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- PDB-5hyb: Crystal structure of myristoylated Y81A mutant MMTV matrix protein -

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Basic information

Entry
Database: PDB / ID: 5hyb
TitleCrystal structure of myristoylated Y81A mutant MMTV matrix protein
ComponentsMatrix ProteinViral matrix protein
KeywordsVIRAL PROTEIN / Myristoylated protein / MMTV mutant
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / structural constituent of virion / nucleotide binding / DNA binding / zinc ion binding
Similarity search - Function
GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
MYRISTIC ACID / DI(HYDROXYETHYL)ETHER / Gag polyprotein
Similarity search - Component
Biological speciesMouse mammary tumor virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.94 Å
AuthorsBrynda, J. / Dostal, J. / Zabransky, A. / Dolezal, M.
Funding support Czech Republic, 6items
OrganizationGrant numberCountry
Czech Science Foundation (GA CR)15-05677S Czech Republic
NPULO1302 Czech Republic
NPULO1304 Czech Republic
RVORVO 61388963 Czech Republic
RVORVO 68378050 Czech Republic
RVORVO: 68378050 Czech Republic
CitationJournal: To Be Published
Title: Crystal structure of myristoylated Y81A mutant MMTV matrix protein
Authors: Brynda, J. / Dostal, J. / Zabransky, A. / Dolezal, M.
History
DepositionFeb 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix Protein
B: Matrix Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4636
Polymers20,7942
Non-polymers6694
Water1,60389
1
B: Matrix Protein
hetero molecules

A: Matrix Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4636
Polymers20,7942
Non-polymers6694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_665x-y+1,-y+1,-z+2/31
2
A: Matrix Protein
hetero molecules

B: Matrix Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4636
Polymers20,7942
Non-polymers6694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_565x-y,-y+1,-z+2/31
Unit cell
Length a, b, c (Å)61.802, 61.802, 89.622
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Matrix Protein / Viral matrix protein / Gag polyprotein


Mass: 10396.958 Da / Num. of mol.: 2 / Mutation: Y81A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mouse mammary tumor virus (strain BR6) / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10258
#2: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-HCl pH 8.5, 25% (v/v) PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 29, 2013
RadiationMonochromator: Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 13822 / % possible obs: 89.7 % / Redundancy: 6 % / Biso Wilson estimate: 35.3 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.6
Reflection shellResolution: 1.93→2.05 Å / Redundancy: 6 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 2.01 / % possible all: 80.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.94→45.95 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.417 / SU ML: 0.149 / SU R Cruickshank DPI: 0.2255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.202
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 955 7 %RANDOM
Rwork0.2123 ---
obs0.2165 12687 90.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.9 Å2 / Biso mean: 27.27 Å2 / Biso min: 12.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.16 Å20 Å2
2---0.31 Å20 Å2
3---0.47 Å2
Refinement stepCycle: final / Resolution: 1.94→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 44 94 1597
Biso mean--33.53 33.43 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191577
X-RAY DIFFRACTIONr_bond_other_d0.0010.021175
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9752115
X-RAY DIFFRACTIONr_angle_other_deg0.93332855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0515190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82323.23971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99915285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6161513
X-RAY DIFFRACTIONr_chiral_restr0.0790.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211691
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02330
LS refinement shellResolution: 1.942→1.992 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.492 45 -
Rwork0.472 611 -
all-656 -
obs--64.76 %

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