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- PDB-3u1a: N-terminal 81-aa fragment of smooth muscle tropomyosin alpha -

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Basic information

Entry
Database: PDB / ID: 3u1a
TitleN-terminal 81-aa fragment of smooth muscle tropomyosin alpha
Componentssmooth muscle tropomyosin alpha
KeywordsCONTRACTILE PROTEIN / Muscle contraction / Actin
Function / homology
Function and homology information


Smooth Muscle Contraction / Striated Muscle Contraction / cytoskeletal protein binding / cardiac muscle contraction / actin filament organization / actin filament / actin filament binding / actin cytoskeleton / protein heterodimerization activity / protein homodimerization activity ...Smooth Muscle Contraction / Striated Muscle Contraction / cytoskeletal protein binding / cardiac muscle contraction / 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: 2 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: smooth muscle tropomyosin alpha
B: smooth muscle tropomyosin alpha
C: smooth muscle tropomyosin alpha
D: smooth muscle tropomyosin alpha


Theoretical massNumber of molelcules
Total (without water)38,4434
Polymers38,4434
Non-polymers00
Water3,891216
1
A: smooth muscle tropomyosin alpha
B: smooth muscle tropomyosin alpha


Theoretical massNumber of molelcules
Total (without water)19,2222
Polymers19,2222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-36 kcal/mol
Surface area12220 Å2
MethodPISA
2
C: smooth muscle tropomyosin alpha
D: smooth muscle tropomyosin alpha


Theoretical massNumber of molelcules
Total (without water)19,2222
Polymers19,2222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-34 kcal/mol
Surface area12270 Å2
MethodPISA
3
A: smooth muscle tropomyosin alpha
B: smooth muscle tropomyosin alpha

C: smooth muscle tropomyosin alpha
D: smooth muscle tropomyosin alpha


Theoretical massNumber of molelcules
Total (without water)38,4434
Polymers38,4434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x+1/2,-y+1/2,-z-11
Buried area8780 Å2
ΔGint-83 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.768, 63.181, 101.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
smooth muscle tropomyosin alpha


Mass: 9610.754 Da / Num. of mol.: 4 / Fragment: unp residues 1-81
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


Mass: 18.015 Da / Num. of mol.: 216 / 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: 49.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1 M Sodium acetate, pH 4.4, 20 mM Calcium chloride, 30-33 % 2-METHYL-2,4-PENTANEDIOL , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 26243 / Num. obs: 25949 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.05 % / Rmerge(I) obs: 0.1058 / Net I/σ(I): 14.59
Reflection shellResolution: 2→2.1 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.4198 / Mean I/σ(I) obs: 4.52 / Num. unique all: 3473 / % possible all: 98.2

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Processing

Software
NameVersionClassification
JDirector(Rigaku)data collection
PHENIXAutosolmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXAutosolphasing
RefinementMethod to determine structure: SAD / Resolution: 2→39.519 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 1253 5.03 %RANDOM
Rwork0.2223 ---
all0.2245 24909 --
obs0.2245 24909 95.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.187 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.047 Å20 Å2-0 Å2
2--0.8771 Å20 Å2
3----7.9241 Å2
Refinement stepCycle: LAST / Resolution: 2→39.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 0 216 2853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092668
X-RAY DIFFRACTIONf_angle_d0.9353557
X-RAY DIFFRACTIONf_dihedral_angle_d19.9561098
X-RAY DIFFRACTIONf_chiral_restr0.073396
X-RAY DIFFRACTIONf_plane_restr0.003483
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2-2.08010.33281250.26472420242089
2.0801-2.17480.27391310.25122446244690
2.1748-2.28940.32291340.22262516251693
2.2894-2.43280.26711380.23462599259995
2.4328-2.62060.30291390.23882626262696
2.6206-2.88430.2621410.2352664266497
2.8843-3.30150.25981440.22432708270898
3.3015-4.15880.24141470.19772782278299
4.1588-39.52630.25481540.21742895289599
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)
10.5054-0.013-0.4230.2741-0.15510.44620.1329-0.12630.0621-0.0563-0.0529-0.0351-0.2759-0.07650.01610.3572-0.00710.01750.1265-0.01980.076820.62087.23019.4895
20.3589-0.0838-0.1470.25130.1360.2926-0.0669-0.1629-0.0278-0.0493-0.04120.0028-0.02210.28660.01490.3554-0.04080.00080.1153-0.010.069221.34125.714712.5096
30.18990.0405-0.15290.34740.0410.20130.04620.06910.0632-0.0515-0.00460.0282-0.07710.1637-0.09670.3760.01420.01590.10850.02740.08462.781624.043-6.9616
40.04740.0630.14270.3014-0.36190.35430.09080.08460.044-0.08640.08290.04630.20060.0182-0.12320.44310.0522-0.00880.18590.00110.11511.994122.5574-9.076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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