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- PDB-4k17: Crystal Structure of mouse CARMIL residues 1-668 -

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Basic information

Entry
Database: PDB / ID: 4k17
TitleCrystal Structure of mouse CARMIL residues 1-668
ComponentsLeucine-rich repeat-containing protein 16A
KeywordsLIPID BINDING PROTEIN / PH domain / LRR domain / lipid binding / protein-protein interaction / phosphatidylserine / phosphatidylinositol / phosphatidylinositol-5-phosphate / plasma membrane
Function / homology
Function and homology information


barbed-end actin filament uncapping / positive regulation of lamellipodium organization / negative regulation of barbed-end actin filament capping / macropinosome / actin filament network formation / macropinocytosis / urate metabolic process / regulation of Arp2/3 complex-mediated actin nucleation / Factors involved in megakaryocyte development and platelet production / ruffle organization ...barbed-end actin filament uncapping / positive regulation of lamellipodium organization / negative regulation of barbed-end actin filament capping / macropinosome / actin filament network formation / macropinocytosis / urate metabolic process / regulation of Arp2/3 complex-mediated actin nucleation / Factors involved in megakaryocyte development and platelet production / ruffle organization / intermediate filament cytoskeleton / lamellipodium assembly / establishment or maintenance of cell polarity / positive regulation of actin filament polymerization / cell leading edge / filamentous actin / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / cell migration / lamellipodium / positive regulation of cell migration / nuclear speck / protein-containing complex binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #1850 / CARMIL, C-terminal domain / CARMIL, pleckstrin homology domain / CARMIL C-terminus / Carmil pleckstrin homology domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe ...Helix Hairpins - #1850 / CARMIL, C-terminal domain / CARMIL, pleckstrin homology domain / CARMIL C-terminus / Carmil pleckstrin homology domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Helix Hairpins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Leucine-rich repeat / Helix non-globular / Leucine-rich repeat domain superfamily / Special / PH-like domain superfamily / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GAMMA-AMINO-BUTANOIC ACID / salicylamide / F-actin-uncapping protein LRRC16A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.895 Å
AuthorsZwolak, A. / Dominguez, R.
CitationJournal: Nat Commun / Year: 2013
Title: CARMIL leading edge localization depends on a non-canonical PH domain and dimerization.
Authors: Zwolak, A. / Yang, C. / Feeser, E.A. / Michael Ostap, E. / Svitkina, T. / Dominguez, R.
History
DepositionApr 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich repeat-containing protein 16A
B: Leucine-rich repeat-containing protein 16A
C: Leucine-rich repeat-containing protein 16A
D: Leucine-rich repeat-containing protein 16A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,3897
Polymers299,1134
Non-polymers2763
Water0
1
A: Leucine-rich repeat-containing protein 16A


Theoretical massNumber of molelcules
Total (without water)74,7781
Polymers74,7781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine-rich repeat-containing protein 16A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9513
Polymers74,7781
Non-polymers1732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Leucine-rich repeat-containing protein 16A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8812
Polymers74,7781
Non-polymers1031
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Leucine-rich repeat-containing protein 16A


Theoretical massNumber of molelcules
Total (without water)74,7781
Polymers74,7781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.168, 67.986, 212.151
Angle α, β, γ (deg.)92.73, 96.95, 110.15
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Leucine-rich repeat-containing protein 16A / CARMIL1 / CARMIL homolog


Mass: 74778.203 Da / Num. of mol.: 4 / Fragment: PH and LRR domains (UNP residues 1-668)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Carmil, Lrrc16, Lrrc16a / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIPL / References: UniProt: Q6EDY6
#2: Chemical ChemComp-OHB / salicylamide / 2-hydroxybenzamide / Salicylamide


Mass: 137.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID / Γ-Aminobutyric acid


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2 / Comment: neurotransmitter, inhibitor*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 16 % PEG3350, 130 mM lithium sulfate, 0.25 % w/v salicylamide, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9784 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 4, 2012 / Details: toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 2.895→50 Å / Num. all: 65054 / Num. obs: 63752 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 13.8
Reflection shellResolution: 2.895→3 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.8 / % possible all: 84.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.895→49.759 Å / Cor.coef. Fo:Fc: 0.9048 / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 1913 -RANDOM
Rwork0.2149 ---
obs-53184 83.4487 %-
Refinement stepCycle: LAST / Resolution: 2.895→49.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20339 0 18 0 20357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.308
X-RAY DIFFRACTIONc_bond_d0.023

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