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- PDB-1nkn: VISUALIZING AN UNSTABLE COILED COIL: THE CRYSTAL STRUCTURE OF AN ... -

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Basic information

Entry
Database: PDB / ID: 1nkn
TitleVISUALIZING AN UNSTABLE COILED COIL: THE CRYSTAL STRUCTURE OF AN N-TERMINAL SEGMENT OF THE SCALLOP MYOSIN ROD
ComponentsS2N51-GCN4
KeywordsCONTRACTILE PROTEIN / alpha helix / coiled coil
Function / homology
Function and homology information


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 / myosin complex / myofibril / TFIID-class transcription factor complex binding ...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 / myosin complex / myofibril / TFIID-class transcription factor complex binding / cytoskeletal motor activity / amino acid biosynthetic process / 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 / RNA polymerase II transcription regulator complex / : / actin filament binding / 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 / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus
Similarity search - Function
: / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Basic region leucine zipper / Myosin S1 fragment, N-terminal / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper ...: / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Basic region leucine zipper / Myosin S1 fragment, N-terminal / 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 / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
General control transcription factor GCN4 / Myosin heavy chain
Similarity search - Component
Biological speciesArgopecten irradians (bay scallop)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, Y. / Brown, J.H. / Reshetnikova, L. / Blazsek, A. / Farkas, L. / Nyitray, L. / Cohen, C.
CitationJournal: Nature / Year: 2003
Title: Visualization of an unstable coiled coil from the scallop myosin rod
Authors: Li, Y. / Brown, J.H. / Reshetnikova, L. / Blazsek, A. / Farkas, L. / Nyitray, L. / Cohen, C.
History
DepositionJan 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE AN APPROPRIATE SEQUENCE DATABASE REFERENCE WAS NOT AVAILABLE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S2N51-GCN4
B: S2N51-GCN4
C: S2N51-GCN4
D: S2N51-GCN4


Theoretical massNumber of molelcules
Total (without water)42,2374
Polymers42,2374
Non-polymers00
Water1,47782
1
A: S2N51-GCN4
B: S2N51-GCN4


Theoretical massNumber of molelcules
Total (without water)21,1182
Polymers21,1182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-47 kcal/mol
Surface area11150 Å2
MethodPISA
2
C: S2N51-GCN4
D: S2N51-GCN4


Theoretical massNumber of molelcules
Total (without water)21,1182
Polymers21,1182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-46 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.034, 73.303, 102.975
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
S2N51-GCN4


Mass: 10559.174 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Argopecten irradians, Saccharomyces cerevisiae
Genus: Argopecten, Saccharomyces / Species: , / Strain: , / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P03069, UniProt: Q17042*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.83 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: sodium chloride, sodium azide, MOPS, PEG 200 MME, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115-20 %PEG2000 MME1reservoir
250 mM1reservoirNaCl
32 mM1reservoirNaN3
444 mMMOPS1reservoirpH6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 14762 / Num. obs: 13342 / % possible obs: 90.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 5.28 / Num. unique all: 1458 / % possible all: 75.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2893 911 -RANDOM
Rwork0.2435 ---
all0.2467 ---
obs0.2467 12880 87.4 %-
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 0 82 2577
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.5-2.550.4153950.3224X-RAY DIFFRACTION1268
2.55-2.60.38051130.2988X-RAY DIFFRACTION1374
2.6-2.660.3244880.2919X-RAY DIFFRACTION1445
2.66-2.720.32871000.2878X-RAY DIFFRACTION1539
2.72-2.790.30551110.2722X-RAY DIFFRACTION1680
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.286
Solvent computation
*PLUS
Displacement parameters
*PLUS

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