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- PDB-2q36: Actin Dimer Cross-linked between Residues 191 and 374 and complex... -

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Basic information

Entry
Database: PDB / ID: 2q36
TitleActin Dimer Cross-linked between Residues 191 and 374 and complexed with Kabiramide C
ComponentsActin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / cross-linked dimer
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'-TRIPHOSPHATE / KABIRAMIDE C / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSawaya, M.R. / Pashkov, I. / Kudryashov, D.S. / Reisler, E. / Yeates, T.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Multiple crystal structures of actin dimers and their implications for interactions in the actin filament.
Authors: Sawaya, M.R. / Kudryashov, D.S. / Pashkov, I. / Adisetiyo, H. / Reisler, E. / Yeates, T.O.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5486
Polymers41,8631
Non-polymers1,6865
Water1,24369
1
A: Actin, alpha skeletal muscle
hetero molecules

A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,09612
Polymers83,7252
Non-polymers3,37110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
Unit cell
Length a, b, c (Å)40.539, 74.276, 144.474
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsthe cross-linked dimer is generated by the following symmetry operator -X,1/2+Y,-1/2-Z

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 41862.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135

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Non-polymers , 5 types, 74 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-KAB / KABIRAMIDE C


Mass: 946.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H75N5O14
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.1 M Tris, 0.2 M lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2005
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→90 Å / Num. all: 15987 / Num. obs: 15987 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.112 / Χ2: 1.065 / Net I/σ(I): 8.8
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.419 / Num. unique all: 1727 / Χ2: 1.089 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2A5X

2a5x


Resolution: 2.5→72.17 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.315 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.446 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 800 5.1 %RANDOM
Rwork0.175 ---
all0.177 15767 --
obs0.177 15767 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.725 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.53 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.5→72.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 109 69 2995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222989
X-RAY DIFFRACTIONr_bond_other_d0.0010.021994
X-RAY DIFFRACTIONr_angle_refined_deg1.5332.0044062
X-RAY DIFFRACTIONr_angle_other_deg0.88534872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7975358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.19323.92125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22715495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.681518
X-RAY DIFFRACTIONr_chiral_restr0.0740.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02582
X-RAY DIFFRACTIONr_nbd_refined0.20.2561
X-RAY DIFFRACTIONr_nbd_other0.190.22059
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21441
X-RAY DIFFRACTIONr_nbtor_other0.0850.21437
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.292
X-RAY DIFFRACTIONr_metal_ion_refined0.1730.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.24
X-RAY DIFFRACTIONr_mcbond_it1.68121865
X-RAY DIFFRACTIONr_mcbond_other0.3312725
X-RAY DIFFRACTIONr_mcangle_it2.50432902
X-RAY DIFFRACTIONr_scbond_it1.61621377
X-RAY DIFFRACTIONr_scangle_it2.43231160
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 64 -
Rwork0.198 1065 -
obs-1129 99.82 %
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)
11.24270.2103-0.46151.19290.01732.10920.0159-0.1520.16250.06470.0386-0.0471-0.2540.0308-0.0546-0.0513-0.0082-0.0384-0.0697-0.045-0.05423.3882-4.7701-11.0904
21.36130.4405-0.02151.88460.01641.291-0.01310.08950.0317-0.189-0.0004-0.09780.04860.11290.0136-0.07910.0203-0.0026-0.02040.0192-0.062910.7206-15.6152-33.3337
32.59140.0604-0.02692.1481.63772.52770-0.1785-0.11060.2521-0.0415-0.01980.2135-0.10210.0414-0.0123-0.014-0.0026-0.06290.0035-0.095-1.3126-35.0932-24.1077
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 365 - 36
2X-RAY DIFFRACTION1AA51 - 13751 - 137
3X-RAY DIFFRACTION1AA337 - 371337 - 371
4X-RAY DIFFRACTION2AA138 - 181138 - 181
5X-RAY DIFFRACTION2AA263 - 336263 - 336
6X-RAY DIFFRACTION3AA182 - 262182 - 262

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