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- PDB-6j5e: Crystal structure of HIV-1 fusion inhibitor SC29EK complexed with... -

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Basic information

Entry
Database: PDB / ID: 6j5e
TitleCrystal structure of HIV-1 fusion inhibitor SC29EK complexed with gp41 NHR (N44)
Components
  • Envelope glycoprotein
  • SC29EK
KeywordsVIRAL PROTEIN/INHIBITOR / HIV fusion inhibitor / six 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 / 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 / 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 / Env polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsLiu, Z.X. / Geng, X.Z. / Qin, B. / Cui, S.
CitationJournal: To Be Published
Title: Crystal structure of HIV-1 fusion inhibitor SC29EK complexed with gp41 NHR (N44)
Authors: Liu, Z.X. / Geng, X.Z. / Qin, B. / Cui, S.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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
G: Envelope glycoprotein
H: SC29EK
I: Envelope glycoprotein
J: SC29EK
K: Envelope glycoprotein
L: SC29EK


Theoretical massNumber of molelcules
Total (without water)26,4306
Polymers26,4306
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-102 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.500, 39.860, 171.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Envelope glycoprotein


Mass: 5037.884 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli / References: UniProt: Q1HMR5, UniProt: P04578*PLUS
#2: Protein/peptide SC29EK


Mass: 3772.257 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1M PH3.5 Citric acid, 16%(w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.33→38.825 Å / Num. obs: 20721 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.19 % / Biso Wilson estimate: 57.985 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.099 / Net I/σ(I): 10.16
Reflection shellResolution: 2.33→2.44 Å / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 3031 / CC1/2: 0.601 / % possible all: 90.6

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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: 2.33→38.825 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.17
RfactorNum. reflection% reflection
Rfree0.2859 1090 5.38 %
Rwork0.233 --
obs0.2359 20260 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.33→38.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 0 10 1766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031781
X-RAY DIFFRACTIONf_angle_d0.4912382
X-RAY DIFFRACTIONf_dihedral_angle_d15.4611110
X-RAY DIFFRACTIONf_chiral_restr0.03262
X-RAY DIFFRACTIONf_plane_restr0.002299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3298-2.43580.3876980.32342214X-RAY DIFFRACTION89
2.4358-2.56420.31811620.29132395X-RAY DIFFRACTION100
2.5642-2.72480.33011420.28372439X-RAY DIFFRACTION100
2.7248-2.93520.30651300.24532418X-RAY DIFFRACTION100
2.9352-3.23040.34111440.26242440X-RAY DIFFRACTION100
3.2304-3.69750.28341380.22722442X-RAY DIFFRACTION99
3.6975-4.65730.26251440.19122422X-RAY DIFFRACTION99
4.6573-38.83060.25911320.22962400X-RAY DIFFRACTION98

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