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- PDB-3lk3: Crystal structure of CapZ bound to the CPI and CSI uncapping moti... -

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Basic information

Entry
Database: PDB / ID: 3lk3
TitleCrystal structure of CapZ bound to the CPI and CSI uncapping motifs 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 / Cytoplasm / 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 / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / 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 / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / macropinosome / Factors involved in megakaryocyte development and platelet production / actin filament network formation / WASH complex / sperm connecting piece / F-actin capping protein complex / macropinocytosis / negative regulation of filopodium assembly / urate metabolic process / regulation of Arp2/3 complex-mediated actin nucleation / cell junction assembly / ruffle organization / barbed-end actin filament capping / actin polymerization or depolymerization / regulation of cell morphogenesis / regulation of lamellipodium assembly / lamellipodium assembly / cortical cytoskeleton / positive regulation of actin filament polymerization / cell leading edge / filamentous actin / brush border / positive regulation of substrate adhesion-dependent cell spreading / cytoskeleton organization / positive regulation of stress fiber assembly / hippocampal mossy fiber to CA3 synapse / actin filament organization / Schaffer collateral - CA1 synapse / cell morphogenesis / Z disc / actin filament binding / cell migration / lamellipodium / Factors involved in megakaryocyte development and platelet production / actin cytoskeleton organization / postsynaptic density / positive regulation of cell migration / nuclear speck / 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 / F-actin-capping protein subunit beta, N-terminal domain ...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 / Leucine rich repeat, ribonuclease inhibitor type / Ribosomal protein S3 C-terminal domain / Leucine Rich repeat / Aspartate Aminotransferase, domain 1 / Leucine-rich repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsHernandez-Valladares, M. / Kim, T. / Kannan, B. / Tung, A. / 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: 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)77,3903
Polymers77,3903
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13770 Å2
ΔGint-68 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.124, 115.535, 61.675
Angle α, β, γ (deg.)90.00, 108.20, 90.00
Int Tables number4
Space group name H-MP1211

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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: 31403.449 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: 12984.595 Da / Num. of mol.: 1 / Fragment: CBR115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARMIL, LRRC16, LRRC16A / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5VZK9
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M KCl, 20% (w/v) PEG 3350 , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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, 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: 2.68→24.27 Å / Num. obs: 17727 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 29.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 8.9 / Num. unique all: 1751 / Rsym value: 0.14 / % possible all: 99.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.5_2) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LK2

3lk2


Resolution: 2.68→20 Å / SU ML: 0.31 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 781 5.2 %RANDOM
Rwork0.1552 ---
obs0.1601 15020 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.708 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 34.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.0888 Å20 Å21.1345 Å2
2--0.648 Å20 Å2
3---0.4409 Å2
Refinement stepCycle: LAST / Resolution: 2.68→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4524 0 0 80 4604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084613
X-RAY DIFFRACTIONf_angle_d1.146232
X-RAY DIFFRACTIONf_dihedral_angle_d19.7231725
X-RAY DIFFRACTIONf_chiral_restr0.078678
X-RAY DIFFRACTIONf_plane_restr0.004816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6795-2.84720.3141300.1992240086
2.8472-3.06660.32061370.1792241387
3.0666-3.37450.26621220.1638243387
3.3745-3.86110.25741220.1338238486
3.8611-4.85820.19031390.1165233384
4.8582-24.27140.20631310.1416227681
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.37140.16780.22080.4818-0.060.3330.005-0.01550.0220.0897-0.00150.0269-0.04060.02880.00020.04820.01290.00740.01630.00320.00356.61136.291812.3917
20.23980.16770.35920.52740.31480.597-0.0302-0.06510.0037-0.02010.01350.0724-0.0214-0.08890.02060.0153-0.02370.00310.0642-0.0180.0436
30.40610.00580.37940.0884-0.1541.3743-0.1487-0.0399-0.0180.0074-0.093-0.0517-0.1198-0.12710.12460.08870.05570.01430.09090.01550.0261
40.69110.08620.17061.1347-0.89421.20830.04270.19960.1717-0.1637-0.2855-0.26770.1790.26010.25190.10220.02830.01510.14910.15460.2018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and resid 7:276
2X-RAY DIFFRACTION2chain 'B' and resid 2:243
3X-RAY DIFFRACTION3chain 'T' and resid 970:1004
4X-RAY DIFFRACTION4chain 'T' and resid 1019:1037

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