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- PDB-2q3i: Crystal structure of the D10-P3/IQN17 complex: a D-peptide inhibi... -

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Basic information

Entry
Database: PDB / ID: 2q3i
TitleCrystal structure of the D10-P3/IQN17 complex: a D-peptide inhibitor of HIV-1 entry bound to the GP41 coiled-coil pocket
Components
  • D-peptide
  • Fusion protein between the Coiled-Coil pocket of HIV GP41 and gcn4-PIQI
KeywordsVIRAL PROTEIN/INHIBITOR / envelope glycoprotein / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMalashkevich, V.N. / Eckert, D.M. / Hong, L.H. / Carr, P.A. / Kim, P.S.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Inhibiting HIV Entry: Discovery of D-Peptide Inhibitors that Target the Gp41 Coiled-Coil Pocket
Authors: Eckert, D.M. / Malashkevich, V.N. / Hong, L.H. / Carr, P.A. / Kim, P.S.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Crystal Structure of GCN4-Piqi, a Trimeric Coiled-Coil with Buried Polar Residues.
Authors: Eckert, D.M. / Malashkevich, V.N. / Kim, P.S.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Core structure of gp41 from the HIV envelope glycoprotein
Authors: Chan, D.C. / Fass, D. / Berger, J.M. / Kim, P.S.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion protein between the Coiled-Coil pocket of HIV GP41 and gcn4-PIQI
D: D-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2713
Polymers7,2362
Non-polymers351
Water2,774154
1
A: Fusion protein between the Coiled-Coil pocket of HIV GP41 and gcn4-PIQI
D: D-peptide
hetero molecules

A: Fusion protein between the Coiled-Coil pocket of HIV GP41 and gcn4-PIQI
D: D-peptide
hetero molecules

A: Fusion protein between the Coiled-Coil pocket of HIV GP41 and gcn4-PIQI
D: D-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8139
Polymers21,7076
Non-polymers1063
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area8800 Å2
ΔGint-86 kcal/mol
Surface area11020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.702, 50.702, 67.858
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-201-

CL

21A-233-

HOH

31A-269-

HOH

41A-281-

HOH

51A-299-

HOH

DetailsThe biological assembly is trimer formed around the crystallographic 3-fold axis

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Components

#1: Protein/peptide Fusion protein between the Coiled-Coil pocket of HIV GP41 and gcn4-PIQI /


Mass: 5468.566 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide synthesis. GCN4-HIV gp41 fusion, called IQN17. The sequence naturally occurs in Saccharomyces cerevisiae and human immunodeficiency virus
References: UniProt: A3F986
#2: Protein/peptide D-peptide


Mass: 1766.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis. D-peptide found by screening.
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: 10% ETHANOL, 1.5 M SODIUM CHLORIDE, pH 7.5, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Mar 31, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→35 Å / Num. obs: 16309 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 4.5 / % possible all: 86.8

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CZQ

1czq


Resolution: 1.5→10 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1639 10 %RANDOM
Rwork0.231 ---
obs0.231 16309 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 111.56 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.6 Å20.561 Å20 Å2
2--0 Å20 Å2
3----13.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms509 0 1 154 664
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d15.7
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it0.962
X-RAY DIFFRACTIONc_mcangle_it1.53
X-RAY DIFFRACTIONc_scbond_it1.853
X-RAY DIFFRACTIONc_scangle_it2.683.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 219 9.8 %
Rwork0.345 2188 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_D.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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