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- PDB-3aae: Crystal structure of Actin capping protein in complex with CARMIL... -

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Basic information

Entry
Database: PDB / ID: 3aae
TitleCrystal structure of Actin capping protein in complex with CARMIL fragment
Components
  • 32mer peptide from Leucine-rich repeat-containing protein 16A
  • F-actin-capping protein subunit alpha-1
  • F-actin-capping protein subunit beta isoforms 1 and 2
KeywordsPROTEIN BINDING / ACTIN CAPPING PROTEIN / BARBED END REGULATION / CARMIL FAMILY PROTEIN / CONFORMATIONAL CHANGE / CELL MOTILITY / Actin capping / Actin-binding / Cytoskeleton / Isopeptide bond / Leucine-rich repeat
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 / : / F-actin capping protein complex / macropinocytosis / urate metabolic process / negative regulation of filopodium assembly / regulation of Arp2/3 complex-mediated actin nucleation / Factors involved in megakaryocyte development and platelet production / cell junction assembly / ruffle organization / barbed-end actin filament capping / actin polymerization or depolymerization / regulation of cell morphogenesis / regulation of lamellipodium assembly / intermediate filament cytoskeleton / lamellipodium assembly / establishment or maintenance of cell polarity / cortical cytoskeleton / positive regulation of actin filament polymerization / 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 / Schaffer collateral - CA1 synapse / cell morphogenesis / Z disc / actin filament binding / cell migration / lamellipodium / actin cytoskeleton organization / postsynaptic density / positive regulation of cell migration / nuclear speck / protein-containing complex binding / membrane / nucleus / plasma membrane / cytoplasm / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsTakeda, S. / Minakata, S. / Narita, A. / Kitazawa, M. / Yamakuni, T. / Maeda, Y. / Nitanai, Y.
CitationJournal: To be Published
Title: Two distinct mechanisms for the regulation of actin capping protein-competitive or allosteric inhibitions
Authors: Takeda, S. / Minakata, S. / Narita, A. / Kitazawa, M. / Yamakuni, T. / Maeda, Y. / Nitanai, Y.
History
DepositionNov 16, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: F-actin-capping protein subunit alpha-1
D: F-actin-capping protein subunit beta isoforms 1 and 2
E: F-actin-capping protein subunit alpha-1
F: F-actin-capping protein subunit beta isoforms 1 and 2
G: F-actin-capping protein subunit alpha-1
H: F-actin-capping protein subunit beta isoforms 1 and 2
I: F-actin-capping protein subunit alpha-1
J: F-actin-capping protein subunit beta isoforms 1 and 2
X: 32mer peptide from Leucine-rich repeat-containing protein 16A
Y: 32mer peptide from Leucine-rich repeat-containing protein 16A
Z: 32mer peptide from Leucine-rich repeat-containing protein 16A
W: 32mer peptide from Leucine-rich repeat-containing protein 16A
V: 32mer peptide from Leucine-rich repeat-containing protein 16A


Theoretical massNumber of molelcules
Total (without water)342,86515
Polymers342,86515
Non-polymers00
Water00
1
A: F-actin-capping protein subunit alpha-1
B: F-actin-capping protein subunit beta isoforms 1 and 2
X: 32mer peptide from Leucine-rich repeat-containing protein 16A


Theoretical massNumber of molelcules
Total (without water)68,5733
Polymers68,5733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11580 Å2
ΔGint-55 kcal/mol
Surface area26080 Å2
MethodPISA
2
C: F-actin-capping protein subunit alpha-1
D: F-actin-capping protein subunit beta isoforms 1 and 2
Y: 32mer peptide from Leucine-rich repeat-containing protein 16A


Theoretical massNumber of molelcules
Total (without water)68,5733
Polymers68,5733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-56 kcal/mol
Surface area26100 Å2
MethodPISA
3
E: F-actin-capping protein subunit alpha-1
F: F-actin-capping protein subunit beta isoforms 1 and 2
Z: 32mer peptide from Leucine-rich repeat-containing protein 16A


