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- PDB-3mud: Structure of the Tropomyosin Overlap Complex from Chicken Smooth ... -

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Basic information

Entry
Database: PDB / ID: 3mud
TitleStructure of the Tropomyosin Overlap Complex from Chicken Smooth Muscle
Components
  • DNA repair protein XRCC4,Tropomyosin alpha-1 chain
  • Tropomyosin alpha-1 chain,Microtubule-associated protein RP/EB family member 1
KeywordsCONTRACTILE PROTEIN / tropomysoin / overlap complex / coiled-coils
Function / homology
Function and homology information


Smooth Muscle Contraction / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / FHA domain binding / mitotic spindle astral microtubule end / positive regulation of ligase activity / DNA ligase IV complex / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin ...Smooth Muscle Contraction / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / FHA domain binding / mitotic spindle astral microtubule end / positive regulation of ligase activity / DNA ligase IV complex / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / protein localization to microtubule / bleb / Striated Muscle Contraction / microtubule plus-end / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / cell projection membrane / mitotic spindle microtubule / regulation of muscle contraction / attachment of mitotic spindle microtubules to kinetochore / ruffle organization / microtubule bundle formation / microtubule plus-end binding / non-motile cilium assembly / protein localization to site of double-strand break / Striated Muscle Contraction / muscle filament sliding / protein localization to centrosome / structural constituent of muscle / sarcomere organization / cellular response to lithium ion / ventricular cardiac muscle tissue morphogenesis / 2-LTR circle formation / mitotic spindle pole / negative regulation of microtubule polymerization / regulation of heart contraction / negative regulation of vascular associated smooth muscle cell migration / spindle midzone / microtubule polymerization / microtubule organizing center / establishment of mitotic spindle orientation / negative regulation of vascular associated smooth muscle cell proliferation / Smooth Muscle Contraction / response to X-ray / regulation of microtubule polymerization or depolymerization / SUMOylation of DNA damage response and repair proteins / cytoskeletal protein binding / spindle assembly / cytoplasmic microtubule / cardiac muscle contraction / stress fiber / positive regulation of stress fiber assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of microtubule polymerization / cytoskeleton organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / positive regulation of cell adhesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein serine/threonine kinase binding / Resolution of Sister Chromatid Cohesion / actin filament organization / negative regulation of cell migration / AURKA Activation by TPX2 / sarcomere / cellular response to reactive oxygen species / actin filament / Nonhomologous End-Joining (NHEJ) / wound healing / RHO GTPases Activate Formins / base-excision repair / double-strand break repair via nonhomologous end joining / structural constituent of cytoskeleton / ruffle membrane / actin filament binding / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / cell migration / double-strand break repair / regulation of cell shape / actin cytoskeleton / site of double-strand break / actin binding / microtubule / cytoskeleton / ciliary basal body / cadherin binding / protein heterodimerization activity / cell division / focal adhesion / centrosome / enzyme binding / Golgi apparatus
Similarity search - Function
Vasodilator-stimulated phosphoprotein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / : / : / : / XRCC4 N-terminal domain ...Vasodilator-stimulated phosphoprotein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / : / : / : / XRCC4 N-terminal domain / XRCC4 coiled-coil / XRCC4 C-terminal region / XRCC4-like, N-terminal domain superfamily / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Tropomyosins signature. / Tropomyosin / Tropomyosin / DNA repair protein XRCC4-like, C-terminal / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Beta Complex / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Tropomyosin alpha-1 chain / Tropomyosin alpha-1 chain / DNA repair protein XRCC4 / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKlenchin, V.A. / Frye, J. / Rayment, I.
CitationJournal: Biochemistry / Year: 2010
Title: Structure of the tropomyosin overlap complex from chicken smooth muscle: insight into the diversity of N-terminal recognition .
Authors: Frye, J. / Klenchin, V.A. / Rayment, I.
History
DepositionMay 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 31, 2017Group: Structure summary
Revision 1.3Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DNA repair protein XRCC4,Tropomyosin alpha-1 chain
B: DNA repair protein XRCC4,Tropomyosin alpha-1 chain
C: Tropomyosin alpha-1 chain,Microtubule-associated protein RP/EB family member 1
D: Tropomyosin alpha-1 chain,Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7906
Polymers56,6324
Non-polymers1582
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-97 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.564, 96.564, 162.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DNA repair protein XRCC4,Tropomyosin alpha-1 chain / X-ray repair cross-complementing protein 4 / Alpha-tropomyosin / Tropomyosin-1


