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- PDB-3l2q: Crystal structure of the Prototype Foamy Virus (PFV) intasome in ... -

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Basic information

Entry
Database: PDB / ID: 3l2q
TitleCrystal structure of the Prototype Foamy Virus (PFV) intasome in apo form
Components
  • 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*TP*GP*TP*A)-3'
  • 5'-D(*TP*AP*CP*AP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3'
  • Integrase
KeywordsRECOMBINATION/DNA / PROTEIN-DNA COMPLEX / TETRAMER / DNA INTEGRATION / ENDONUCLEASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / NUCLEUS / TRANSFERASE / VIRAL NUCLEOPROTEIN / VIRION / ZINC / DNA-BINDING / ZINC BINDING / HHCC MOTIF / VIRAL PROTEIN / RECOMBINATION / RECOMBINATION-DNA complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / host cell cytoplasm / viral entry into host cell / host cell nucleus / RNA binding / identical protein binding / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #110 / Endonuclease III; domain 1 - #70 / Spumavirus aspartic protease (A9) / Foamy virus protease (FV PR) domain profile. / Retroviral integrase, C-terminal SH3 domain / Retroviral integrase C-terminal SH3 domain / Spumavirus aspartic protease A9 / Integrase zinc-binding domain / Integrase zinc binding domain / Arc Repressor Mutant, subunit A ...Arc Repressor Mutant, subunit A - #110 / Endonuclease III; domain 1 - #70 / Spumavirus aspartic protease (A9) / Foamy virus protease (FV PR) domain profile. / Retroviral integrase, C-terminal SH3 domain / Retroviral integrase C-terminal SH3 domain / Spumavirus aspartic protease A9 / Integrase zinc-binding domain / Integrase zinc binding domain / Arc Repressor Mutant, subunit A / RNase H-like domain found in reverse transcriptase / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / Endonuclease III; domain 1 / SH3 type barrels. - #140 / Ribonuclease H-like superfamily/Ribonuclease H / Helix non-globular / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / RNase H type-1 domain profile. / Special / SH3 type barrels. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA (> 10) / DNA / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHuman spumaretrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.25 Å
AuthorsHare, S. / Gupta, S.S. / Cherepanov, P.
CitationJournal: Nature / Year: 2010
Title: Retroviral intasome assembly and inhibition of DNA strand transfer
Authors: Hare, S. / Gupta, S.S. / Valkov, E. / Engelman, A. / Cherepanov, P.
History
DepositionDec 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrase
B: Integrase
C: 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*TP*GP*TP*A)-3'
D: 5'-D(*TP*AP*CP*AP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2838
Polymers99,9424
Non-polymers3424
Water0
1
A: Integrase
B: Integrase
C: 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*TP*GP*TP*A)-3'
D: 5'-D(*TP*AP*CP*AP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3'
hetero molecules

A: Integrase
B: Integrase
C: 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*TP*GP*TP*A)-3'
D: 5'-D(*TP*AP*CP*AP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,56716
Polymers199,8838
Non-polymers6838
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area23380 Å2
ΔGint-130 kcal/mol
Surface area54030 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)158.250, 158.250, 124.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A119 - 200
2114B119 - 200
1214A241 - 257
2214B241 - 257
1314A263 - 273
2314B263 - 273

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Components

#1: Protein Integrase / / IN / p42In


Mass: 44456.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human spumaretrovirus / Strain: HSRV2 / Gene: pol / Plasmid: pSSH6P-PFV-INFL / Production host: Escherichia coli (E. coli) / Strain (production host): PC2 / References: UniProt: P14350
#2: DNA chain 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*TP*GP*TP*A)-3'


Mass: 5864.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 19 nucleotide preprocessed PFV donor DNA
#3: DNA chain 5'-D(*TP*AP*CP*AP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3'


Mass: 5163.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 17 nucleotide preprocessed PFV donor DNA
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3

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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: 3.91 Å3/Da / Density % sol: 68.52 % / Mosaicity: 0.67 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.35M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50mM Mes-NaOH, pH 6.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC / Detector: AREA DETECTOR / Date: Oct 13, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.25→38.979 Å / Num. all: 25432 / Num. obs: 25432 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.116
Reflection shellResolution: 3.25→3.43 Å / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DLR
Resolution: 3.25→38.38 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 1 / SU B: 33.55 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.678 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22087 1288 5.1 %RANDOM
Rwork0.19673 ---
obs0.19793 24121 99.68 %-
all-25488 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.738 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å2-0 Å2-0 Å2
2--2.05 Å20 Å2
3----4.1 Å2
Refinement stepCycle: LAST / Resolution: 3.25→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4149 732 19 0 4900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225104
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3152.1537119
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66223.488172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2115676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0471523
X-RAY DIFFRACTIONr_chiral_restr0.0730.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0223612
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4191.52657
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80824339
X-RAY DIFFRACTIONr_scbond_it0.96532447
X-RAY DIFFRACTIONr_scangle_it1.7194.52780
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 860 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.350.5
medium thermal0.422
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 75 -
Rwork0.317 1742 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.46721.0853.28261.00411.75114.54220.2342-0.0823-0.0751-0.073-0.42090.14730.1818-0.55890.18670.2482-0.0718-0.03760.354-0.08750.2178-67.927.131-56.086
20.88820.04110.37552.17720.30521.7036-0.1067-0.2656-0.05520.07320.07150.03650.2909-0.10670.03520.1519-0.04520.06080.25150.03160.0819-35.30738.782-5.258
32.41040.0658-0.91421.27490.93877.5744-0.2191-0.2959-0.73710.2394-0.21250.05161.2179-0.11670.43160.4143-0.25160.110.3910.02240.387-54.51827.164-27.65
43.8848-0.64980.14341.6936-0.58222.1246-0.2057-0.5154-0.09450.320.1550.11650.2281-0.01250.05070.24360.03710.0830.46620.01730.0288-24.59336.86915.51
50.10670.6281-0.13794.8170.22011.70690.0426-0.04670.04340.0226-0.09360.2588-0.2298-0.12240.0510.1425-0.0802-0.02050.2823-0.02170.1988-43.01761.172-15.377
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 111
2X-RAY DIFFRACTION2A112 - 308
3X-RAY DIFFRACTION3A309 - 392
4X-RAY DIFFRACTION4B112 - 308
5X-RAY DIFFRACTION5C1 - 19
6X-RAY DIFFRACTION5D1 - 17

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