subunit, N-terminal domain
Domain ID domain_id3aaeF02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily210 — F-actin capping protein, beta subunit
Domain ID domain_id3aaeG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1140 — Ribosomal protein S3 C-terminal domain
Homologous superfamily homologous superfamily60 — F-actin capping protein, alpha subunit
Domain ID domain_id3aaeG02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily210 — F-actin capping protein, beta subunit
Domain ID domain_id3aaeH01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily570 — F-actin capping protein, alpha/beta subunit, N-terminal domain
Domain ID domain_id3aaeH02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily210 — F-actin capping protein, beta subunit
Domain ID domain_id3aaeI01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1140 — Ribosomal protein S3 C-terminal domain
Homologous superfamily homologous superfamily60 — F-actin capping protein, alpha subunit
Domain ID domain_id3aaeI02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily210 — F-actin capping protein, beta subunit
Domain ID domain_id3aaeJ01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily570 — F-actin capping protein, alpha/beta subunit, N-terminal domain
Domain ID domain_id3aaeJ02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily210 — F-actin capping protein, beta subunit

8. Citations (1)

9. Files and Curves (10)