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- PDB-2q5u: Crystal structure of IQN17 -

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Basic information

Entry
Database: PDB / ID: 2q5u
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 / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / 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. / 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 1, 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: 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)16,4414
Polymers16,4063
Non-polymers351
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-60 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.515, 47.895, 136.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsUnit cell contains biological assembly, trimer

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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.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 21% PEG4000, 0.15 M ammonium sulfate, 0.1 M sodium acetate, pH 4.8, 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
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: 1.5→30 Å / Num. all: 24434 / Num. obs: 24434 / % possible obs: 100 % / Redundancy: 5.5 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2221 / Rsym value: 0.32 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.3.0034refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1CZQ

1czq


Resolution: 1.5→18.69 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.855 / SU B: 1.603 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29999 2418 10.1 %RANDOM
Rwork0.24389 ---
obs0.24946 21525 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.688 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 10 224 1385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221165
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7782.0121547
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8915136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.35225.88251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57415297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.162159
X-RAY DIFFRACTIONr_chiral_restr0.1030.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02779
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2460.2649
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2838
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2114
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2860.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4481.5714
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13721117
X-RAY DIFFRACTIONr_scbond_it3.9613502
X-RAY DIFFRACTIONr_scangle_it6.4724.5428
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.499→1.537 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 190 -
Rwork0.259 1574 -
obs--99.1 %

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