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- PDB-3lk2: Crystal structure of CapZ bound to the uncapping motif from CARMIL -

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Basic information

Entry
Database: PDB / ID: 3lk2
TitleCrystal structure of CapZ bound to the uncapping motif from CARMIL
Components
  • F-actin-capping protein subunit alpha-1
  • F-actin-capping protein subunit beta isoforms 1 and 2
  • Leucine-rich repeat-containing protein 16A
KeywordsPROTEIN BINDING / CapZ / CARMIL / actin filaments / uncapping / actin-filament regulators / protein-protein complex / Actin capping / Actin-binding / Cytoskeleton
Function / homology
Function and homology information


barbed-end actin filament uncapping / positive regulation of lamellipodium organization / negative regulation of barbed-end actin filament capping / Advanced glycosylation endproduct receptor signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / RHOD GTPase cycle / RHOF GTPase cycle / COPI-mediated anterograde transport / macropinosome ...barbed-end actin filament uncapping / positive regulation of lamellipodium organization / negative regulation of barbed-end actin filament capping / Advanced glycosylation endproduct receptor signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / RHOD GTPase cycle / RHOF GTPase cycle / COPI-mediated anterograde transport / macropinosome / Factors involved in megakaryocyte development and platelet production / actin filament network formation / F-actin capping protein complex / WASH complex / macropinocytosis / negative regulation of filopodium assembly / regulation of Arp2/3 complex-mediated actin nucleation / urate metabolic process / cell junction assembly / ruffle organization / actin polymerization or depolymerization / barbed-end actin filament capping / regulation of cell morphogenesis / regulation of lamellipodium assembly / lamellipodium assembly / positive regulation of actin filament polymerization / cortical cytoskeleton / cell leading edge / filamentous actin / brush border / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / cytoskeleton organization / hippocampal mossy fiber to CA3 synapse / actin filament organization / cell morphogenesis / Schaffer collateral - CA1 synapse / Z disc / actin filament binding / cell migration / lamellipodium / Factors involved in megakaryocyte development and platelet production / actin cytoskeleton organization / postsynaptic density / nuclear speck / positive regulation of cell migration / protein-containing complex binding / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
CARMIL, C-terminal domain / CARMIL, pleckstrin homology domain / CARMIL C-terminus / Carmil pleckstrin homology domain / : / F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site ...CARMIL, C-terminal domain / CARMIL, pleckstrin homology domain / CARMIL C-terminus / Carmil pleckstrin homology domain / : / F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / Ribosomal protein S3 C-terminal domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Aspartate Aminotransferase, domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Leucine-rich repeat / Leucine-rich repeat domain superfamily / PH-like domain superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta isoforms 1 and 2 / F-actin-uncapping protein LRRC16A
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHernandez-Valladares, M. / Kim, T. / Kannan, B. / Tung, A. / Aguda, A.H. / Larsson, M. / Cooper, J.A. / Robinson, R.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural characterization of a capping protein interaction motif defines a family of actin filament regulators.
Authors: Hernandez-Valladares, M. / Kim, T. / Kannan, B. / Tung, A. / Aguda, A.H. / Larsson, M. / Cooper, J.A. / Robinson, R.C.
History
DepositionJan 27, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-actin-capping protein subunit alpha-1
B: F-actin-capping protein subunit beta isoforms 1 and 2
T: Leucine-rich repeat-containing protein 16A


Theoretical massNumber of molelcules
Total (without water)66,2383
Polymers66,2383
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-57 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.9, 71.8, 154.1
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein F-actin-capping protein subunit alpha-1 / CapZ 36/32 / Beta-actinin subunit I


Mass: 33001.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZA1 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P13127
#2: Protein F-actin-capping protein subunit beta isoforms 1 and 2 / CapZ B1 and B2 / CapZ 36/32 / Beta-actinin subunit II


Mass: 27315.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZB / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P14315
#3: Protein Leucine-rich repeat-containing protein 16A / CARMIL homolog


Mass: 5920.755 Da / Num. of mol.: 1 / Fragment: CPI, capping protein interacting motif / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human)
References: UniProt: Q5VZK9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% w/v PEG 20000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2008 / Details: phosphor screen, fiber-optic taper and CCD chip
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 31702 / Num. obs: 31671 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 20.4
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 8.1 / Num. unique all: 1514 / Rsym value: 0.37 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IZN

1izn


Resolution: 2.2→19.71 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.784 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1603 5.1 %RANDOM
Rwork0.209 ---
all0.215 29998 --
obs0.215 29998 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 0 260 4632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224461
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9526030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04424.867226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.5215801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2091528
X-RAY DIFFRACTIONr_chiral_restr0.10.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213404
X-RAY DIFFRACTIONr_mcbond_it0.6061.52715
X-RAY DIFFRACTIONr_mcangle_it1.18324389
X-RAY DIFFRACTIONr_scbond_it2.05431746
X-RAY DIFFRACTIONr_scangle_it3.3564.51641
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 119 -
Rwork0.25 2103 -
obs-2103 98.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.71150.76760.32931.7604-0.13270.8920.14640.0355-0.1976-0.1071-0.0850.13470.1997-0.1155-0.06140.1650.08590.01390.13540.01180.097110.77239.681959.5338
21.77911.12530.16412.1035-0.13471.1607-0.08840.16310.0593-0.26590.0488-0.0687-0.12010.08240.03960.14950.07050.06060.12140.02920.058430.014436.635755.7395
36.20043.3973-1.0945.6543-2.17132.2334-0.08890.65010.2649-0.41150.16460.66910.0528-0.2013-0.07570.28130.1554-0.03010.24480.01490.236813.627536.397151.2431
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 276
2X-RAY DIFFRACTION2B2 - 243
3X-RAY DIFFRACTION3T970 - 1002

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