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- PDB-9sjq: Single-chain chimeric protein mimicking the interaction between H... -

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Basic information

Entry
Database: PDB / ID: 9sjq
TitleSingle-chain chimeric protein mimicking the interaction between HR1 and HR2 in HIV gp41 (pH 6.5)
ComponentsTransmembrane protein gp41,Y26L-covNHR
KeywordsVIRAL PROTEIN / GP41 / HIV-1
Function / homology
Function and homology information


Dectin-2 family / symbiont-mediated perturbation of host defense response / 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 ...Dectin-2 family / symbiont-mediated perturbation of host defense response / 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
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCamara-Artigas, A. / Gavira, J.A. / Conejero-Lara, F. / Polo-Megias, D. / Salinas-Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Other governmentPID2019. 107515RB.C21 Spain
CitationJournal: Protein Sci. / Year: 2026
Title: Investigating the role of a conserved hydrophobic pocket of gp41 in the anti-HIV activity of fusion inhibitors.
Authors: Polo-Megias, D. / Cano-Munoz, M. / Sanchez-Martinez, L. / Lestani, S. / Moog, C. / Decoville, T. / Salinas-Garcia, M.C. / Gavira, J.A. / Camara-Artigas, A. / Conejero-Lara, F.
History
DepositionAug 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane protein gp41,Y26L-covNHR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9674
Polymers23,6791
Non-polymers2883
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-25 kcal/mol
Surface area11810 Å2
Unit cell
Length a, b, c (Å)53.755, 79.713, 62.900
Angle α, β, γ (deg.)90.000, 94.200, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

21A-527-

HOH

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Components

#1: Protein Transmembrane protein gp41,Y26L-covNHR / TM / Glycoprotein 41 / gp41


Mass: 23678.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The chimeric protein consists of the fusion between the C-terminal heptad repeat region (CHR) of HIV-1 envelope's gp41 subunit (segment Tyr638-Leu663) and a 'de novo'-designed single-chain ...Details: The chimeric protein consists of the fusion between the C-terminal heptad repeat region (CHR) of HIV-1 envelope's gp41 subunit (segment Tyr638-Leu663) and a 'de novo'-designed single-chain protein construct that mimics the gp41 N-terminal heptad repeat (NHR) (segment Asn541-Leu592) in a trimeric coiled-coil conformation
Source: (gene. exp.) Human immunodeficiency virus type 1 (BRU ISOLATE)
Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: P03377
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2M ammonium sulfate, 0.1M MES, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→19.93 Å / Num. obs: 41887 / % possible obs: 99.1 % / Redundancy: 2.8 % / Biso Wilson estimate: 22.63 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.046 / Rrim(I) all: 0.066 / Net I/σ(I): 8.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2032 / CC1/2: 0.94 / Rpim(I) all: 0.487 / Rrim(I) all: 0.705 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimless0.8.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.93 Å / SU ML: 0.185 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 22.0381
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 2127 5.08 %
Rwork0.1806 39706 -
obs0.1822 41833 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.17 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 15 143 1733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661615
X-RAY DIFFRACTIONf_angle_d0.89832173
X-RAY DIFFRACTIONf_chiral_restr0.0382244
X-RAY DIFFRACTIONf_plane_restr0.0257289
X-RAY DIFFRACTIONf_dihedral_angle_d16.5129647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.33911530.27332584X-RAY DIFFRACTION98.7
1.53-1.570.2891440.25062626X-RAY DIFFRACTION99.11
1.57-1.620.261540.21962638X-RAY DIFFRACTION98.52
1.62-1.660.24011440.19052630X-RAY DIFFRACTION98.65
1.66-1.720.20141490.16952609X-RAY DIFFRACTION97.8
1.72-1.780.2271490.16732622X-RAY DIFFRACTION99.28
1.78-1.850.19431520.16182669X-RAY DIFFRACTION99.61
1.85-1.930.2241310.1722619X-RAY DIFFRACTION99.13
1.93-2.040.24381440.1712642X-RAY DIFFRACTION99.25
2.04-2.160.23381270.16582677X-RAY DIFFRACTION98.8
2.16-2.330.17941330.14842657X-RAY DIFFRACTION99.79
2.33-2.560.2231290.1572708X-RAY DIFFRACTION99.68
2.56-2.930.20061360.17542652X-RAY DIFFRACTION99.5
2.93-3.690.21051420.19032700X-RAY DIFFRACTION99.23
3.69-19.930.20021400.19192673X-RAY DIFFRACTION98.12

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