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- PDB-1mn8: Structure of Moloney Murine Leukaemia Virus Matrix Protein -

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Basic information

Entry
Database: PDB / ID: 1mn8
TitleStructure of Moloney Murine Leukaemia Virus Matrix Protein
ComponentsCore protein p15
KeywordsVIRAL PROTEIN / HELICAL BUNDLE
Function / homology
Function and homology information


host cell uropod / host cell late endosome membrane / viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / structural constituent of virion / host cell plasma membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gamma-retroviral matrix domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / DNA polymerase; domain 1 / Retroviral matrix protein ...Gamma-retroviral matrix domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / DNA polymerase; domain 1 / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMoloney murine leukemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1 Å
AuthorsRiffel, N. / Harlos, K. / Iourin, O. / Rao, Z. / Kingsman, A. / Stuart, D. / Fry, E.
CitationJournal: Structure / Year: 2002
Title: Atomic resolution structure of Moloney murine leukaemia virus matrix protein and its relationship to other retroviral matrix proteins.
Authors: Riffel, N. / Harlos, K. / Iourin, O. / Rao, Z. / Kingsman, A. / Stuart, D. / Fry, E.
History
DepositionSep 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 ...chem_comp_atom / chem_comp_bond / database_2 / 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: Core protein p15
B: Core protein p15
C: Core protein p15
D: Core protein p15


Theoretical massNumber of molelcules
Total (without water)45,7924
Polymers45,7924
Non-polymers00
Water10,251569
1
A: Core protein p15


Theoretical massNumber of molelcules
Total (without water)11,4481
Polymers11,4481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Core protein p15


Theoretical massNumber of molelcules
Total (without water)11,4481
Polymers11,4481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Core protein p15


Theoretical massNumber of molelcules
Total (without water)11,4481
Polymers11,4481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Core protein p15


Theoretical massNumber of molelcules
Total (without water)11,4481
Polymers11,4481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.8, 49.5, 50.8
Angle α, β, γ (deg.)71.9, 81.9, 80.0
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Core protein p15 / M-MuLV Matrix protein p15


Mass: 11448.051 Da / Num. of mol.: 4 / Fragment: M-MuLV C-terminally truncated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Genus: Gammaretrovirus / Species: Murine leukemia virus / Gene: p15 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (D3) / References: UniProt: P03332
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 6

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES-Na pH 7.5, 1.4M sodium citrate, 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13 mg/mlprotein1drop
20.1 MHEPES-Na1reservoirpH7.5
31.4 Msodium citrate1reservoir
4100 mM1reservoirNaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9777
SYNCHROTRONSRS PX14.220.978
Detector
TypeIDDetector
ADSC QUANTUM 41CCD
ADSC QUANTUM 42CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97771
20.9781
ReflectionResolution: 1→20 Å / Num. all: 141760 / Num. obs: 141760 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.1
Reflection shellResolution: 1→1.04 Å / Mean I/σ(I) obs: 0.9
Reflection
*PLUS
% possible obs: 86 %
Reflection shell
*PLUS
Highest resolution: 1 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SHELXL-97refinement
RefinementMethod to determine structure: MIR / Resolution: 1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.169 --
all0.133 141625 -
obs-141625 86 %
Refinement stepCycle: LAST / Resolution: 1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 0 569 3732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d2.5
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.133
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.5

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