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- PDB-1izn: Crystal Structure of Actin Filament Capping Protein CapZ -

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Basic information

Entry
Database: PDB / ID: 1izn
TitleCrystal Structure of Actin Filament Capping Protein CapZ
Components
  • CapZ alpha-1 subunit
  • CapZ beta-1 subunit
KeywordsPROTEIN BINDING / HETERODIMER / CAPPING PROTEIN / ACTIN FILAMENT BARBED END CAPPING
Function / homology
Function and homology information


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 / Factors involved in megakaryocyte development and platelet production / COPI-mediated anterograde transport / negative regulation of filopodium assembly / sperm head-tail coupling apparatus / F-actin capping protein complex ...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 / Factors involved in megakaryocyte development and platelet production / COPI-mediated anterograde transport / negative regulation of filopodium assembly / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / regulation of lamellipodium assembly / regulation of cell morphogenesis / lamellipodium assembly / cortical cytoskeleton / brush border / cytoskeleton organization / hippocampal mossy fiber to CA3 synapse / Schaffer collateral - CA1 synapse / Z disc / cell morphogenesis / actin filament binding / lamellipodium / actin cytoskeleton organization / postsynaptic density / membrane / plasma membrane / cytosol
Similarity search - Function
Capz alpha-1 subunit / 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 ...Capz alpha-1 subunit / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Aspartate Aminotransferase, domain 1 / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Special / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta isoforms 1 and 2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsYamashita, A. / Maeda, K. / Maeda, Y.
CitationJournal: EMBO J. / Year: 2003
Title: Crystal structure of CapZ: structural basis for actin filament barbed end capping
Authors: Yamashita, A. / Maeda, K. / Maeda, Y.
History
DepositionOct 10, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CapZ alpha-1 subunit
B: CapZ beta-1 subunit
C: CapZ alpha-1 subunit
D: CapZ beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0588
Polymers128,8104
Non-polymers2484
Water9,242513
1
A: CapZ alpha-1 subunit
B: CapZ beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5294
Polymers64,4052
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-44 kcal/mol
Surface area26630 Å2
MethodPISA
2
C: CapZ alpha-1 subunit
D: CapZ beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5294
Polymers64,4052
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-43 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.200, 57.200, 99.200
Angle α, β, γ (deg.)90.00, 113.00, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChains A and B, C and D are biological heterodimer assemblies respectively.

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Components

#1: Protein CapZ alpha-1 subunit / F-ACTIN CAPPING PROTEIN ALPHA-1 SUBUNIT


Mass: 33001.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)plysS / References: UniProt: P13127
#2: Protein CapZ beta-1 subunit / F-actin capping protein beta subunit isoform 1


Mass: 31403.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken)
Description: The cDNAs encoding alpha-1 and beta-1 subunits were cloned in a single vector
Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)plysS / References: UniProt: P14315
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG3350, magnesium nitrate, MES-NAOH, Jeffamine M-600, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
25 mMTris-HCl1droppH8.0
31 mMdithiothreitol1drop
45 %Jeffamine M-6001drop
518 %PEG33501reservoir
60.2 M1reservoirMg(NO3)2
70.1 MMES-NaOH1reservoirpH6.0

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 24, 2002 / Details: CYLINDRICAL BEND MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 61111 / Num. obs: 61088 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.75 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 26
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.265 / % possible all: 100
Reflection
*PLUS
Num. measured all: 228951
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2970 4.93 %RANDOM
Rwork0.222 ---
all-60190 --
obs-60190 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.24 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 43.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.994 Å20 Å2-2.679 Å2
2--1.989 Å20 Å2
3----0.994 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8743 0 16 513 9272
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.378
X-RAY DIFFRACTIONc_dihedral_angle_d23.156
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.4441.5
X-RAY DIFFRACTIONc_mcangle_it2.4262
X-RAY DIFFRACTIONc_scbond_it1.9362
X-RAY DIFFRACTIONc_scangle_it2.9162.5
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.34 279 4.7 %
Rwork0.276 5661 -
obs-5940 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NO3.PARAMNO3.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.156
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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