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- PDB-5z0w: Crystal structure of HIV-1 fusion inhibitor SC29EK complexed with... -

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Basic information

Entry
Database: PDB / ID: 5z0w
TitleCrystal structure of HIV-1 fusion inhibitor SC29EK complexed with gp41 NHR (N36)
Components
  • peptide-C
  • peptide-N
KeywordsVIRAL PROTEIN/INHIBITOR / HIV fusion inhibitor / 6 helix bundle / VIRAL PROTEIN-INHIBITOR 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 / virus-mediated perturbation of host defense response / host cell endosome membrane ...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 / virus-mediated perturbation of host defense response / 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 / 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
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
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.896 Å
AuthorsLiu, Z.X. / Qin, B. / Cui, S.
CitationJournal: J. Virol. / Year: 2018
Title: Mechanism of HIV-1 Resistance to an Electronically Constrained alpha-Helical Peptide Membrane Fusion Inhibitor
Authors: Wu, X. / Liu, Z. / Ding, X. / Yu, D. / Wei, H. / Qin, B. / Zhu, Y. / Chong, H. / Cui, S. / He, Y.
History
DepositionDec 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Feb 7, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 28, 2018Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
E: peptide-N
F: peptide-C


Theoretical massNumber of molelcules
Total (without water)7,8732
Polymers7,8732
Non-polymers00
Water41423
1
E: peptide-N
F: peptide-C

E: peptide-N
F: peptide-C

E: peptide-N
F: peptide-C


Theoretical massNumber of molelcules
Total (without water)23,6196
Polymers23,6196
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Buried area11030 Å2
ΔGint-87 kcal/mol
Surface area9630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.925, 56.925, 51.454
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11E-102-

HOH

21E-103-

HOH

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Components

#1: Protein/peptide peptide-N


Mass: 4126.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#2: Protein/peptide peptide-C


Mass: 3746.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris-cl PH8.0, 28%w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 1.896→35.597 Å / Num. obs: 4928 / % possible obs: 99.5 % / Redundancy: 4.53 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Net I/av σ(I): 11.21 / Net I/σ(I): 11.21
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 4.24 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 1.68 / Num. unique obs: 768 / CC1/2: 0.741 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H0N

5h0n


Resolution: 1.896→35.597 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.67
RfactorNum. reflection% reflection
Rfree0.257 245 5 %
Rwork0.2057 --
obs0.208 4897 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.896→35.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms553 0 0 23 576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008559
X-RAY DIFFRACTIONf_angle_d0.81747
X-RAY DIFFRACTIONf_dihedral_angle_d23.391347
X-RAY DIFFRACTIONf_chiral_restr0.04582
X-RAY DIFFRACTIONf_plane_restr0.00493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8964-2.38920.28621350.21872301X-RAY DIFFRACTION99
2.3892-35.60320.24871100.20252351X-RAY DIFFRACTION100

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