Theoretical massNumber of molelcules
Total (without water)68,5733
Polymers68,5733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11490 Å2
ΔGint-53 kcal/mol
Surface area24500 Å2
MethodPISA
4
G: F-actin-capping protein subunit alpha-1
H: F-actin-capping protein subunit beta isoforms 1 and 2
W: 32mer peptide from Leucine-rich repeat-containing protein 16A


Theoretical massNumber of molelcules
Total (without water)68,5733
Polymers68,5733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11140 Å2
ΔGint-49 kcal/mol
Surface area24510 Å2
MethodPISA
5
I: F-actin-capping protein subunit alpha-1
J: F-actin-capping protein subunit beta isoforms 1 and 2
V: 32mer peptide from Leucine-rich repeat-containing protein 16A


Theoretical massNumber of molelcules
Total (without water)68,5733
Polymers68,5733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-50 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.153, 104.358, 186.633
Angle α, β, γ (deg.)90.00, 119.09, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
12B
22D
32F
42H
52J
13X
23Y
33Z
43W
53V
14B
24D
15X
25Y
35Z
45W
55V

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A8 - 276
2112C8 - 276
3112E8 - 276
4112G8 - 276
5112I8 - 276
1122B4 - 249
2122D4 - 249
3122F4 - 249
4122H4 - 249
5122J4 - 249
1133X986 - 999
2133Y986 - 999
3133Z986 - 999
4133W986 - 999
5133V986 - 999
1145B252 - 264
2145D252 - 264
1155X974 - 985
2155Y974 - 985
3155Z974 - 985
4155W974 - 985
5155V974 - 985

NCS ensembles :
ID
1
2
3
4
5
DetailsTHE ORIGOMETRIC STATE OF THE ACTIN CAPPING PROTEIN IS A HETERO DIMER COMPOSE OF SUBUNIT A (CHAIN A) AND SUBUNIT B (CHAIN B) IN VIVO AND IN VITRO.

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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.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZA1 / Plasmid: PETDUET1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 (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.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZB / Plasmid: PETDUET1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 (DE3) / References: UniProt: P14315
#3: Protein/peptide
32mer peptide from Leucine-rich repeat-containing protein 16A / CARMIL / CAPPING PROTEIN ARP2/3 MYOSIN I LINKER / CARMIL homolog


Mass: 4167.751 Da / Num. of mol.: 5 / Fragment: CP-BINDING MOTIF, residues 971-1002
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lrrc16a / Plasmid: PGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 (DE3) / References: UniProt: Q6EDY6

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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: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14% PEG 3350, 180MM TRI-AMMONIUM CITRATE, 100MM MES-NAOH, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 23, 2008 / Details: mirrors
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→49.7 Å / Num. obs: 58413 / % possible obs: 99.5 % / Redundancy: 7.6 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 16.4
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 5.56 / Num. unique all: 5823 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
DPSdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AA0

