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- PDB-5n88: Crystal structure of antibody bound to viral protein -

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Basic information

Entry
Database: PDB / ID: 5n88
TitleCrystal structure of antibody bound to viral protein
Components
  • (PC4 and SFRS1-interacting protein) x 2
  • VH59 antibody
KeywordsIMMUNE SYSTEM / MLL: HIV: intracellular antibody: integrase: LEDGF / AIDS
Function / homology
Function and homology information


supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Formation of WDR5-containing histone-modifying complexes / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin ...supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Formation of WDR5-containing histone-modifying complexes / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin / nuclear periphery / euchromatin / response to heat / DNA-binding transcription factor binding / response to oxidative stress / transcription coactivator activity / chromatin remodeling / chromatin binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain
Similarity search - Domain/homology
PC4 and SFRS1-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsBao, L. / Hannon, C. / Cruz-Migoni, A. / Ptchelkine, D. / Sun, M.-y. / Derveni, M. / Bunjobpol, W. / Chambers, J.S. / Simmons, A. / Phillips, S.E.V. / Rabbitts, T.H.
CitationJournal: Sci Rep / Year: 2017
Title: Intracellular immunization against HIV infection with an intracellular antibody that mimics HIV integrase binding to the cellular LEDGF protein.
Authors: Bao, L. / Hannon, C. / Cruz-Mignoni, A. / Ptchelkine, D. / Sun, M.Y. / Miller, A. / Bunjobpol, W. / Quevedo, C.E. / Derveni, M. / Chambers, J. / Simmons, A. / Phillips, S.E.V. / Rabbitts, T.H.
History
DepositionFeb 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: VH59 antibody
D: PC4 and SFRS1-interacting protein
A: VH59 antibody
E: PC4 and SFRS1-interacting protein


Theoretical massNumber of molelcules
Total (without water)46,4254
Polymers46,4254
Non-polymers00
Water5,765320
1
H: VH59 antibody
E: PC4 and SFRS1-interacting protein


Theoretical massNumber of molelcules
Total (without water)23,2272
Polymers23,2272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-11 kcal/mol
Surface area10350 Å2
MethodPISA
2
D: PC4 and SFRS1-interacting protein
A: VH59 antibody


Theoretical massNumber of molelcules
Total (without water)23,1972
Polymers23,1972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-13 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.061, 41.408, 58.660
Angle α, β, γ (deg.)104.040, 96.070, 100.490
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody VH59 antibody


Mass: 13886.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1 / Plasmid: pRK-172 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
#2: Protein PC4 and SFRS1-interacting protein / CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived ...CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52


Mass: 9310.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2 / Plasmid: pRK-172 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O75475
#3: Protein PC4 and SFRS1-interacting protein / CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived ...CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52


Mass: 9340.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2 / Plasmid: pRK-172 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O75475
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 1.73 Å3/Da / Density % sol: 28.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5 / Details: 25.0% PEG 3350, 10mM Tris pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 115544 / % possible obs: 90.4 % / Redundancy: 3.73 % / Net I/σ(I): 2.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→14.92 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.29 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.16 / Details: Refmac5
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 1562 5.2 %RANDOM
Rwork0.1878 ---
obs0.1909 28647 88.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 76.12 Å2 / Biso mean: 20.012 Å2 / Biso min: 7.19 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.7→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 0 320 3572
Biso mean---29.66 -
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193320
X-RAY DIFFRACTIONr_bond_other_d0.0020.023180
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.9524475
X-RAY DIFFRACTIONr_angle_other_deg1.0773.0017307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6735413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56623.741147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70815615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6891524
X-RAY DIFFRACTIONr_chiral_restr0.1140.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023742
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02786
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 121 -
Rwork0.251 2162 -
all-2283 -
obs--90.81 %

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