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- PDB-6fm2: CARP domain of mouse cyclase-associated protein 1 (CAP1) bound to... -

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Basic information

Entry
Database: PDB / ID: 6fm2
TitleCARP domain of mouse cyclase-associated protein 1 (CAP1) bound to ADP-actin
Components
  • Actin, alpha skeletal muscle
  • Adenylyl cyclase-associated protein 1
KeywordsSTRUCTURAL PROTEIN / Complex / Actin Cytoskeleton / Nucleotide Exchange / Actin Turnover
Function / homology
Function and homology information


ameboidal-type cell migration / cytoskeletal motor activator activity / cortical actin cytoskeleton / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / skeletal muscle thin filament assembly ...ameboidal-type cell migration / cytoskeletal motor activator activity / cortical actin cytoskeleton / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / 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 / 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 / calcium-dependent protein binding / lamellipodium / cell body / actin binding / actin cytoskeleton organization / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / extracellular region / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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, 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 / Pectate Lyase C-like - #70 / 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 / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Pectate Lyase C-like / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / 3 Solenoid / 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 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Adenylyl cyclase-associated protein 1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesMus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKotila, T.M. / Kogan, K. / Lappalainen, P.
Funding support Finland, United States, 5items
OrganizationGrant numberCountry
Academy of Finland272130 Finland
Academy of Finland307415 Finland
European Research Council290974 Finland
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM063691 United States
National Science Foundation (United States)DMR-1420382 United States
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis of actin monomer re-charging by cyclase-associated protein.
Authors: Kotila, T. / Kogan, K. / Enkavi, G. / Guo, S. / Vattulainen, I. / Goode, B.L. / Lappalainen, P.
History
DepositionJan 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,8464
Polymers59,3952
Non-polymers4522
Water1,42379
1
A: Actin, alpha skeletal muscle
B: Adenylyl cyclase-associated protein 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)119,6928
Polymers118,7894
Non-polymers9034
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area12640 Å2
ΔGint-82 kcal/mol
Surface area40830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.833, 73.833, 453.377
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#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) / Plasmid details: Pel-Freez / Tissue: MuscleSkeletal muscle / References: UniProt: P68135
#2: Protein Adenylyl cyclase-associated protein 1 / CAP 1


Mass: 17519.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cap1, Cap / Plasmid: pPL974 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40124
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl, 0.2 M LiCl, 20% (w/v) PEG8000 / PH range: 8.0-8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→45.34 Å / Num. obs: 19109 / % possible obs: 98.2 % / Redundancy: 6 % / Biso Wilson estimate: 94.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.035 / Rrim(I) all: 0.087 / Net I/σ(I): 11.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.371 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2749 / CC1/2: 0.777 / Rpim(I) all: 0.585 / Rrim(I) all: 1.494 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1k4z, 3tpq

