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- PDB-4k42: Crystal structure of actin in complex with synthetic AplC tail an... -

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Basic information

Entry
Database: PDB / ID: 4k42
TitleCrystal structure of actin in complex with synthetic AplC tail analogue SF01 [(3R,4S,5R,6S,10R,11R,12R)-11-(acetyloxy)-1-(benzyloxy)-14-[formyl(methyl)amino]-5-hydroxy-4,6,10,12-tetramethyl-9-oxotetradecan-3-yl propanoate]
ComponentsActin, alpha skeletal muscle
KeywordsCONTRACTILE PROTEIN / cell motility / gelsolin
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
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 ...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 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-NWM / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPereira, J.H. / Petchprayoon, C. / Moriarty, N.W. / Fink, S.J. / Cecere, G. / Paterson, I. / Adams, P.D. / Marriott, G.
CitationJournal: Chemmedchem / Year: 2014
Title: Structural and biochemical studies of actin in complex with synthetic macrolide tail analogues.
Authors: Pereira, J.H. / Petchprayoon, C. / Hoepker, A.C. / Moriarty, N.W. / Fink, S.J. / Cecere, G. / Paterson, I. / Adams, P.D. / Marriott, G.
History
DepositionApr 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_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 / _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: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,63116
Polymers167,4504
Non-polymers4,18012
Water1,892105
1
A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9084
Polymers41,8631
Non-polymers1,0453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9084
Polymers41,8631
Non-polymers1,0453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9084
Polymers41,8631
Non-polymers1,0453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9084
Polymers41,8631
Non-polymers1,0453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.650, 67.343, 207.853
Angle α, β, γ (deg.)90.00, 92.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 41862.613 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-NWM / (3R,4S,5R,6S,10R,11R,12R)-11-(acetyloxy)-1-(benzyloxy)-14-[formyl(methyl)amino]-5-hydroxy-4,6,10,12-tetramethyl-9-oxotetradecan-3-yl propanoate


Mass: 577.749 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H51NO8
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M BIS-TRIS pH 5.5, 25% Polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 28543 / % possible obs: 84.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.9→2.95 Å / % possible all: 83.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→49.192 Å / SU ML: 0.44 / σ(F): 1.34 / Phase error: 31.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2713 1086 5.05 %RANDOM
Rwork0.2277 ---
obs0.2299 28543 83.95 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→49.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11282 0 276 105 11663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511802
X-RAY DIFFRACTIONf_angle_d0.86516008
X-RAY DIFFRACTIONf_dihedral_angle_d18.6364540
X-RAY DIFFRACTIONf_chiral_restr0.0471794
X-RAY DIFFRACTIONf_plane_restr0.0042024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.99930.37531460.30672629X-RAY DIFFRACTION83
2.9993-3.11940.33591390.29042671X-RAY DIFFRACTION83
3.1194-3.26130.35961450.27812658X-RAY DIFFRACTION83