3aa0


Resolution: 3.3→49.7 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.843 / Occupancy max: 1 / Occupancy min: 1 / SU B: 27.301 / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.576 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27092 2955 5.1 %RANDOM
Rwork0.24333 ---
obs0.24472 55462 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.82 Å2 / Biso mean: 50.947 Å2 / Biso min: 27.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å21.07 Å2
2--0.51 Å20 Å2
3---1.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.67 Å
Refinement stepCycle: LAST / Resolution: 3.3→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22177 0 0 0 22177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02222623
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.95330582
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36152743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38724.7281159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.693154069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.58615157
X-RAY DIFFRACTIONr_chiral_restr0.080.23310
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117294
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6121.513744
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.144222231
X-RAY DIFFRACTIONr_scbond_it1.01838879
X-RAY DIFFRACTIONr_scangle_it1.8944.58351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1076TIGHT POSITIONAL0.030.05
1C1076TIGHT POSITIONAL0.030.05
1E1076TIGHT POSITIONAL0.030.05
1G1076TIGHT POSITIONAL0.030.05
1I1076TIGHT POSITIONAL0.030.05
1A1109MEDIUM POSITIONAL0.060.5
1C1109MEDIUM POSITIONAL0.040.5
1E1109MEDIUM POSITIONAL0.040.5
1G1109MEDIUM POSITIONAL0.040.5
1I1109MEDIUM POSITIONAL0.050.5
1A1076TIGHT THERMAL0.060.5
1C1076TIGHT THERMAL0.060.5
1E1076TIGHT THERMAL0.040.5
1G1076TIGHT THERMAL0.050.5
1I1076TIGHT THERMAL0.050.5
1A1109MEDIUM THERMAL0.072
1C1109MEDIUM THERMAL0.062
1E1109MEDIUM THERMAL0.052
1G1109MEDIUM THERMAL0.052
1I1109MEDIUM THERMAL0.062
2B984TIGHT POSITIONAL0.040.05
2D984TIGHT POSITIONAL0.030.05
2F984TIGHT POSITIONAL0.030.05
2H984TIGHT POSITIONAL0.030.05
2J984TIGHT POSITIONAL0.030.05
2B952MEDIUM POSITIONAL0.040.5
2D952MEDIUM POSITIONAL0.050.5
2F952MEDIUM POSITIONAL0.050.5
2H952MEDIUM POSITIONAL0.040.5
2J952MEDIUM POSITIONAL0.040.5
2B984TIGHT THERMAL0.080.5
2D984TIGHT THERMAL0.050.5
2F984TIGHT THERMAL0.050.5
2H984TIGHT THERMAL0.060.5
2J984TIGHT THERMAL0.060.5
2B952MEDIUM THERMAL0.092
2D952MEDIUM THERMAL0.062
2F952MEDIUM THERMAL0.052
2H952MEDIUM THERMAL0.072
2J952MEDIUM THERMAL0.072
3X52TIGHT POSITIONAL0.030.05
3Y52TIGHT POSITIONAL0.020.05
3Z52TIGHT POSITIONAL0.030.05
3W52TIGHT POSITIONAL0.030.05
3V52TIGHT POSITIONAL0.030.05
3X65LOOSE POSITIONAL0.035
3Y65LOOSE POSITIONAL0.035
3Z65LOOSE POSITIONAL0.035
3W65LOOSE POSITIONAL0.035
3V65LOOSE POSITIONAL0.035
3X52TIGHT THERMAL0.060.5
3Y52TIGHT THERMAL0.030.5
3Z52TIGHT THERMAL0.040.5
3W52TIGHT THERMAL0.050.5
3V52TIGHT THERMAL0.070.5
3X65LOOSE THERMAL0.0810
3Y65LOOSE THERMAL0.0410
3Z65LOOSE THERMAL0.0410
3W65LOOSE THERMAL0.0510
3V65LOOSE THERMAL0.0510
4B52MEDIUM POSITIONAL0.30.5
4D64LOOSE POSITIONAL1.115
4B52MEDIUM THERMAL0.512
4D64LOOSE THERMAL0.5310
5X32MEDIUM POSITIONAL0.450.5
5Y32MEDIUM POSITIONAL0.360.5
5Z32MEDIUM POSITIONAL0.30.5
5W32MEDIUM POSITIONAL0.520.5
5V32MEDIUM POSITIONAL0.460.5
5X33LOOSE POSITIONAL1.515
5Y33LOOSE POSITIONAL1.235
5Z33LOOSE POSITIONAL1.295
5W33LOOSE POSITIONAL1.375
5V33LOOSE POSITIONAL1.455
5X32MEDIUM THERMAL1.32
5Y32MEDIUM THERMAL0.532
5Z32MEDIUM THERMAL0.222
5W32MEDIUM THERMAL0.442
5V32MEDIUM THERMAL0.332
5X33LOOSE THERMAL0.9510
5Y33LOOSE THERMAL0.3410
5Z33LOOSE THERMAL0.3310
5W33LOOSE THERMAL0.3810
5V33LOOSE THERMAL0.3110
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 217 -
Rwork0.312 4072 -
all-4289 -
obs--99.26 %

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