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

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Basic information

Entry
Database: PDB / ID: 9sjp
TitleSingle-chain chimeric protein mimicking the interaction between HR1 and HR2 in HIV gp41 bound to ANS
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
8-ANILINO-1-NAPHTHALENE SULFONATE / ANILINE / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,3388
Polymers47,3582
Non-polymers9806
Water8,467470
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.500, 53.100, 58.000
Angle α, β, γ (deg.)70.020, 69.930, 71.650
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 23678.775 Da / Num. of mol.: 2
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 1 / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: P03377
#2: Chemical ChemComp-2AN / 8-ANILINO-1-NAPHTHALENE SULFONATE


Mass: 299.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ANL / ANILINE


Mass: 93.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 30% w/v PEG 8000, 0.1 M MES

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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, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.15→19.47 Å / Num. obs: 154137 / % possible obs: 88.9 % / Redundancy: 1.8 % / Biso Wilson estimate: 14.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.031 / Rrim(I) all: 0.043 / Net I/σ(I): 12.5
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6335 / CC1/2: 0.844 / Rpim(I) all: 0.518 / Rrim(I) all: 0.733 / % possible all: 73.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.21.2_5419refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→19.47 Å / SU ML: 0.0989 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 16.5453
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1727 7840 5.09 %
Rwork0.1497 146266 -
obs0.1508 154106 88.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.74 Å2
Refinement stepCycle: LAST / Resolution: 1.15→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 64 470 3688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01233302
X-RAY DIFFRACTIONf_angle_d1.26644444
X-RAY DIFFRACTIONf_chiral_restr0.0737493
X-RAY DIFFRACTIONf_plane_restr0.0177588
X-RAY DIFFRACTIONf_dihedral_angle_d16.10991314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.27122050.23053824X-RAY DIFFRACTION69.29
1.16-1.180.26732400.23194531X-RAY DIFFRACTION82.93
1.18-1.190.22622890.21994542X-RAY DIFFRACTION83.64
1.19-1.210.20762560.20734699X-RAY DIFFRACTION85.27
1.21-1.220.22532550.20614704X-RAY DIFFRACTION86.65
1.22-1.240.21512530.20014814X-RAY DIFFRACTION87.71
1.24-1.260.22512650.18774954X-RAY DIFFRACTION88.59
1.26-1.280.2142330.17354813X-RAY DIFFRACTION88.76
1.28-1.30.19492440.16444960X-RAY DIFFRACTION89.74
1.3-1.320.17732750.15134968X-RAY DIFFRACTION90.29
1.32-1.340.18222680.14944892X-RAY DIFFRACTION90.59
1.34-1.360.16512530.14435058X-RAY DIFFRACTION91.1
1.36-1.390.17412880.14524978X-RAY DIFFRACTION91.34
1.39-1.420.16252720.14684998X-RAY DIFFRACTION91.54
1.42-1.450.19662760.14724982X-RAY DIFFRACTION91.19
1.45-1.480.15592600.13285023X-RAY DIFFRACTION90.84
1.48-1.520.15182820.11154946X-RAY DIFFRACTION90.45
1.52-1.560.13012670.11214978X-RAY DIFFRACTION91.12
1.56-1.610.14232540.1155006X-RAY DIFFRACTION90.88
1.61-1.660.15232720.11494955X-RAY DIFFRACTION90.9
1.66-1.720.15952600.12434984X-RAY DIFFRACTION90.7
1.72-1.790.15522720.13075020X-RAY DIFFRACTION91.68
1.79-1.870.14712590.13184999X-RAY DIFFRACTION91.44
1.87-1.970.1852730.13815006X-RAY DIFFRACTION90.88
1.97-2.090.14522660.13414904X-RAY DIFFRACTION90.02
2.09-2.250.14632660.1274927X-RAY DIFFRACTION89.91
2.25-2.480.14752730.12974936X-RAY DIFFRACTION89.9
2.48-2.830.18142560.1474963X-RAY DIFFRACTION90.39
2.83-3.570.16492570.16134972X-RAY DIFFRACTION90.44
3.57-19.470.21562510.18344930X-RAY DIFFRACTION89.64

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