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- PDB-5hfm: Gp41-targeting HIV-1 fusion inhibitors with hook-like Ile-Asp-Leu tail -

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Basic information

Entry
Database: PDB / ID: 5hfm
TitleGp41-targeting HIV-1 fusion inhibitors with hook-like Ile-Asp-Leu tail
ComponentsEnvelope glycoprotein gp160,gp41 CHR region
KeywordsVIRAL PROTEIN / HIV-1 fusion inhibitor / Ile-Asp-Leu tail / hook-like 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 / host cell plasma membrane / structural molecule activity / virion membrane / 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
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.298 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 gp160,gp41 CHR region
B: Envelope glycoprotein gp160,gp41 CHR region
C: Envelope glycoprotein gp160,gp41 CHR region
D: Envelope glycoprotein gp160,gp41 CHR region
E: Envelope glycoprotein gp160,gp41 CHR region
F: Envelope glycoprotein gp160,gp41 CHR region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0088
Polymers56,6816
Non-polymers3262
Water2,558142
1
A: Envelope glycoprotein gp160,gp41 CHR region
B: Envelope glycoprotein gp160,gp41 CHR region
C: Envelope glycoprotein gp160,gp41 CHR region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5044
Polymers28,3413
Non-polymers1631
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-76 kcal/mol
Surface area12740 Å2
MethodPISA
2
D: Envelope glycoprotein gp160,gp41 CHR region
E: Envelope glycoprotein gp160,gp41 CHR region
F: Envelope glycoprotein gp160,gp41 CHR region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5044
Polymers28,3413
Non-polymers1631
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-74 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.112, 39.076, 90.602
Angle α, β, γ (deg.)90.03, 89.98, 120.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Envelope glycoprotein gp160,gp41 CHR region / Env polyprotein


Mass: 9446.845 Da / Num. of mol.: 6 / Fragment: UNP residues 539-581
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: isolate LW123 / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: Q70626, UniProt: P04578*PLUS
#2: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.2 / Details: 1.4 M Sodium Potassium Phosphate

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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: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.298→33.9 Å / Num. obs: 18969 / % possible obs: 92.3 % / Redundancy: 1.6 % / Net I/σ(I): 16.4

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.298→33.85 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2467 969 5.11 %
Rwork0.2003 --
obs0.2029 18969 92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.298→33.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 22 142 3940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033832
X-RAY DIFFRACTIONf_angle_d0.4975134
X-RAY DIFFRACTIONf_dihedral_angle_d18.1751496
X-RAY DIFFRACTIONf_chiral_restr0.032566
X-RAY DIFFRACTIONf_plane_restr0.001656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2979-2.4190.38021110.27282351X-RAY DIFFRACTION84
2.419-2.57050.34381350.2582569X-RAY DIFFRACTION92
2.5705-2.76890.36311370.25392649X-RAY DIFFRACTION94
2.7689-3.04730.27091510.23372657X-RAY DIFFRACTION95
3.0473-3.48790.24971470.21112683X-RAY DIFFRACTION96
3.4879-4.39290.22281550.16352630X-RAY DIFFRACTION95
4.3929-33.85410.19371330.17542461X-RAY DIFFRACTION88

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