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- PDB-4i2l: New HIV entry inhibitor MTSFT/T23 complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4i2l
TitleNew HIV entry inhibitor MTSFT/T23 complex
Components
  • GP41
  • inhibitor MTSFT
KeywordsVIRAL PROTEIN/ANTIVIRAL PROTEIN / 6-helix bundle / coiled-coil / membrane / fusion inhibitor / M-T hook / 6-helix-bundle / tryptophan-methionine / VIRAL PROTEIN-ANTIVIRAL PROTEIN complex
Function / homology
Function and homology information


Dectin-2 family / 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 / 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 ...Dectin-2 family / 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 / 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.426 Å
AuthorsYao, X. / Chong, H.H. / Waltersperger, S. / Wang, M.T. / He, Y.X. / Cui, S.
CitationJournal: To be Published
Title: Potent antiviral activity of the novel HIV entry inhibitor MTSFT
Authors: Yao, X. / Chong, H.H. / Waltersperger, S. / Wang, M.T. / He, Y.X. / Cui, S.
History
DepositionNov 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: GP41
D: inhibitor MTSFT


Theoretical massNumber of molelcules
Total (without water)9,6522
Polymers9,6522
Non-polymers00
Water97354
1
C: GP41
D: inhibitor MTSFT

C: GP41
D: inhibitor MTSFT

C: GP41
D: inhibitor MTSFT


Theoretical massNumber of molelcules
Total (without water)28,9566
Polymers28,9566
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area11930 Å2
ΔGint-83 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.948, 43.948, 238.439
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-602-

HOH

21C-615-

HOH

31D-704-

HOH

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Components

#1: Protein/peptide GP41 / / Transmembrane protein gp41 / TM / Glycoprotein 41


Mass: 4873.639 Da / Num. of mol.: 1 / Fragment: N-peptide T23, UNP RESIDUES 549-589 / Source method: obtained synthetically
Details: HIV gp41 NHR 550-590 sequence occurs naturally in HIV-1 virus
Source: (synth.) Human immunodeficiency virus type 1 / References: UniProt: P04580
#2: Protein/peptide inhibitor MTSFT


Mass: 4778.199 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Sequence of MTSFT does not occur naturally in HIV-1, but designed based on sequence of HIV-1 gp41 CHR
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1M MES pH 6.4, 26 %(v/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 21, 2012
RadiationMonochromator: Bartels Monochromator Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.426→37.584 Å / Num. obs: 17074 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.03 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 24.76
Reflection shellResolution: 1.43→1.51 Å / Redundancy: 4.66 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.07 / % possible all: 98.1

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VIE

3vie


Resolution: 1.426→37.584 Å / SU ML: 0.22 / σ(F): 1.64 / Phase error: 24.25 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2421 855 5.01 %
Rwork0.216 --
obs0.2173 17074 99.4 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.778 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.098 Å20 Å20 Å2
2--7.098 Å20 Å2
3---2.1598 Å2
Refinement stepCycle: LAST / Resolution: 1.426→37.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms671 0 0 54 725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003722
X-RAY DIFFRACTIONf_angle_d0.566975
X-RAY DIFFRACTIONf_dihedral_angle_d18.008290
X-RAY DIFFRACTIONf_chiral_restr0.037105
X-RAY DIFFRACTIONf_plane_restr0.002128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4264-1.51580.31191390.2522260598
1.5158-1.63290.28821380.2255264099
1.6329-1.79720.26121410.2072661100
1.7972-2.05720.22041420.17592712100
2.0572-2.59180.20241440.16512743100
2.5918-37.59730.25011510.242858100

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