Mass: 19743.168 Da / Num. of mol.: 2 / Mutation: I134T, L249N,I134T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Gallus gallus (chicken)
Gene: XRCC4, TPM1 / Plasmid: pET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pRIL / References: UniProt: Q13426, UniProt: P04268
#2: Protein Tropomyosin alpha-1 chain,Microtubule-associated protein RP/EB family member 1 / Alpha-tropomyosin / Tropomyosin-1 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 8572.687 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPM1, C15orf13, TMSA, MAPRE1 / Plasmid: pET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pRIL / References: UniProt: P09493, UniProt: Q15691
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 3.35 Å3/Da / Density % sol: 63.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% MePEG 2000, 100 mM Bis-Tris, 120 mM MgSO4 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: SBC-3 / Detector: CCD / Date: Aug 6, 2009
RadiationMonochromator: Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 39926 / Num. obs: 39647 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 49.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 17.9 % / Mean I/σ(I) obs: 5.8 / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0088refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FU1

1fu1


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.66 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25049 1982 5 %RANDOM
Rwork0.20699 ---
obs0.20913 37461 98.98 %-
all-37847 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.235 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2--0.82 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3421 0 9 398 3828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223485
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.9644677
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5865431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90225.74169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18415660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2251513
X-RAY DIFFRACTIONr_chiral_restr0.0690.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022587
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.70252152
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.023503434
X-RAY DIFFRACTIONr_scbond_it6.78771333
X-RAY DIFFRACTIONr_scangle_it10.197701242
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 144 -
Rwork0.235 2694 -
obs--99.09 %
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)
11.94161.0860.50912.85871.23072.9708-0.0178-0.12610.01930.19420.11890.07860.08710.2382-0.10110.0810.01490.02620.1281-0.05220.0739-5.1634-3.2071-22.1735
24.9681.6993-4.86330.7229-1.80364.930.0704-0.21210.12160.0046-0.00360.01160.01810.1705-0.06680.2495-0.07430.03410.2178-0.08970.1694-32.5298-22.8126-14.5423
35.01753.37222.07744.78512.06232.51060.0362-0.09350.2635-0.1651-0.29950.73890.0849-0.35490.26330.1032-0.0241-0.08050.1251-0.07620.2241-32.7244-19.2933-43.3288
41.31961.0141-0.65681.1357-0.56980.34840.2169-0.2370.11140.1666-0.13160.216-0.13550.1334-0.08530.1916-0.0504-0.05310.1725-0.02840.2585-31.2127-18.6119-23.8622
55.64554.1258-5.90887.7124-6.339211.09470.0391-0.4098-0.11471.13930.02730.5496-0.7381-0.3606-0.06630.32260.07960.18130.2315-0.02110.1419-61.9317-38.448129.6862
65.80372.2625-3.24634.3764-1.97876.5203-0.1539-0.172-0.15090.68940.13390.82060.1589-0.82540.020.28430.04890.23950.25160.01880.3215-65.3004-44.285525.8142
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 0
2X-RAY DIFFRACTION1A2 - 113
3X-RAY DIFFRACTION2A114 - 135
4X-RAY DIFFRACTION2A248 - 284
5X-RAY DIFFRACTION3B-1 - 0
6X-RAY DIFFRACTION3B2 - 90
7X-RAY DIFFRACTION4B91 - 135
8X-RAY DIFFRACTION4B248 - 284
9X-RAY DIFFRACTION5C-2 - 29
10X-RAY DIFFRACTION5C215 - 230
11X-RAY DIFFRACTION6D-2 - 29
12X-RAY DIFFRACTION6D215 - 230

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