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- PDB-6rsw: HFD domain of mouse CAP1 bound to the pointed end of G-actin -

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Basic information

Entry
Database: PDB / ID: 6rsw
TitleHFD domain of mouse CAP1 bound to the pointed end of G-actin
Components
  • Actin, alpha skeletal muscle
  • Adenylyl cyclase-associated protein 1
  • Twinfilin-1
KeywordsCONTRACTILE PROTEIN / Actin binding protein
Function / homology
Function and homology information


regulation of actin phosphorylation / ameboidal-type cell migration / RHOBTB2 GTPase cycle / sequestering of actin monomers / negative regulation of actin filament polymerization / barbed-end actin filament capping / actin filament depolymerization / regulation of lamellipodium assembly / cytoskeletal motor activator activity / cortical actin cytoskeleton ...regulation of actin phosphorylation / ameboidal-type cell migration / RHOBTB2 GTPase cycle / sequestering of actin monomers / negative regulation of actin filament polymerization / barbed-end actin filament capping / actin filament depolymerization / regulation of lamellipodium assembly / cytoskeletal motor activator activity / cortical actin cytoskeleton / myofibril / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / positive regulation of cardiac muscle hypertrophy / troponin I binding / actin filament bundle / filamentous actin / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / cAMP-mediated signaling / adenylate cyclase binding / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / Neutrophil degranulation / receptor-mediated endocytosis / filopodium / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell morphogenesis / positive regulation of neuron projection development / calcium-dependent protein binding / actin filament binding / cell-cell junction / actin cytoskeleton / lamellipodium / cell body / actin binding / actin cytoskeleton organization / protein tyrosine kinase activity / hydrolase activity / protein domain specific binding / calcium ion binding / protein-containing complex binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / extracellular region / ATP binding / identical protein binding / 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 / Twinfilin / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / ATPase, nucleotide binding domain / Alpha Horseshoe / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Adenylyl cyclase-associated protein 1 / Actin, alpha skeletal muscle / Twinfilin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Twinfilin-1
C: Adenylyl cyclase-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7048
Polymers77,7523
Non-polymers9525
Water11,746652
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-34 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.370, 54.490, 87.830
Angle α, β, γ (deg.)90.00, 93.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Twinfilin-1 / Protein A6


Mass: 16567.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Twf1, Ptk9 / Plasmid: pPL1340 / Details (production host): pSUMO / Production host: Escherichia coli (E. coli) / References: UniProt: Q91YR1
#3: Protein Adenylyl cyclase-associated protein 1 / CAP 1


Mass: 19308.041 Da / Num. of mol.: 1 / Mutation: C92S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cap1, Cap / Plasmid: pPL1337 / Details (production host): pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40124

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Non-polymers , 4 types, 657 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES, 0.1 mM KCl, 10% PEG4000 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 30, 2018
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.95→41.45 Å / Num. obs: 60448 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 35.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.038 / Rrim(I) all: 0.096 / Net I/σ(I): 12.88
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.073 / Mean I/σ(I) obs: 1.58 / Num. unique obs: 1209 / CC1/2: 0.923 / Rpim(I) all: 0.47 / Rrim(I) all: 1.174 / % possible all: 99.87

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSVERSION Jan 26, 2018 BUILT=20180409data reduction
XSCALEVERSION Jan 26, 2018 BUILT=20180409data scaling
BALBES1.0.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3daw, 1s0p

3daw

1s0p


Resolution: 1.95→41.45 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.142 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.194 3003 4.97 %RANDOM
Rwork0.166 ---
obs0.168 60448 100 %-
Displacement parametersBiso mean: 45.07 Å2
Baniso -1Baniso -2Baniso -3
1--9.3197 Å20 Å2-9.1276 Å2
2--2.9166 Å20 Å2
3---6.4031 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.95→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5417 0 70 652 6139
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015611HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.997600HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1986SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes956HARMONIC5
X-RAY DIFFRACTIONt_it5611HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion17.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion738SEMIHARMONIC5
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_contact7016SEMIHARMONIC4
LS refinement shellResolution: 1.95→1.96 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2309 -3.97 %
Rwork0.2002 1161 -
all0.2015 1209 -
obs--99.51 %
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)
10.693-0.2331-0.26590.7720.23710.6861-0.0197-0.12030.02120.05950.062-0.10630.06760.1244-0.0423-0.00830.00410.0069-0.0447-0.0155-0.067311.581-7.964215.0898
21.336-0.7308-0.49891.82761.55241.98590.0047-0.0682-0.0192-0.01540.1496-0.1512-0.11870.2088-0.15430.0028-0.03480.0114-0.0397-0.0344-0.10978.208815.913939.5656
32.3278-0.4725-0.18581.9756-0.09061.98220.11310.2464-0.0892-0.3762-0.122-0.24180.14460.08840.0089-0.06350.03720.1086-0.13010.0116-0.059833.9385-22.0115-10.5713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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