[English] 日本語
Yorodumi
- PDB-3mtu: Structure of the Tropomyosin Overlap Complex from Chicken Smooth ... -

+
Open data


ID or keywords:

Loading...

-
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


viral scaffold / Smooth Muscle Contraction / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / Striated Muscle Contraction / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore ...viral scaffold / Smooth Muscle Contraction / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / Striated Muscle Contraction / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / non-motile cilium assembly / microtubule bundle formation / microtubule plus-end binding / protein localization to centrosome / microtubule organizing center / negative regulation of microtubule polymerization / virion assembly / mitotic spindle pole / microtubule polymerization / cytoplasmic microtubule / establishment of mitotic spindle orientation / regulation of microtubule polymerization or depolymerization / spindle assembly / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cardiac muscle contraction / 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 / positive regulation of microtubule polymerization / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / cytoskeletal protein binding / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / actin filament / actin filament organization / protein localization / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / actin filament binding / actin cytoskeleton / cell migration / microtubule / 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 / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #400 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more