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- PDB-2q7c: Crystal structure of IQN17 -

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Basic information

Entry
Database: PDB / ID: 2q7c
TitleCrystal structure of IQN17
Componentsfusion protein between yeast variant GCN4 and HIVgp41
KeywordsVIRAL PROTEIN / ENVELOPE GLYCOPROTEIN / COILED COIL / VIRAL PROTEIN/VIRAL PROTEIN INHIBITOR
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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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: 2 Å
AuthorsMalashkevich, V.N. / Eckert, D.M. / Hong, L.H. / 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
DepositionJun 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fusion protein between yeast variant GCN4 and HIVgp41
B: fusion protein between yeast variant GCN4 and HIVgp41
C: fusion protein between yeast variant GCN4 and HIVgp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5487
Polymers16,4063
Non-polymers1424
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-76 kcal/mol
Surface area9350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.986, 39.846, 135.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide fusion protein between yeast variant GCN4 and HIVgp41 / IQN17


Mass: 5468.566 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: SYNTHETIC PEPTIDE. THE SEQUENCE NATURALLY OCCURS IN SACCHAROMYCES CEREVISIAE AND HUMAN IMMUNODEFICIENCY VIRUS.
References: UniProt: A3F986
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG4000, 1.5 M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 2000 / Details: X4A
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 9644 / % possible obs: 98.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.048 / Χ2: 1.066 / Net I/σ(I): 19.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.070.2099111.12894.4
2.07-2.150.1659271.00499.6
2.15-2.250.1359600.97799.9
2.25-2.370.0989600.92100
2.37-2.520.0869631.016100
2.52-2.710.0729621.09299.9
2.71-2.990.0529710.98499.7
2.99-3.420.0439760.91899.5
3.42-4.310.03410031.21498.3
4.31-350.03210111.49692.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å24.57 Å
Translation2.5 Å24.57 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0034refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.021 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30954 463 4.8 %RANDOM
Rwork0.23414 ---
obs0.23779 9139 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.254 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å20 Å20 Å2
2---0.79 Å20 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 0 13 84 1262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221183
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9981574
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7695136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.7925.6653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91215296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.933159
X-RAY DIFFRACTIONr_chiral_restr0.1330.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02799
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.2539
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2806
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3320.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1851.5746
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.326201116
X-RAY DIFFRACTIONr_scbond_it13.53520543
X-RAY DIFFRACTIONr_scangle_it6.5894.5456
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 29 -
Rwork0.252 609 -
obs-950 89.86 %

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