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- PDB-3u1c: Anti-parallel dimer of N-terminal 98-aa fragment of smooth muscle... -

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Basic information

Entry
Database: PDB / ID: 3u1c
TitleAnti-parallel dimer of N-terminal 98-aa fragment of smooth muscle tropomyosin alpha
ComponentsTropomyosin alpha-1 chain
KeywordsCONTRACTILE PROTEIN / Anti-parallel coiled coil
Function / homology
Function and homology information


Smooth Muscle Contraction / Striated Muscle Contraction / cardiac muscle contraction / cytoskeletal protein binding / actin filament organization / actin filament / actin filament binding / actin cytoskeleton / protein heterodimerization activity / protein homodimerization activity ...Smooth Muscle Contraction / Striated Muscle Contraction / cardiac muscle contraction / cytoskeletal protein binding / actin filament organization / actin filament / actin filament binding / actin cytoskeleton / protein heterodimerization activity / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Tropomyosins signature. / Tropomyosin / Tropomyosin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Tropomyosin alpha-1 chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsJampani, N. / Dominguez, R.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural analysis of smooth muscle tropomyosin alpha and beta isoforms.
Authors: Rao, J.N. / Rivera-Santiago, R. / Li, X.E. / Lehman, W. / Dominguez, R.
History
DepositionSep 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tropomyosin alpha-1 chain
B: Tropomyosin alpha-1 chain


Theoretical massNumber of molelcules
Total (without water)23,1922
Polymers23,1922
Non-polymers00
Water2,684149
1
A: Tropomyosin alpha-1 chain

A: Tropomyosin alpha-1 chain


Theoretical massNumber of molelcules
Total (without water)23,1922
Polymers23,1922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area4830 Å2
ΔGint-44 kcal/mol
Surface area14070 Å2
MethodPISA
2
B: Tropomyosin alpha-1 chain

B: Tropomyosin alpha-1 chain


Theoretical massNumber of molelcules
Total (without water)23,1922
Polymers23,1922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area4960 Å2
ΔGint-42 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.654, 76.654, 79.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-130-

HOH

21A-155-

HOH

31A-162-

HOH

41B-152-

HOH

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Components

#1: Protein Tropomyosin alpha-1 chain


Mass: 11595.910 Da / Num. of mol.: 2 / Fragment: unp residues 1-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: PTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P04268
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M Sodium acetate, pH 4.0, 40 mM Calcium chloride, 32-35 % 2-METHYL-2,4-PENTANEDIOL, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID10.9795
SYNCHROTRONCHESS A120.9772
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELNov 8, 2010
2CCDMar 28, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111) ChannelSINGLE WAVELENGTHMx-ray1
2Si (111) ChannelSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97721
ReflectionResolution: 1.75→25 Å / Num. all: 24608 / Num. obs: 23590 / % possible obs: 95.9 % / Redundancy: 17.76 % / Rmerge(I) obs: 0.0757 / Net I/σ(I): 24.9
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 12.69 % / Rmerge(I) obs: 0.4364 / Mean I/σ(I) obs: 4.59 / Num. unique all: 3675 / % possible all: 94.8

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Processing

Software
NameVersionClassification
JDirector(Rigaku)data collection
ADSCQuantumdata collection
SHELXDphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→25 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 31.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2843 1049 5.03 %RANDOM
Rwork0.2457 ---
all0.2477 20857 --
obs0.2477 20857 92.24 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.254 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.4834 Å20 Å2-0 Å2
2--8.4834 Å20 Å2
3----16.9668 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1618 0 0 149 1767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091686
X-RAY DIFFRACTIONf_angle_d1.142258
X-RAY DIFFRACTIONf_dihedral_angle_d17.714708
X-RAY DIFFRACTIONf_chiral_restr0.076251
X-RAY DIFFRACTIONf_plane_restr0.004309
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8001-1.89490.43451220.33452268226876
1.8949-2.01360.34781450.30712693269389
2.0136-2.1690.31391530.26882920292097
2.169-2.38710.31271550.26692935293597
2.3871-2.73220.28711570.25142985298598
2.7322-3.44090.28331600.23053044304498
3.4409-25.10230.25071570.22832963296391
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)
1-0.1202-0.1268-0.06420.2871-0.95871.3682-0.0986-0.0065-0.01280.080.0946-0.0051-0.3713-0.33610.02580.1760.00570.00560.23290.010.16524.778985.1503-3.7086
2-0.1011-0.0169-0.1506-0.00490.18140.9470.02480.0324-0.0481-0.04610.04270.0069-0.17570.16780.01740.36580.0821-0.01950.1944-0.03010.2198-20.685495.5393-23.2965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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