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

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Basic information

Entry
Database: PDB / ID: 3mtu
TitleStructure of the Tropomyosin Overlap Complex from Chicken Smooth Muscle
Components
  • Capsid assembly scaffolding protein,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 / viral scaffold / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / Striated Muscle Contraction / mitotic spindle microtubule ...Smooth Muscle Contraction / viral scaffold / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / Striated Muscle Contraction / mitotic spindle microtubule / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / microtubule bundle formation / non-motile cilium assembly / protein localization to centrosome / negative regulation of microtubule polymerization / virion assembly / mitotic spindle pole / microtubule organizing center / microtubule polymerization / establishment of mitotic spindle orientation / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / spindle assembly / cytoskeletal protein binding / cardiac muscle contraction / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of microtubule polymerization / 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 / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / actin filament organization / actin filament / RHO GTPases Activate Formins / actin filament binding / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / cell migration / actin cytoskeleton / microtubule / ciliary basal body / cadherin binding / protein heterodimerization activity / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / protein homodimerization activity / DNA binding / RNA binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #400 / Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #400 / Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / 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 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHANOL / Tropomyosin alpha-1 chain / Capsid assembly scaffolding protein / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
Homo sapiens (human)
Bacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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
DepositionApr 30, 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 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Tropomyosin alpha-1 chain,Microtubule-associated protein RP/EB family member 1
B: Tropomyosin alpha-1 chain,Microtubule-associated protein RP/EB family member 1
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
E: Capsid assembly scaffolding protein,Tropomyosin alpha-1 chain
F: Capsid assembly scaffolding protein,Tropomyosin alpha-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,71824
Polymers52,7666
Non-polymers95218
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-67 kcal/mol
Surface area18410 Å2
MethodPISA
2
A: Tropomyosin alpha-1 chain,Microtubule-associated protein RP/EB family member 1
B: Tropomyosin alpha-1 chain,Microtubule-associated protein RP/EB family member 1
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
F: Capsid assembly scaffolding protein,Tropomyosin alpha-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,76223
Polymers43,8105
Non-polymers95218
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-29 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.131, 285.328, 43.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

21D-304-

HOH

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: 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: 8713.371 Da / Num. of mol.: 4
Fragment: Fusion protein of residues 1-29 of chicken smooth muscle tropomyosin and residues 215-257 of human EB1 protein,Fusion protein of residues 1-29 of chicken smooth muscle tropomyosin and ...Fragment: Fusion protein of residues 1-29 of chicken smooth muscle tropomyosin and residues 215-257 of human EB1 protein,Fusion protein of residues 1-29 of chicken smooth muscle tropomyosin and residues 215-257 of human EB1 protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Homo sapiens (human)
Gene: TPM1, MAPRE1 / Plasmid: pET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pRIL / References: UniProt: P04268, UniProt: Q15691
#2: Protein Capsid assembly scaffolding protein,Tropomyosin alpha-1 chain / Gene product 7 / gp7 / Head morphogenesis protein / Protein p7 / Scaffold protein / Alpha- ...Gene product 7 / gp7 / Head morphogenesis protein / Protein p7 / Scaffold protein / Alpha-tropomyosin / Tropomyosin-1


Mass: 8956.418 Da / Num. of mol.: 2
Fragment: Fusion protein of residues 2-45 of phage phi29 Gp7 protein and residues 256-284 of chicken smooth muscle tropomyosin,Fusion protein of residues 2-45 of phage phi29 Gp7 protein and residues ...Fragment: Fusion protein of residues 2-45 of phage phi29 Gp7 protein and residues 256-284 of chicken smooth muscle tropomyosin,Fusion protein of residues 2-45 of phage phi29 Gp7 protein and residues 256-284 of chicken smooth muscle tropomyosin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Gallus gallus (chicken)
Plasmid: pET31B / Gene: TPM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pRIL / References: UniProt: P13848, UniProt: P04268

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Non-polymers , 4 types, 365 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% MePEG 5000, 100 mM MES, pH 6.0, 140 mM CaCl2, 2% methanol , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 15, 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: 2.1→30 Å / Num. all: 33163 / Num. obs: 33097 / % possible obs: 99.8 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 23
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 3.6 / % possible all: 99.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MLPHAREphasing
REFMAC5.5.0088refinement
HKL-3000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→29.87 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.393 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24113 1666 5 %RANDOM
Rwork0.20096 ---
obs0.20298 31424 99.64 %-
all-31538 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.25 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.193 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20 Å2
2---0.91 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 59 347 3726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223438
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.9874586
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9565414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.06826.888196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67615689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2511516
X-RAY DIFFRACTIONr_chiral_restr0.0680.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022569
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_it2.56232071
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.922503314
X-RAY DIFFRACTIONr_scbond_it6.25651367
X-RAY DIFFRACTIONr_scangle_it9.817701267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.098→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 118 -
Rwork0.202 2237 -
obs--97.64 %
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)
10.1312-0.2580.00374.905-0.52980.17220.07490.04780.02030.1504-0.06240.1864-0.0109-0.0249-0.01250.06430.01440.02810.1053-0.00020.031911.54784.50442.11
20.06770.30150.07917.72161.18080.32380.08660.001-0.0121-0.0047-0.1406-0.09150.0207-0.07760.0540.10640.0284-0.02010.1315-0.00510.041312.04981.79744.038
30.1217-0.5689-0.32748.10292.3491.01280.0419-0.017-0.004-0.0435-0.0311-0.0903-0.07690.0049-0.01080.0628-0.0093-0.03180.1243-0.01350.021612.15364.55621.278
40.01250.1261-0.00994.7034-0.83490.87090.02570.013-0.0011-0.1257-0.02690.0928-0.0456-0.02980.00120.05790.0277-0.00780.12790.00150.03379.89364.48922.429
50.2618-0.7791-0.104211.66820.06890.5496-0.0613-0.0265-0.0489-1.35480.109-0.12430.24410.0426-0.04770.33210.01010.02510.0816-0.02160.075722.82713.28832.906
66.8174-12.1873-2.909621.91865.28081.9678-0.2567-0.08920.19880.65260.1386-0.44630.5622-0.19540.11810.4397-0.1499-0.02390.0828-0.04850.199723.50612.9338.249
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 257
2X-RAY DIFFRACTION2B-2 - 257
3X-RAY DIFFRACTION3C-2 - 257
4X-RAY DIFFRACTION4D-2 - 257
5X-RAY DIFFRACTION5E1 - 284
6X-RAY DIFFRACTION6F1 - 284

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