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- PDB-2kz7: Solution structure of the CARMIL CAH3a/b domain bound to capping ... -

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Basic information

Entry
Database: PDB / ID: 2kz7
TitleSolution structure of the CARMIL CAH3a/b domain bound to capping protein (CP)
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 / TROSY / Paramagnetic relaxation enhancement / protein-protein complex
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 / macropinosome / Factors involved in megakaryocyte development and platelet production ...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 / macropinosome / Factors involved in megakaryocyte development and platelet production / COPI-mediated anterograde transport / negative regulation of filopodium assembly / actin filament network formation / F-actin capping protein complex / WASH complex / sperm head-tail coupling apparatus / macropinocytosis / urate metabolic process / Factors involved in megakaryocyte development and platelet production / barbed-end actin filament capping / cell junction assembly / ruffle organization / actin polymerization or depolymerization / intermediate filament cytoskeleton / regulation of lamellipodium assembly / regulation of cell morphogenesis / lamellipodium assembly / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / cortical cytoskeleton / filamentous actin / brush border / positive regulation of stress fiber assembly / cytoskeleton organization / positive regulation of substrate adhesion-dependent cell spreading / hippocampal mossy fiber to CA3 synapse / cell morphogenesis / Schaffer collateral - CA1 synapse / Z disc / actin filament binding / cell migration / lamellipodium / actin cytoskeleton organization / postsynaptic density / nuclear speck / positive regulation of cell migration / protein-containing complex binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
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 / 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)
Mus musculus (house mouse)
MethodSOLUTION NMR / molecular dynamics, simulated annealing, torsion angle dynamics
AuthorsZwolak, A. / Tjandra, N.
CitationJournal: To be Published
Title: Solution structure of the CARMIL CAH3a/b domain bound to capping protein (CP)
Authors: Zwolak, A. / Uruno, T. / Piszczek, G.P. / Hammer III, J.A. / Tjandra, N.
History
DepositionJun 12, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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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
C: Leucine-rich repeat-containing protein 16A


Theoretical massNumber of molelcules
Total (without water)73,8553
Polymers73,8553
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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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: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P14315
#3: Protein Leucine-rich repeat-containing protein 16A / CARMIL homolog


Mass: 9449.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lrrc16a, Carmil, Lrrc16 / Plasmid: pGEX4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6EDY6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.35 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% D2O93% H2O/7% D2O
20.35 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% D2O93% H2O/7% D2O
30.35 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% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mMCPalpha subunit[U-99% 15N; U-80% 2H]1
0.35 mMCPbeta subunit[U-99% 15N; U-80% 2H]1
0.39 mMCARMIL CAH3a/b domain[U-2H]1
0.35 mMCARMIL CAH3a/b domain[U-99% 15N; U-80% 2H]2
0.39 mMCPalpha subunit[U-2H]2
0.39 mMCPbeta subunit[U-2H]2
0.35 mMCPalpha subunit[U-99% 15N; U-80% 2H]3
0.35 mMCPbeta subunit[U-99% 15N; U-80% 2H]3
0.39 mMCARMIL CAH3a/b domain[U-2H; spin labeled at 1 or 5 postions]3
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettchemical shift assignment
PIPPGarrettchemical shift calculation
PIPPGarrettpeak picking
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics, simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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