3.2613-3.43320.32071360.26192665X-RAY DIFFRACTION82
3.4332-3.64830.30911380.2312679X-RAY DIFFRACTION83
3.6483-3.92990.2641270.2172654X-RAY DIFFRACTION82
3.9299-4.32510.19591520.19052604X-RAY DIFFRACTION82
4.3251-4.95050.21811580.17932650X-RAY DIFFRACTION82
4.9505-6.23510.27031400.22052701X-RAY DIFFRACTION83
6.2351-49.1920.24221590.20563192X-RAY DIFFRACTION95
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)
11.78360.6680.66012.40680.52973.9944-0.0024-0.43440.16260.3752-0.14680.56870.7731-0.23920.24810.4012-0.10380.08320.3935-0.11160.2378-7.57369.478-75.0316
22.13081.19971.76636.2744-0.53931.90290.09690.2650.15971.1494-1.18980.47380.0041-1.37290.10080.437-0.11910.0680.8598-0.45621.1032-24.693815.2852-79.3406
31.7752-0.27670.58813.2767-1.10721.4219-0.1863-0.39240.50360.057-0.08240.8718-0.0064-0.31720.01070.24810.01730.02270.118-0.18560.9643-11.171820.0304-79.1358
41.1355-0.56170.92371.55880.53321.5825-0.1183-0.04890.20970.3178-0.22330.21280.0376-0.45430.20230.2858-0.04620.00360.3095-0.09970.3510.3415.9584-77.2789
51.02350.0968-0.24431.17620.05051.7772-0.52980.25370.5417-0.40810.08350.1914-0.0964-0.2990.17430.26770.0587-0.00320.0979-0.02650.4767-3.932210.4986-96.0214
61.8230.0719-0.06140.6177-0.1310.4908-0.0094-0.1496-0.1094-0.1223-0.06650.1997-0.0796-0.07710.0812-0.5001-0.068-0.03090.4187-0.13350.462-13.8839-1.2446-99.8744
71.62210.21770.73741.43750.31631.00760.1290.1969-0.0902-0.09-0.09220.1277-0.04670.0406-0.00040.11740.00330.01730.1538-0.0270.2409-1.19092.1466-99.8267
81.14380.4648-0.04131.36030.21542.4882-0.0559-0.3606-0.02990.4929-0.03590.0669-0.08430.36030.0040.19450.01430.00580.2202-0.01870.31827.610712.5119-77.9146
91.1313-0.16260.46130.4693-0.37450.6041-0.1602-0.53890.3297-0.31760.3261-0.4982-0.6712-0.15850.16380.67520.0444-0.00930.5397-0.06430.0437-27.7238-1.2968-66.1113
103.8816-0.7882-0.49430.418-0.44271.2187-0.253-0.30050.54280.05860.9047-0.7365-0.27191.20120.99050.523-0.015-0.23931.1801-0.41210.3559-9.3249-9.1201-60.4555
113.12531.5562-0.53433.7034-0.05370.3383-0.42-0.1697-0.48970.36050.2277-0.8104-0.46111.0305-0.09150.4734-0.1344-0.18340.5479-0.15760.1164-23.7198-5.5901-56.8865
120.98980.07350.28311.10240.78560.6452-0.0548-0.0241-0.38690.1638-0.02540.2978-0.25260.27870.08180.4233-0.04530.02090.38750.01020.1802-34.4395-9.8205-59.5229
131.65020.1018-0.84460.7545-0.24951.74760.00710.069-0.3037-0.00330.1003-0.19920.08270.2698-0.08510.2672-0.07-0.01320.3667-0.14330.2182-27.1518-25.257-76.708
141.4267-0.5082-0.7591.6384-0.40191.6054-0.13-0.00950.02480.31970.17540.0852-0.4941-0.09830.00690.3826-0.0347-0.0040.3485-0.03010.2546-39.4922-6.9697-62.6542
152.87240.32271.59032.0816-0.00691.9252-0.59931.11170.3394-1.3677-0.1179-0.14510.1070.92890.11751.00580.01510.08540.58470.04170.54838.4213-26.7942-30.8252
161.80980.60870.59321.02251.19841.5072-0.61310.3316-0.0975-0.9808-0.0524-0.97370.42491.17870.25450.77670.15610.23720.91370.44611.171926.8569-19.6935-24.3891
173.0516-0.44892.15651.57690.77864.182-0.04050.94960.1129-0.6637-0.393-0.8879-0.3870.9790.43261.08730.06660.19550.49520.20160.715812.414-16.8674-28.5738
180.821-0.08960.31911.4961-0.27971.1204-0.11760.32180.1887-0.0116-0.08640.0288-0.4580.2590.1250.95090.07950.04690.4540.06090.54773.2121-14.893-28.8861
192.56680.06130.86632.2649-1.24852.0952-0.1109-0.23320.1355-0.2269-0.1219-0.2939-0.1858-0.01580.02970.4925-0.03920.01860.27540.0550.53114.9269-24.9395-10.3176
