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- PDB-9hs7: Anti-HIV-1 chimeric miniprotein mimicking the N-terminal half of ... -

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Basic information

Entry
Database: PDB / ID: 9hs7
TitleAnti-HIV-1 chimeric miniprotein mimicking the N-terminal half of gp41 NHR with an extended region targeting the MPER
ComponentsTransmembrane protein gp41
KeywordsANTIVIRAL PROTEIN / HEPTAD-REPEAT REGION OF GP41
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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
DI(HYDROXYETHYL)ETHER / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsCamara-Artigas, A. / Gavira, J.A. / Conejero-Lara, F. / Polo-Megias, D. / Salinas-Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2019.107515RB.C21 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Potent HIV-1 miniprotein inhibitors targeting highly conserved gp41 epitopes.
Authors: Polo-Megias, D. / Cano-Munoz, M. / Gantner, P. / Laumond, G. / Decoville, T. / Grezzani, J. / La Rocchia, I. / Salinas-Garcia, M.C. / Camara-Artigas, A. / Gavira, J.A. / Conejero-Lara, F. / Moog, C.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transmembrane protein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5542
Polymers15,4481
Non-polymers1061
Water63135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint1 kcal/mol
Surface area8060 Å2
Unit cell
Length a, b, c (Å)65.435, 65.435, 88.769
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Transmembrane protein gp41 / TM / Glycoprotein 41 / gp41


Mass: 15447.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (BRU ISOLATE)
Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: P19551
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.55 Å3/Da / Density % sol: 66.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M sodium phosphate monobasic monohydrate, 0.1M potassium phosphate monobasic, 2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.698→19.29 Å / Num. obs: 11436 / % possible obs: 94.1 % / Redundancy: 10.2 % / Biso Wilson estimate: 25.17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.024 / Net I/σ(I): 15.9
Reflection shellResolution: 1.698→1.908 Å / Redundancy: 10 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 572 / CC1/2: 0.752 / Rpim(I) all: 0.33 / % possible all: 86.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.698→19.29 Å / SU ML: 0.1752 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.0149
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2391 551 4.82 %
Rwork0.2008 10881 -
obs0.2027 11432 86.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.62 Å2
Refinement stepCycle: LAST / Resolution: 1.698→19.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms964 0 7 35 1006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139996
X-RAY DIFFRACTIONf_angle_d1.40131333
X-RAY DIFFRACTIONf_chiral_restr0.0605155
X-RAY DIFFRACTIONf_plane_restr0.0209177
X-RAY DIFFRACTIONf_dihedral_angle_d16.5585399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.870.3414180.2777416X-RAY DIFFRACTION86.9
1.87-2.140.2418540.25211064X-RAY DIFFRACTION18.98
2.14-2.690.29621880.26513701X-RAY DIFFRACTION65.44
2.69-19.290.22192910.17845700X-RAY DIFFRACTION99.95

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