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- PDB-6psa: PIE12 D-PEPTIDE AGAINST HIV ENTRY (IN COMPLEX WITH IQN17 Q577R RE... -

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Basic information

Entry
Database: PDB / ID: 6psa
TitlePIE12 D-PEPTIDE AGAINST HIV ENTRY (IN COMPLEX WITH IQN17 Q577R RESISTANCE MUTANT)
Components
  • IQN17
  • PIE12 D-peptide
KeywordsVIRAL PROTEIN/INHIBITOR / HIV / HELIX / HIV ENTRY INHIBITOR / IQN17 PIE12 / D-PEPTIDE INHIBITOR / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


FCERI mediated MAPK activation / Synthesis and processing of ENV and VPU / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / symbiont-mediated evasion of host immune response / mediator complex binding / positive regulation of establishment of T cell polarity ...FCERI mediated MAPK activation / Synthesis and processing of ENV and VPU / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / symbiont-mediated evasion of host immune response / mediator complex binding / positive regulation of establishment of T cell polarity / Oxidative Stress Induced Senescence / Alpha-defensins / Dectin-2 family / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / Binding and entry of HIV virion / cellular response to nutrient levels / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / cellular response to amino acid starvation / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / clathrin-dependent endocytosis of virus by host cell / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / viral protein processing / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / symbiont entry into host cell / DNA-binding transcription factor activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / chromatin binding / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / membrane
Similarity search - Function
: / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like ...: / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
polypeptide(D) / polypeptide(D) (> 10) / General control transcription factor GCN4 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciessynthetic construct (others)
Saccharomyces cerevisiae (brewer's yeast)
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHill, C.P. / Whitby, F.G. / Kay, M. / Weinstock, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Retrovirology / Year: 2019
Title: Characterization of resistance to a potent D-peptide HIV entry inhibitor.
Authors: Smith, A.R. / Weinstock, M.T. / Siglin, A.E. / Whitby, F.G. / Francis, J.N. / Hill, C.P. / Eckert, D.M. / Root, M.J. / Kay, M.S.
History
DepositionJul 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: PIE12 D-peptide
A: IQN17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6434
Polymers7,5722
Non-polymers712
Water1,33374
1
H: PIE12 D-peptide
A: IQN17
hetero molecules

H: PIE12 D-peptide
A: IQN17
hetero molecules

H: PIE12 D-peptide
A: IQN17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,92812
Polymers22,7166
Non-polymers2136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10350 Å2
ΔGint-83 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.843, 48.843, 67.634
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Polypeptide(D) PIE12 D-peptide


Mass: 2029.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide IQN17


Mass: 5542.534 Da / Num. of mol.: 1
Fragment: GP41 HYDROPHOBIC POCKET, RESIDUES 565-581, GCN4, RESIDUES 249-276
Mutation: Q577R / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (brewer's yeast), (synth.) Human immunodeficiency virus type 1
References: UniProt: P03069, UniProt: P04578
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: HAMPTON RESEARCH SALT RX SCREEN, CONDITION B4 - 1.8M AMMONIUM CITRATE DIBASIC, 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.6
Temp details: K

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97591 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2011
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97591 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 14574 / % possible obs: 98.5 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 26.2
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.375 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→13.21 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.07
RfactorNum. reflection% reflection
Rfree0.217 1454 10.02 %
Rwork0.176 --
obs0.18 14513 98.1 %
Solvent computationShrinkage radii: 1.13 Å / VDW probe radii: 1.2 Å / Bsol: 66.47 Å2 / ksol: 0.56 e/Å3
Displacement parametersBiso mean: 26.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.7698 Å20 Å20 Å2
2--2.7698 Å20 Å2
3----5.5396 Å2
Refinement stepCycle: LAST / Resolution: 1.3→13.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms530 0 2 74 606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008539
X-RAY DIFFRACTIONf_angle_d1.123713
X-RAY DIFFRACTIONf_dihedral_angle_d14.871215
X-RAY DIFFRACTIONf_chiral_restr0.0576
X-RAY DIFFRACTIONf_plane_restr0.00588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3001-1.34650.30461610.31171299X-RAY DIFFRACTION99
1.3465-1.40040.25991420.22921330X-RAY DIFFRACTION99
1.4004-1.4640.23841590.17761300X-RAY DIFFRACTION100
1.464-1.54110.22611400.14091294X-RAY DIFFRACTION97
1.5411-1.63750.18721490.14881361X-RAY DIFFRACTION100
1.6375-1.76370.21271280.15631334X-RAY DIFFRACTION100
1.7637-1.94060.22781530.15241322X-RAY DIFFRACTION100
1.9406-2.22030.19211430.15451346X-RAY DIFFRACTION100
2.2203-2.7930.22161520.15791328X-RAY DIFFRACTION100
2.793-13.2070.21391270.2041145X-RAY DIFFRACTION86

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