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- PDB-6rsq: Helical folded domain of mouse CAP1 -

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Basic information

Entry
Database: PDB / ID: 6rsq
TitleHelical folded domain of mouse CAP1
ComponentsAdenylyl cyclase-associated protein 1
KeywordsCONTRACTILE PROTEIN / Actin binding protein
Function / homology
Function and homology information


ameboidal-type cell migration / cortical actin cytoskeleton / cAMP-mediated signaling / adenylate cyclase binding / receptor-mediated endocytosis / Neutrophil degranulation / actin filament organization / cell morphogenesis / actin binding / actin cytoskeleton organization ...ameboidal-type cell migration / cortical actin cytoskeleton / cAMP-mediated signaling / adenylate cyclase binding / receptor-mediated endocytosis / Neutrophil degranulation / actin filament organization / cell morphogenesis / actin binding / actin cytoskeleton organization / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Adenylate cyclase-associated CAP, N-terminal domain / Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / Adenylate cyclase associated (CAP) N terminal / CAP protein signature 1. / CAP protein signature 2. / Adenylate cyclase-associated CAP / Adenylate cyclase-associated CAP, C-terminal ...Adenylate cyclase-associated CAP, N-terminal domain / Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / Adenylate cyclase associated (CAP) N terminal / CAP protein signature 1. / CAP protein signature 2. / Adenylate cyclase-associated CAP / Adenylate cyclase-associated CAP, C-terminal / Adenylate cyclase associated (CAP) C terminal / Adenylate cyclase-associated CAP, C-terminal superfamily / CARP motif / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Adenylyl cyclase-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsKotila, T. / Kogan, K. / Lappalainen, P.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland320161 Finland
Academy of Finland307415 Finland
CitationJournal: Nat Commun / Year: 2019
Title: Mechanism of synergistic actin filament pointed end depolymerization by cyclase-associated protein and cofilin.
Authors: Kotila, T. / Wioland, H. / Enkavi, G. / Kogan, K. / Vattulainen, I. / Jegou, A. / Romet-Lemonne, G. / Lappalainen, P.
History
DepositionMay 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: 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: Adenylyl cyclase-associated protein 1
B: Adenylyl cyclase-associated protein 1
C: Adenylyl cyclase-associated protein 1
D: Adenylyl cyclase-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0237
Polymers89,7474
Non-polymers2763
Water2,072115
1
A: Adenylyl cyclase-associated protein 1
D: Adenylyl cyclase-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0574
Polymers44,8732
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-19 kcal/mol
Surface area15730 Å2
MethodPISA
2
B: Adenylyl cyclase-associated protein 1
C: Adenylyl cyclase-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9653
Polymers44,8732
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-21 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.510, 91.410, 106.870
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
Adenylyl cyclase-associated protein 1 / CAP 1


Mass: 22436.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cap1, Cap / Plasmid: pPL1063 / Details (production host): pCoofy18 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40124
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: 0.1M sodium cacodylate, 12% PEG4000 (w/v), pH 6.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2016
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.37→41.26 Å / Num. obs: 33463 / % possible obs: 99.81 % / Redundancy: 7 % / Biso Wilson estimate: 58.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1376 / Rpim(I) all: 0.05559 / Rrim(I) all: 0.1486 / Net I/σ(I): 10.63
Reflection shellResolution: 2.37→2.455 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.786 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 3266 / CC1/2: 0.868 / Rpim(I) all: 0.7036 / Rrim(I) all: 1.921 / % possible all: 99.81

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSVERSION Jan 26, 2018 BUILT=20180409data reduction
XSCALEVERSION Jan 26, 2018 BUILT=20180409data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1s0p

1s0p


Resolution: 2.37→41.26 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.319 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.225
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1606 4.8 %RANDOM
Rwork0.186 ---
obs0.188 33463 100 %-
Displacement parametersBiso mean: 64.96 Å2
Baniso -1Baniso -2Baniso -3
1-9.0993 Å20 Å20 Å2
2---10.4915 Å20 Å2
3---1.3921 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.37→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5565 0 18 115 5698
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015710HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.077724HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1979SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes958HARMONIC5
X-RAY DIFFRACTIONt_it5710HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion18.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion718SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6721SEMIHARMONIC4
LS refinement shellResolution: 2.37→2.39 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.247 -4.93 %
Rwork0.2056 637 -
all0.2077 670 -
obs--99.85 %
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)
11.6905-0.1139-0.08542.3578-0.23921.2360.07740.10710.1445-0.2534-0.04830.2863-0.0089-0.1285-0.029-0.1539-0.0198-0.0296-0.00180.0606-0.0572-14.4228-1.4314-30.0807
24.27691.01370.41942.45780.0842.10990.2027-0.48520.33680.1883-0.15650.08790.0398-0.0762-0.0462-0.31320.0472-0.01420.1009-0.1593-0.150414.04018.357147.3687
32.79730.26271.0941.63970.34843.5120.1972-0.0186-0.35110.04090.0228-0.2370.23940.0947-0.22-0.269-0.0018-0.0258-0.0455-0.124-0.02152.267-6.698531.4955
41.66840.00280.1031.76910.16522.32910.0387-0.04320.01470.059-0.00960.02310.05960.0365-0.029-0.17910.00030.0402-0.01420.0409-0.0593-2.8985-17.0301-14.7468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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