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- PDB-2q31: Actin Dimer Cross-linked Between Residues 41 and 374 and proteoly... -

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Basic information

Entry
Database: PDB / ID: 2q31
TitleActin Dimer Cross-linked Between Residues 41 and 374 and proteolytically cleaved by subtilisin between residues 47 and 48.
ComponentsActin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / cross-linked dimer / proteolytically cleaved
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 / LATRUNCULIN A / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / difference Fourier / Resolution: 2.7 Å
AuthorsSawaya, M.R. / Pashkov, I. / Kudryashov, D.S. / Reisler, E. / Yeates, T.O.
Citation
Journal: 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.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actin.
Authors: Kudryashov, D.S. / Sawaya, M.R. / Adisetiyo, H. / Norcross, T. / Hegyi, G. / 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_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
B: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6638
Polymers83,7252
Non-polymers1,9386
Water55831
1
A: Actin, alpha skeletal muscle
hetero molecules

A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6638
Polymers83,7252
Non-polymers1,9386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
2
B: Actin, alpha skeletal muscle
hetero molecules

B: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6638
Polymers83,7252
Non-polymers1,9386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Unit cell
Length a, b, c (Å)108.253, 71.984, 54.703
Angle α, β, γ (deg.)90.000, 104.680, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LAR / End label comp-ID: LAR / Refine code: 1 / Auth seq-ID: 5 - 402 / Label seq-ID: 5

Dom-IDAuth asym-IDLabel asym-ID
1AA - E
2BB - H
DetailsBiological unit 1 is generated by a unit cell translation along the "c" axis applied to chain A. Biological unit 2 is generated by a unit cell translation along the "c" axis applied to chain B.

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Components

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


Mass: 41862.613 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-LAR / LATRUNCULIN A / 4-(17-HYDROXY-5,12-DIMETHYL-3-OXO-2,16-DIOXABICYCLO[13.3.1]NONADECA-4,8,10-TRIEN-17-YL)-2-THIAZOLIDINONE / Latrunculin


Mass: 421.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H31NO5S / Comment: toxin*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% MPD, 0.1 M sodium acetate, 0.01M calcium chloride, pH 4.6, 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: 2.7→90 Å / Num. all: 19970 / Num. obs: 19970 / % possible obs: 87.5 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.176 / Χ2: 1.042 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.82.10.41812621.022155.8
2.8-2.912.10.42615120.94166.3
2.91-3.042.30.39717321.051176.5
3.04-3.22.40.39118890.986184.5
3.2-3.42.70.35121780.978195
3.4-3.6630.28422220.993198.2
3.66-4.033.20.23422671.055199.8
4.03-4.623.20.15922881.18199.3
4.62-5.823.20.12722721.036199.5
5.82-903.30.09123481.049199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
BOSdata collection
RefinementMethod to determine structure: difference Fourier
Starting model: pdb entry 2Q1N

2q1n


Resolution: 2.7→43.07 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.826 / SU B: 33.536 / SU ML: 0.415 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R Free: 0.547 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 764 5 %RANDOM
Rwork0.249 ---
obs0.251 15349 68.09 %-
all-19970 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.744 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20.44 Å2
2---1.53 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5245 0 122 31 5398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225488
X-RAY DIFFRACTIONr_bond_other_d0.0010.023671
X-RAY DIFFRACTIONr_angle_refined_deg1.0351.9927464
X-RAY DIFFRACTIONr_angle_other_deg0.79638980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2135667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.43924.174230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.65715916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8381530
X-RAY DIFFRACTIONr_chiral_restr0.0570.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021068
X-RAY DIFFRACTIONr_nbd_refined0.1930.21243
X-RAY DIFFRACTIONr_nbd_other0.1730.24046
X-RAY DIFFRACTIONr_nbtor_refined0.170.22706
X-RAY DIFFRACTIONr_nbtor_other0.0810.22580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2162
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0610.23
X-RAY DIFFRACTIONr_mcbond_it0.55523501
X-RAY DIFFRACTIONr_mcbond_other0.18621349
X-RAY DIFFRACTIONr_mcangle_it0.79735417
X-RAY DIFFRACTIONr_scbond_it0.53422362
X-RAY DIFFRACTIONr_scangle_it0.80632047
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4512 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.010.05
TIGHT THERMAL0.020.5
LS refinement shellResolution: 2.7→2.846 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.496 26 -
Rwork0.321 425 -
obs-451 13.74 %
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)
17.16670.1572-1.09882.21261.36654.3289-0.1876-0.3936-0.31420.20230.01230.59070.0415-0.31010.1754-0.014-0.0969-0.00630.10980.08310.276119.694630.083416.516
27.61790.78721.29181.97830.04645.2952-0.16410.8306-0.0644-0.43070.0001-0.03890.19110.22680.164-0.0347-0.0918-0.03550.13820.0636-0.025143.387233.29968.3344
311.62652.0854-2.31453.9307-0.21034.69380.0313-1.44920.78770.2659-0.04840.0719-0.13-0.22550.017-0.03770.0007-0.00470.2843-0.0526-0.094146.069839.791131.8782
46.0948-0.51450.11151.34531.01335.8099-0.18630.66030.1464-0.333-0.07960.4521-0.4276-0.02380.26590.06160.0434-0.1425-0.01670.08370.2787-4.49814.255115.7022
510.3896-1.13340.24211.86730.22725.6609-0.0122-1.13310.13210.40560.18450.2408-0.2539-0.2439-0.1723-0.05220.06770.03670.0760.0663-0.055812.16161.08934.4383
68.5523-1.10642.98612.6769-1.04786.92350.16971.4263-0.3104-0.3942-0.0023-0.23840.17610.5265-0.1673-0.04880.00340.03760.3276-0.0585-0.095726.0493-5.375115.2273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 375 - 37
2X-RAY DIFFRACTION1AA66 - 13766 - 137
3X-RAY DIFFRACTION1AA337 - 347337 - 347
4X-RAY DIFFRACTION2AA138 - 181138 - 181
5X-RAY DIFFRACTION2AA263 - 336263 - 336
6X-RAY DIFFRACTION3AA182 - 262182 - 262
7X-RAY DIFFRACTION4BB5 - 375 - 37
8X-RAY DIFFRACTION4BB66 - 13766 - 137
9X-RAY DIFFRACTION4BB337 - 347337 - 347
10X-RAY DIFFRACTION5BB138 - 181138 - 181
11X-RAY DIFFRACTION5BB263 - 336263 - 336
12X-RAY DIFFRACTION6BB182 - 262182 - 262

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