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- PDB-3vie: HIV-gp41 fusion inhibitor Sifuvirtide -

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Basic information

Entry
Database: PDB / ID: 3vie
TitleHIV-gp41 fusion inhibitor Sifuvirtide
Components
  • Envelope glycoprotein gp160
  • Sifuvirtide
KeywordsVIRAL PROTEIN/ANTIVIRAL PROTEIN / 6-helix bundle / membrane fusion inhibition / HIV / VIRAL PROTEIN-ANTIVIRAL PROTEIN complex
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
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYao, X. / Waltersperger, S. / Wang, M.T. / Cui, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Broad antiviral activity and crystal structure of HIV-1 fusion inhibitor sifuvirtide
Authors: Yao, X. / Chong, H. / Zhang, C. / Waltersperger, S. / Wang, M. / Cui, S. / He, Y.
History
DepositionSep 29, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Structure summary
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Nov 8, 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_ref_seq_dif
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_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein gp160
C: Envelope glycoprotein gp160
E: Envelope glycoprotein gp160
B: Sifuvirtide
D: Sifuvirtide
F: Sifuvirtide


Theoretical massNumber of molelcules
Total (without water)26,6106
Polymers26,6106
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12010 Å2
ΔGint-96 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.787, 49.179, 55.818
Angle α, β, γ (deg.)90.00, 90.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Envelope glycoprotein gp160


Mass: 4152.843 Da / Num. of mol.: 3 / Fragment: NHR domain, UNP residues 554-589 / Source method: obtained synthetically / Details: NHR 35-70 sequence occurs naturally in HIV-1 / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YP39, UniProt: P04578*PLUS
#2: Protein/peptide Sifuvirtide


Mass: 4717.020 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: Sequence of Sifuvirtide has been designed based on sequence of HIV-1 gp41 CHR
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris HCl, 10% w/v PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2011
RadiationMonochromator: Bartels Monochromator Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.701→44.391 Å / Num. obs: 24817 / % possible obs: 93.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.18 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 18.53
Reflection shellResolution: 1.701→1.8 Å / Redundancy: 1.24 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.51 / % possible all: 63.3

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ENV

1env


Resolution: 1.8→34.936 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.25 / σ(F): 0.81 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 1109 5 %
Rwork0.1818 --
obs0.1837 22201 98.81 %
all-24817 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.439 Å2 / ksol: 0.463 e/Å3
Displacement parametersBiso max: 113.7 Å2 / Biso mean: 31.7329 Å2 / Biso min: 12.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.7408 Å20 Å2-2.8535 Å2
2--6.6726 Å2-0 Å2
3----7.4134 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 0 93 1963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182210
X-RAY DIFFRACTIONf_angle_d1.493016
X-RAY DIFFRACTIONf_dihedral_angle_d16.919926
X-RAY DIFFRACTIONf_chiral_restr0.117312
X-RAY DIFFRACTIONf_plane_restr0.006410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8820.25761290.2012435256492
1.882-1.98120.2251380.184626332771100
1.9812-2.10530.24341410.167526622803100
2.1053-2.26780.2171380.157126372775100
2.2678-2.4960.23981410.15626672808100
2.496-2.8570.20621400.168726712811100
2.857-3.59890.20251420.158526852827100
3.5989-34.94250.21391400.21222702284299

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