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- PDB-3vu6: Short peptide HIV entry inhibitor MT-SC22EK with a M-T hook -

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Basic information

Entry
Database: PDB / ID: 3vu6
TitleShort peptide HIV entry inhibitor MT-SC22EK with a M-T hook
Components
  • MTSC22
  • Transmembrane protein gp41Transmembrane protein
KeywordsMEMBRANE PROTEIN/INHIBITOR / 6-helix bundle / coiled-coil / membrane / fusion inhibitor / M-T hook / HIV entry / MEMBRANE PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


host cell periphery / CD4 receptor binding / 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 / host cell perinuclear region of cytoplasm ...host cell periphery / CD4 receptor binding / 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 / host cell perinuclear region of cytoplasm / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / 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 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.324 Å
AuthorsYao, X. / Chong, H.H. / Waltersperger, S. / Wang, M.T. / He, Y.X. / Cui, S.
CitationJournal: Faseb J. / Year: 2013
Title: Short-peptide fusion inhibitors with high potency against wild-type and enfuvirtide-resistant HIV-1
Authors: Chong, H.H. / Yao, X. / Qiu, Z. / Sun, J. / Zhang, M. / Waltersperger, S. / Wang, M.T. / Liu, S.-L. / Cui, S. / He, Y.X.
History
DepositionJun 19, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 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 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane protein gp41
B: MTSC22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7033
Polymers7,6072
Non-polymers961
Water84747
1
A: Transmembrane protein gp41
B: MTSC22
hetero molecules

A: Transmembrane protein gp41
B: MTSC22
hetero molecules

A: Transmembrane protein gp41
B: MTSC22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1099
Polymers22,8216
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area10330 Å2
ΔGint-92 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.910, 44.910, 182.908
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-601-

SO4

21A-701-

HOH

31A-735-

HOH

41A-744-

HOH

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Components

#1: Protein/peptide Transmembrane protein gp41 / Transmembrane protein


Mass: 4489.252 Da / Num. of mol.: 1 / Fragment: UNP residues 553-590 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 / References: UniProt: P03375
#2: Protein/peptide MTSC22


Mass: 3117.608 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Sequence of MTSC22 does not occur naturally in HIV-1, but designed based on sequence of HIV-1 gp41 CHR
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.5 Å3/Da / Density % sol: 64.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.22M lithium sulphate, 0.1M Tris, 26% PEG4000, pH 8.5, 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 22, 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: 2.324→38.893 Å / Num. all: 5295 / Num. obs: 5295 / % possible obs: 99.75 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 18.58
Reflection shellResolution: 2.32→2.46 Å / Redundancy: 9.38 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 5.79 / Num. unique all: 1424 / % possible all: 99

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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: 1ENV

1env


Resolution: 2.324→38.893 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.811 / SU ML: 0.27 / σ(F): 2.21 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 265 5.01 %RANDOM
Rwork0.2159 ---
all0.2173 5295 --
obs0.2173 5292 99.75 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.019 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 118.69 Å2 / Biso mean: 44.9606 Å2 / Biso min: 13.13 Å2
Baniso -1Baniso -2Baniso -3
1-5.8689 Å2-0 Å2-0 Å2
2--5.8689 Å2-0 Å2
3----11.7377 Å2
Refinement stepCycle: LAST / Resolution: 2.324→38.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms536 0 5 47 588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012547
X-RAY DIFFRACTIONf_angle_d1.147734
X-RAY DIFFRACTIONf_chiral_restr0.06581
X-RAY DIFFRACTIONf_plane_restr0.00589
X-RAY DIFFRACTIONf_dihedral_angle_d18.792211
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3245-2.92840.26251260.213224062532
2.9284-38.89860.23951390.216926212760

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