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- PDB-1d1u: USE OF AN N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS ... -

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Basic information

Entry
Database: PDB / ID: 1d1u
TitleUSE OF AN N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE TO FACILITATE CRYSTALLIZATION AND ANALYSIS OF A PSEUDO-16-MER DNA MOLECULE CONTAINING G-A MISPAIRS
Components
  • DNA (5'-D(*AP*CP*GP*GP*CP*AP*CP*GP*AP*G)-3')
  • DNA (5'-D(*CP*TP*CP*GP*TP*G)-3')
  • PROTEIN (REVERSE TRANSCRIPTASE)
KeywordsHYDROLASE/DNA / G-A MISPAIR / SYN-ADENINE / NUCLEIC ACID / PROTEIN-DNA COMPLEX / SINGLE-STRAND OVERHANG / REVERSE TRANSCRIPTASE / MOLONEY MURINE LEUKEMIA VIRUS / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion assembly / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion assembly / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / structural constituent of virion / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal 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 ...Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal 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 / : / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsCote, M.L. / Yohannan, S. / Georgiadis, M.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Use of an N-terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing G-A mispairs.
Authors: Cote, M.L. / Yohannan, S.J. / Georgiadis, M.M.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Crystal Structures of the N-Terminal Fragment from Moloney Murine Leukemia Virus Reverse Transcriptase Complexed with Nucleic Acid: Functional Implications for Template-Primer Binding to the Fingers Domain
Authors: Najmudin, S. / Cote, M.L. / Sun, D. / Yohannan, S. / Montano, S.P. / Gu, J. / Georgiadis, M.M.
History
DepositionSep 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*TP*CP*GP*TP*G)-3')
C: DNA (5'-D(*AP*CP*GP*GP*CP*AP*CP*GP*AP*G)-3')
A: PROTEIN (REVERSE TRANSCRIPTASE)


Theoretical massNumber of molelcules
Total (without water)33,8143
Polymers33,8143
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.738, 145.491, 46.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: DNA chain DNA (5'-D(*CP*TP*CP*GP*TP*G)-3')


Mass: 1800.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC
#2: DNA chain DNA (5'-D(*AP*CP*GP*GP*CP*AP*CP*GP*AP*G)-3')


Mass: 3079.031 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE SEQUENCE 5'-CTCGTG-3' WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS 392 DNA/RNA SYNTHESIZER
#3: Protein PROTEIN (REVERSE TRANSCRIPTASE)


Mass: 28934.287 Da / Num. of mol.: 1 / Fragment: FINGERS AND PALM DOMAIN OF MMLV RT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Genus: Gammaretrovirus / Species: Murine leukemia virus / Gene: MMLV REVERSE TRANSCRIPTASE / Production host: Escherichia coli (E. coli) / References: UniProt: P03355, DNA-directed DNA polymerase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.45 mMprotein1drop
20.9 mMoligonucleotide1drop
33.6 mMddCTP1drop
410 %PEG40001reservoir
50.1 M1reservoirNaCl
60.05 MADA1reservoir

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 17117 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 22.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.278 / % possible all: 98.5
Reflection shell
*PLUS
% possible obs: 98.5 % / Mean I/σ(I) obs: 4.6

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: MODEL WAS REFINED WITH TWO DIFFERENT SIDE-CHAIN CONFORMATIONS FOR TYR 64 (IN THE A MOLECULE). BOTH WERE HELD AT 50% OCCUPANCY. THE 5'- TERMINAL ADENINE OF THE "C" CHAIN MAY HAVE EITHER THE ...Details: MODEL WAS REFINED WITH TWO DIFFERENT SIDE-CHAIN CONFORMATIONS FOR TYR 64 (IN THE A MOLECULE). BOTH WERE HELD AT 50% OCCUPANCY. THE 5'- TERMINAL ADENINE OF THE "C" CHAIN MAY HAVE EITHER THE SYN- OR ANTI- CONFORMATION. THE DEPOSITED DATA HAVE ADENINE C7 IN THE ANTI- CONFORMATION. INDEPENDENT REFINEMENTS OF THE STRUCTURAL MODEL WITH EITHER A SYN- OR AN ANTI-CONFORMATION FOR THE 5'-TERMINAL ADENINE ((A7) IN THE "C" CHAIN) YIELDED ELECTRON DENSITY MAPS WHICH GAVE NO PREFERENCE FOR ONE CONFORMATION OVER THE OTHER, AND NO INDICATION OF PARTIAL OCCUPANCIES FOR BOTH. THE INDEPENDENT REFINEMENTS YIELDED THE SAME REFINEMENT STATISTICS. THE DEPOSITED DATA CONTAIN THE ADENINE (A7) IN THE ANTI-CONFORMATION. THE COORDINATES FOR THE SYN-ADENINE ARE AVAILABLE UPON REQUEST FROM THE AUTHORS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 861 5 %RANDOM
Rwork0.23 ---
obs0.23 17117 99 %-
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 324 0 175 2540
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13

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