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- PDB-5hfl: Gp41-targeting HIV-1 fusion inhibitors with helical Ile-Asp-Leu tail -

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Basic information

Entry
Database: PDB / ID: 5hfl
TitleGp41-targeting HIV-1 fusion inhibitors with helical Ile-Asp-Leu tail
ComponentsEnvelope glycoprotein,gp41 CHR region
KeywordsVIRAL PROTEIN / HIV-1 / fusion inhibitor / Ile-Asp-Leu tail / helical tail
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / 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 / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / membrane / plasma membrane
Similarity search - Function
Helix Hairpins - #210 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Env polyprotein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.294 Å
AuthorsZhu, Y. / Ye, S. / Zhang, R.
CitationJournal: Sci Rep / Year: 2016
Title: Rational improvement of gp41-targeting HIV-1 fusion inhibitors: an innovatively designed Ile-Asp-Leu tail with alternative conformations
Authors: Zhu, Y. / Su, S. / Qin, L. / Wang, Q. / Shi, L. / Ma, Z. / Tang, J. / Jiang, S. / Lu, L. / Ye, S. / Zhang, R.
History
DepositionJan 7, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein,gp41 CHR region
B: Envelope glycoprotein,gp41 CHR region
C: Envelope glycoprotein,gp41 CHR region
D: Envelope glycoprotein,gp41 CHR region
E: Envelope glycoprotein,gp41 CHR region
F: Envelope glycoprotein,gp41 CHR region


Theoretical massNumber of molelcules
Total (without water)51,8216
Polymers51,8216
Non-polymers00
Water3,081171
1
A: Envelope glycoprotein,gp41 CHR region
B: Envelope glycoprotein,gp41 CHR region
C: Envelope glycoprotein,gp41 CHR region


Theoretical massNumber of molelcules
Total (without water)25,9113
Polymers25,9113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-65 kcal/mol
Surface area11460 Å2
MethodPISA
2
D: Envelope glycoprotein,gp41 CHR region
E: Envelope glycoprotein,gp41 CHR region
F: Envelope glycoprotein,gp41 CHR region


Theoretical massNumber of molelcules
Total (without water)25,9113
Polymers25,9113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-69 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.449, 114.471, 42.936
Angle α, β, γ (deg.)90.00, 91.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Envelope glycoprotein,gp41 CHR region


Mass: 8636.868 Da / Num. of mol.: 6 / Fragment: UNP residues 35-70
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: A1YNW7, UniProt: P04578*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsresidue 622-627 is fusion linker, and residue 654-656 is artificial tail.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.2
Details: 0.2 M NaCl, 0.1 M Na2HPO4, citric acid, 15-20%(w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.294→42.915 Å / Num. obs: 17227 / % possible obs: 99.6 % / Redundancy: 3.4 % / Net I/σ(I): 10.5

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.294→42.915 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2629 1711 9.93 %
Rwork0.2142 --
obs0.2194 17226 93.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.294→42.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 0 171 3587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023453
X-RAY DIFFRACTIONf_angle_d0.4474629
X-RAY DIFFRACTIONf_dihedral_angle_d15.2771337
X-RAY DIFFRACTIONf_chiral_restr0.037512
X-RAY DIFFRACTIONf_plane_restr0.001585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2942-2.36170.28861370.2371217X-RAY DIFFRACTION87
2.3617-2.43790.33931420.23121201X-RAY DIFFRACTION90
2.4379-2.5250.30131430.22451293X-RAY DIFFRACTION94
2.525-2.62610.30991380.22971227X-RAY DIFFRACTION90
2.6261-2.74560.34181230.25481189X-RAY DIFFRACTION86
2.7456-2.89040.26541440.21881302X-RAY DIFFRACTION95
2.8904-3.07140.28741450.2271356X-RAY DIFFRACTION97
3.0714-3.30850.30581460.21841357X-RAY DIFFRACTION98
3.3085-3.64130.26421460.22171286X-RAY DIFFRACTION95
3.6413-4.16780.2521450.20171306X-RAY DIFFRACTION95
4.1678-5.24950.18511490.17651384X-RAY DIFFRACTION99
5.2495-42.92240.24441530.21891397X-RAY DIFFRACTION99

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