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- PDB-3nnq: Crystal Structure of the N-terminal domain of Moloney murine leuk... -

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Basic information

Entry
Database: PDB / ID: 3nnq
TitleCrystal Structure of the N-terminal domain of Moloney murine leukemia virus integrase, Northeast Structural Genomics Consortium Target OR3
ComponentsN-terminal domain of Moloney murine leukemia virus integrase
KeywordsVIRAL PROTEIN / retroviral integrase / Zn finger / Moloney murine leukemia virus / structural genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Endonuclease III; domain 1 - #70 / 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 ...Endonuclease III; domain 1 - #70 / 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 / Endonuclease III; domain 1 / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.693 Å
AuthorsGuan, R. / Xiao, R. / Acton, T. / Jiang, M. / Roth, M. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2017
Title: X-ray crystal structure of the N-terminal region of Moloney murine leukemia virus integrase and its implications for viral DNA recognition.
Authors: Guan, R. / Aiyer, S. / Cote, M.L. / Xiao, R. / Jiang, M. / Acton, T.B. / Roth, M.J. / Montelione, G.T.
History
DepositionJun 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Jul 26, 2023Group: Database references / Derived calculations / Refinement description
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-terminal domain of Moloney murine leukemia virus integrase
B: N-terminal domain of Moloney murine leukemia virus integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6636
Polymers27,4142
Non-polymers2494
Water64936
1
A: N-terminal domain of Moloney murine leukemia virus integrase
B: N-terminal domain of Moloney murine leukemia virus integrase
hetero molecules

A: N-terminal domain of Moloney murine leukemia virus integrase
B: N-terminal domain of Moloney murine leukemia virus integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,32612
Polymers54,8284
Non-polymers4988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
Buried area4800 Å2
ΔGint-42 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.818, 112.818, 115.528
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-136-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 12 - 104 / Label seq-ID: 12 - 104

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 12:104 )AA
2chain B and (resseq 12:104 )BB
DetailsAuthors state that the biological unit is a dimer, not a tetramer. The dimer in the asymmetric unit may not be the real dimer in solution, however.

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Components

#1: Protein N-terminal domain of Moloney murine leukemia virus integrase / Integrase p46


Mass: 13707.008 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Gene: gag-pol / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03355
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.0 M Sodium Malonate, 0.1 M Sodium Acetate,0.05% Anapoe X-305, pH 5.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97917, 0.97940, 0.96863
DetectorDetector: CCD / Date: Oct 24, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979171
20.97941
30.968631
ReflectionResolution: 2.693→50 Å / Num. all: 7989 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.2 % / Biso Wilson estimate: 74.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 44.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 3.43 / Num. unique all: 795 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PHENIXdev_403refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.693→49.724 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.42 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2744 783 10 %10% data, random
Rwork0.2292 ---
obs0.2337 7829 97.74 %-
all-7989 --
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 88.865 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 192.72 Å2 / Biso mean: 94.1634 Å2 / Biso min: 15.22 Å2
Baniso -1Baniso -2Baniso -3
1--3.7665 Å20 Å20 Å2
2---3.7665 Å20 Å2
3---7.5329 Å2
Refinement stepCycle: LAST / Resolution: 2.693→49.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 10 36 1620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041628
X-RAY DIFFRACTIONf_angle_d0.6742194
X-RAY DIFFRACTIONf_chiral_restr0.048240
X-RAY DIFFRACTIONf_plane_restr0.002268
X-RAY DIFFRACTIONf_dihedral_angle_d13.741598
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A772X-RAY DIFFRACTIONPOSITIONAL0.015
12B772X-RAY DIFFRACTIONPOSITIONAL0.015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6934-2.86220.35731180.30911067118590
2.8622-3.08310.34421310.28721172130399
3.0831-3.39330.32011320.27411871319100
3.3933-3.88420.2721310.22131183131499
3.8842-4.8930.2631340.191612011335100
4.893-49.73230.23831370.21781236137398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.30480.131-0.09720.5822-0.35630.39860.315-0.43320.73090.27060.3043-0.2965-0.3942-0.05630.25680.14630.08960.1260.6774-0.40020.4821-31.1161-20.654423.5604
20.30010.1759-0.19670.7879-0.49160.32070.2510.7394-0.1844-0.3199-0.3588-0.79320.1152-0.3588-0.02090.31020.0220.13840.9028-0.4470.66540.743-34.64976.9312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA12 - 201
2X-RAY DIFFRACTION2chain BB12 - 201

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