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- PDB-2q1n: Actin Dimer Cross-linked Between Residues 41 and 374 -

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Basic information

Entry
Database: PDB / ID: 2q1n
TitleActin Dimer Cross-linked Between Residues 41 and 374
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 / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / LATRUNCULIN A / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSawaya, M.R. / Pashkov, I. / Kudryashov, D.S. / Adisetiyo, H. / 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 25, 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 / pdbx_struct_conn_angle / 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 / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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

Downloads & links

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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)85,74110
Polymers83,7252
Non-polymers2,0168
Water41423
1
A: Actin, alpha skeletal muscle
hetero molecules

A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,74110
Polymers83,7252
Non-polymers2,0168
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)85,74110
Polymers83,7252
Non-polymers2,0168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Unit cell
Length a, b, c (Å)108.057, 71.813, 54.787
Angle α, β, γ (deg.)90.000, 104.700, 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: GLU / Beg label comp-ID: GLU / End auth comp-ID: LAR / End label comp-ID: LAR / Refine code: 2 / Auth seq-ID: 4 - 403 / Label seq-ID: 4

Dom-IDAuth asym-IDLabel asym-ID
1AA - F
2BB - J
DetailsA unit cell translation along the "c" axis generates the cross-linked dimer.

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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.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*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


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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% MPD, 0.1M sodium acetate, 0.02 M 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: 23524 / Num. obs: 23524 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 71.8 Å2 / Rmerge(I) obs: 0.093 / Χ2: 1.038 / Net I/σ(I): 9.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3 % / Rmerge(I) obs: 0.471 / Num. unique all: 2291 / Χ2: 1.035 / % possible all: 97.1

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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: 2.7→52.26 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.876 / SU B: 30.078 / SU ML: 0.34 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1147 5.1 %RANDOM
Rwork0.228 ---
all0.231 22428 --
obs0.231 22428 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.45 Å2
Baniso -1Baniso -2Baniso -3
1--7.56 Å20 Å2-1.07 Å2
2--6.18 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.7→52.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5401 0 124 23 5548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225649
X-RAY DIFFRACTIONr_bond_other_d0.0020.023789
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9897682
X-RAY DIFFRACTIONr_angle_other_deg0.87639260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.755685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18623.975239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62315945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1171533
X-RAY DIFFRACTIONr_chiral_restr0.0680.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021107
X-RAY DIFFRACTIONr_nbd_refined0.20.21274
X-RAY DIFFRACTIONr_nbd_other0.1850.23978
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22764
X-RAY DIFFRACTIONr_nbtor_other0.0810.22842
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2149
X-RAY DIFFRACTIONr_metal_ion_refined0.1830.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.26
X-RAY DIFFRACTIONr_mcbond_it2.16823579
X-RAY DIFFRACTIONr_mcbond_other0.43721384
X-RAY DIFFRACTIONr_mcangle_it3.06535568
X-RAY DIFFRACTIONr_scbond_it2.51122428
X-RAY DIFFRACTIONr_scangle_it3.532114
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
2023TIGHT POSITIONAL0.020.05
2622MEDIUM POSITIONAL0.210.5
2023TIGHT THERMAL0.110.5
2622MEDIUM THERMAL0.492
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 72 -
Rwork0.32 1563 -
obs-1635 98.49 %
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)
16.8959-0.04390.25991.33110.96763.9033-0.0955-0.2328-0.27970.1057-0.04070.35390.0657-0.49460.1362-0.1846-0.0917-0.0023-0.19140.04980.041719.663830.07816.5649
26.05911.19552.8151.9077-0.34264.8774-0.11340.8257-0.1576-0.35160.190.02640.06120.3929-0.0766-0.2039-0.10280.0176-0.12620.0472-0.214243.31233.27398.3532
313.52250.0563-0.81713.0884-0.0360.0497-0.0313-1.60980.56580.1818-0.0462-0.0667-0.0491-0.46980.0775-0.0808-0.03330.0256-0.1416-0.0312-0.247645.9939.749531.9341
44.96-1.1537-0.16741.27370.73724.5503-0.08020.54950.274-0.2436-0.0730.3718-0.2045-0.15040.1532-0.1540.0442-0.1059-0.19450.09330.0811-4.54694.254115.6947
57.4007-1.00090.41931.6405-0.29462.8708-0.2495-0.970.0290.30640.28220.3399-0.1788-0.1236-0.0326-0.18270.10210.04530.02420.1045-0.231812.07621.122934.4453
67.6339-0.66452.89950.9565-0.27953.15120.14771.1695-0.427-0.15250.0402-0.11480.2721-0.2266-0.1879-0.14060.01640.0463-0.0276-0.068-0.23725.9723-5.362115.2067
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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