1k4z

3tpq


Resolution: 2.8→39.57 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.922 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.734 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.42 / SU Rfree Blow DPI: 0.318 / SU Rfree Cruickshank DPI: 0.31
RfactorNum. reflection% reflectionSelection details
Rfree0.234 912 4.8 %RANDOM
Rwork0.183 ---
obs0.186 18983 98.2 %-
Displacement parametersBiso mean: 128.69 Å2
Baniso -1Baniso -2Baniso -3
1--21.7511 Å20 Å20 Å2
2---21.7511 Å20 Å2
3---43.5022 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: 1 / Resolution: 2.8→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 39 79 4228
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014229HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.225737HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1486SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes109HARMONIC2
X-RAY DIFFRACTIONt_gen_planes618HARMONIC5
X-RAY DIFFRACTIONt_it4229HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion21.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion576SEMIHARMONIC5
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_contact4904SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.338 138 5.04 %
Rwork0.237 2600 -
all0.243 2738 -
obs--99.93 %
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)
14.5144-2.2069-1.49461.21820.79835.0285-0.77190.5988-0.7004-0.2599-0.24220.37710.9768-0.52411.01410.65450.09290.239-0.8977-0.1037-0.608-33.15867.50329.1121
25.333-5.9214-7.49174.51391.498611.9664-0.98230.664-0.50350.00880.51320.57990.498-1.36410.46911.10290.2736-0.5167-0.4753-0.0126-0.2995-44.767631.431311.2
39.0463-7.43748.17142.3486-3.45858.7953-0.0560.67270.3199-0.30210.0109-1.0843-0.35790.39470.0450.82850.0767-0.1122-0.65120.0566-0.7196-33.941326.80774.6654
41.6697-1.7719-0.71964.84330.31486.5838-0.7210.4262-0.4969-0.64820.08350.63410.089-0.89580.63750.48910.10710.0276-0.6733-0.1031-0.5378-38.436113.374913.3157
50.11771.1881-1.19871.80680.23522.896-0.8389-0.138-0.5976-0.34540.13860.21061.16080.01240.70030.3570.31780.3929-0.84710.0704-0.5476-28.7837.122323.8142
63.15870.47-3.53895.4026-0.72466.9385-0.0515-0.57430.1978-0.86240.4035-0.4151-1.32621.0116-0.3520.4-0.00230.4102-0.7644-0.0089-0.6483-12.142822.61766.3785
71.9899-0.0364-13.60955.60354.39870.0061-0.085-0.0570.2874-0.0240.2385-0.630.01780.7924-0.15350.4129-0.21450.49140.3153-0.0142-0.15995.433518.85132.9478
81.91941.6827-2.67051.3032-0.11828.2334-0.6454-0.5652-0.4262-0.45910.271-0.60960.27141.88530.37440.15110.44830.4235-0.45740.0907-0.5608-7.915911.940516.6488
94.6741-0.0215-0.35281.61080.73194.7306-0.3696-0.1184-1.0905-0.1925-0.32090.37761.1191-0.85990.69050.50890.05240.4269-1.04820.0047-0.561-36.7180.212621.6919
10-3.69193.4576-1.50615.22313.93243.72140.4312-0.069-0.2489-0.4758-0.80980.44330.2909-1.11050.37860.97510.36320.7319-0.86740.3321-0.2147-37.6273-7.540640.6596
115.2832-2.430924.18240.02994.3794-0.6325-0.4558-0.49650.6316-0.00630.11281.8223-0.14090.63880.62530.6520.6395-0.69330.3625-0.479-32.138-2.301745.1177
125.96360.0064-9.1422-0.63233.26861.93130.0125-0.3108-0.309-0.0512-0.3783-0.1721.1576-0.60750.36580.54850.8660.4925-0.23020.3977-0.5007-28.57243.782546.027
13-1.8980.3457-10.142111.2904-0.51250.1780.0998-0.31660.47310.1151-0.31460.2038-0.2385-0.50580.21480.17150.41360.2909-0.53880.0223-0.3936-37.20699.741240.8973
142.36170.5130.86673.6697-1.07810.1541-0.1164-0.601-0.4805-0.1769-0.60270.15741.12880.67870.7192-0.03350.74820.2149-0.35680.252-0.608-27.728412.122846.1279
15-0.10521.55010.87043.00686.707210.9278-0.0347-0.50950.00060.34810.0741-0.52-0.30310.9176-0.0394-0.13880.77370.1176-0.10370.23-0.6381-25.591818.18754.1024
1611.75091.0610.48699.80817.82230-0.2483-0.77230.27860.0080.7396-0.3237-0.68530.4104-0.49130.29170.3868-0.1914-0.6209-0.0561-0.5303-28.074833.457134.3243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|5 - A|36 }
2X-RAY DIFFRACTION2{ A|37 - A|53 }
3X-RAY DIFFRACTION3{ A|54 - A|68 }
4X-RAY DIFFRACTION4{ A|69 - A|107 }
5X-RAY DIFFRACTION5{ A|108 - A|175 }
6X-RAY DIFFRACTION6{ A|176 - A|224 }
7X-RAY DIFFRACTION7{ A|225 - A|237 }
8X-RAY DIFFRACTION8{ A|238 - A|334 }
9X-RAY DIFFRACTION9{ A|335 - A|375 }
10X-RAY DIFFRACTION10{ B|317 - B|333 }
11X-RAY DIFFRACTION11{ B|334 - B|374 }
12X-RAY DIFFRACTION12{ B|375 - B|388 }
13X-RAY DIFFRACTION13{ B|389 - B|394 }
14X-RAY DIFFRACTION14{ B|395 - B|436 }
15X-RAY DIFFRACTION15{ B|437 - B|455 }
16X-RAY DIFFRACTION16{ B|456 - B|473 }

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