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- PDB-2z5h: Crystal structure of the head-to-tail junction of tropomyosin com... -

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Basic information

Entry
Database: PDB / ID: 2z5h
TitleCrystal structure of the head-to-tail junction of tropomyosin complexed with a fragment of TnT
Components
  • General control protein GCN4 and Tropomyosin alpha-1 chain
  • Tropomyosin alpha-1 chain and General control protein GCN4
  • Troponin T, fast skeletal muscle isoforms
KeywordsCONTRACTILE PROTEIN / actin / troponin / tropomyosin / cytoskeleton / cardiomyopathy / four-helix bundle
Function / homology
Function and homology information


troponin C binding / troponin complex / regulation of muscle contraction / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter ...troponin C binding / troponin complex / regulation of muscle contraction / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / sarcomere organization / tropomyosin binding / troponin I binding / TFIID-class transcription factor complex binding / amino acid biosynthetic process / skeletal muscle contraction / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to amino acid starvation / actin filament / RNA polymerase II transcription regulator complex / : / actin filament binding / actin cytoskeleton / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Troponin T / Tropomyosins signature. / Tropomyosin / Troponin / Troponin domain superfamily / Tropomyosin / Troponin / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. ...Troponin T / Tropomyosins signature. / Tropomyosin / Troponin / Troponin domain superfamily / Tropomyosin / Troponin / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
General control transcription factor GCN4 / Troponin T, fast skeletal muscle isoforms / Tropomyosin alpha-1 chain
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Oryctolagus cuniculus (rabbit)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsMurakami, K. / Nozawa, K. / Tomii, K. / Kudou, N. / Igarashi, N. / Shirakihara, Y. / Wakatsuki, S. / Stewart, M. / Yasunaga, T. / Wakabayashi, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structural basis for tropomyosin overlap in thin (actin) filaments and the generation of a molecular swivel by troponin-T
Authors: Murakami, K. / Stewart, M. / Nozawa, K. / Tomii, K. / Kudou, N. / Igarashi, N. / Shirakihara, Y. / Wakatsuki, S. / Yasunaga, T. / Wakabayashi, T.
History
DepositionJul 12, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Database references / Derived calculations
Revision 1.3Aug 16, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Revision 1.4Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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: General control protein GCN4 and Tropomyosin alpha-1 chain
B: General control protein GCN4 and Tropomyosin alpha-1 chain
C: General control protein GCN4 and Tropomyosin alpha-1 chain
D: General control protein GCN4 and Tropomyosin alpha-1 chain
E: General control protein GCN4 and Tropomyosin alpha-1 chain
F: General control protein GCN4 and Tropomyosin alpha-1 chain
G: General control protein GCN4 and Tropomyosin alpha-1 chain
H: General control protein GCN4 and Tropomyosin alpha-1 chain
I: Tropomyosin alpha-1 chain and General control protein GCN4
T: Troponin T, fast skeletal muscle isoforms


Theoretical massNumber of molelcules
Total (without water)59,65710
Polymers59,65710
Non-polymers00
Water99155
1
A: General control protein GCN4 and Tropomyosin alpha-1 chain
B: General control protein GCN4 and Tropomyosin alpha-1 chain
I: Tropomyosin alpha-1 chain and General control protein GCN4
T: Troponin T, fast skeletal muscle isoforms


Theoretical massNumber of molelcules
Total (without water)23,3174
Polymers23,3174
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: General control protein GCN4 and Tropomyosin alpha-1 chain
D: General control protein GCN4 and Tropomyosin alpha-1 chain


Theoretical massNumber of molelcules
Total (without water)12,1142
Polymers12,1142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-29 kcal/mol
Surface area7750 Å2
MethodPISA
3
E: General control protein GCN4 and Tropomyosin alpha-1 chain
F: General control protein GCN4 and Tropomyosin alpha-1 chain


Theoretical massNumber of molelcules
Total (without water)12,1142
Polymers12,1142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-29 kcal/mol
Surface area7490 Å2
MethodPISA
4
G: General control protein GCN4 and Tropomyosin alpha-1 chain
H: General control protein GCN4 and Tropomyosin alpha-1 chain


Theoretical massNumber of molelcules
Total (without water)12,1142
Polymers12,1142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-30 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.809, 158.308, 163.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein
General control protein GCN4 and Tropomyosin alpha-1 chain / TM


Mass: 6056.825 Da / Num. of mol.: 8
Fragment: C terminal domain of GCN4 and Tropomyosin alpha-1 chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Oryctolagus cuniculus (rabbit)
Genus: Saccharomyces, Oryctolagus / Species: , / Strain: , / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P03069, UniProt: P58772
#2: Protein/peptide Tropomyosin alpha-1 chain and General control protein GCN4 / TM


Mass: 4537.393 Da / Num. of mol.: 1
Fragment: N terminal domain of Tropomyosin alpha-1 chain and C terminal domain of GCN4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Genus: Oryctolagus, Saccharomyces / Species: , / Strain: , / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P58772, UniProt: P03069
#3: Protein Troponin T, fast skeletal muscle isoforms / / TnT


Mass: 6665.503 Da / Num. of mol.: 1 / Fragment: Residues 58-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P12620
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 4.71 Å3/Da / Density % sol: 73.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→113.96 Å / Num. obs: 25479 / % possible obs: 96.5 % / Redundancy: 4.9 % / Biso Wilson estimate: 70.8 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2375 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→113.96 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.907 / SU B: 12.013 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.509 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24701 1251 5.1 %RANDOM
Rwork0.23676 ---
obs0.23729 23334 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.192 Å2
Baniso -1Baniso -2Baniso -3
1-6.18 Å20 Å20 Å2
2---3 Å20 Å2
3----3.18 Å2
Refinement stepCycle: LAST / Resolution: 2.89→113.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 0 0 55 3940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223914
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1242.0085236
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96326.699206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.99115828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9911513
X-RAY DIFFRACTIONr_chiral_restr0.1080.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022850
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3050.21781
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.22663
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.360.2152
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3270.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.48722415
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.35633742
X-RAY DIFFRACTIONr_scbond_it4.57621617
X-RAY DIFFRACTIONr_scangle_it7.13331494
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.89→2.965 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 78 -
Rwork0.297 1519 -
obs--86.46 %

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