202.71740.69520.15841.3225-0.11480.38850.3698-0.01940.1340.291-0.2204-0.511-0.16020.2414-0.07310.73880.0378-0.03090.31950.09250.719418.2502-36.4786-4.4803
211.2902-0.1487-0.4580.7890.61691.26510.6112-0.1406-0.6870.0509-1.0637-0.2234-0.48010.29910.27280.5791-0.07270.04730.61510.1660.846823.9757-44.5819-4.1402
222.5651-1.44320.22342.1322-0.08651.2251-0.0172-0.4505-0.2171-0.0298-0.00570.164-0.12270.23670.06040.5615-0.0672-0.01350.41370.05720.44970.3397-29.8309-4.4593
231.6970.21950.74441.3119-0.44711.581-0.0440.39580.3198-0.4137-0.22550.11010.0605-0.28730.13211.03970.0375-0.04590.3260.04960.5776-3.3533-22.2283-26.0169
243.36041.2568-1.22114.1815-0.90512.1563-0.34570.94610.7632-0.07470.93051.097-1.0067-0.93950.00771.12690.43670.13460.96980.42080.9092-26.057829.2056-38.8009
252.8011-0.32880.8652.0853-1.3133.00290.43460.29350.2905-0.06060.4290.3986-0.5181-0.07250.46160.9230.41080.18012.42490.48620.8893-43.193423.5678-43.2657
264.38770.25750.18562.5304-1.07651.76270.17561.90651.1233-0.04370.27710.4922-1.2443-1.9335-0.61371.17590.31280.05991.48240.33430.7378-26.690526.8476-46.8027
272.42711.2579-1.20322.1533-0.39291.36890.22140.94860.3032-0.3640.17420.2843-0.7514-0.631-0.33161.02440.176-0.0520.760.08830.5592-15.928822.7358-44.1454
283.64620.4991-1.32132.1296-0.3062.268-0.30060.1331-1.5665-0.4277-0.1476-0.2147-0.2265-0.47440.07870.78660.0933-0.16980.6052-0.01550.7092-22.37638.63-34.5629
292.54080.86310.13381.5732-1.37412.6497-0.1183-0.2012-0.1690.09670.1355-0.22220.0914-0.5429-0.05150.69040.0014-0.03990.62340.07650.4755-25.23536.4199-24.5353
302.53411.4708-0.93522.1097-0.07691.48860.30540.25320.0709-0.2284-0.3815-0.0717-0.35270.01050.15450.91630.07860.06770.66360.03530.5569-11.907721.3559-36.334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 165 )
5X-RAY DIFFRACTION5chain 'A' and (resid 166 through 196 )
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 230 )
7X-RAY DIFFRACTION7chain 'A' and (resid 231 through 318 )
8X-RAY DIFFRACTION8chain 'A' and (resid 319 through 374 )
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 28 )
10X-RAY DIFFRACTION10chain 'B' and (resid 29 through 68 )
11X-RAY DIFFRACTION11chain 'B' and (resid 69 through 112 )
12X-RAY DIFFRACTION12chain 'B' and (resid 113 through 165 )
13X-RAY DIFFRACTION13chain 'B' and (resid 166 through 318 )
14X-RAY DIFFRACTION14chain 'B' and (resid 319 through 374 )
15X-RAY DIFFRACTION15chain 'C' and (resid 5 through 28 )
16X-RAY DIFFRACTION16chain 'C' and (resid 29 through 68 )
17X-RAY DIFFRACTION17chain 'C' and (resid 69 through 112 )
18X-RAY DIFFRACTION18chain 'C' and (resid 113 through 145 )
19X-RAY DIFFRACTION19chain 'C' and (resid 146 through 196 )
20X-RAY DIFFRACTION20chain 'C' and (resid 197 through 230 )
21X-RAY DIFFRACTION21chain 'C' and (resid 231 through 251 )
22X-RAY DIFFRACTION22chain 'C' and (resid 252 through 318 )
23X-RAY DIFFRACTION23chain 'C' and (resid 319 through 374 )
24X-RAY DIFFRACTION24chain 'D' and (resid 5 through 37 )
25X-RAY DIFFRACTION25chain 'D' and (resid 38 through 68 )
26X-RAY DIFFRACTION26chain 'D' and (resid 69 through 112 )
27X-RAY DIFFRACTION27chain 'D' and (resid 113 through 165 )
28X-RAY DIFFRACTION28chain 'D' and (resid 166 through 196 )
29X-RAY DIFFRACTION29chain 'D' and (resid 197 through 294 )
30X-RAY DIFFRACTION30chain 'D' and (resid 295 through 374 )

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