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- PDB-3f50: HIV gp41 six-helix bundle composed of an alpha/beta-peptide analo... -

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Basic information

Entry
Database: PDB / ID: 3f50
TitleHIV gp41 six-helix bundle composed of an alpha/beta-peptide analogue of the CHR domain in complex with an NHR domain alpha-peptide
Components
  • Envelope glycoprotein gp160
  • alpha/beta-peptide analogue of the HIV gp41 CHR domain
KeywordsVIRAL PROTEIN / alpha/beta-peptide / helix bundle / AIDS / Apoptosis / Cell membrane / Cleavage on pair of basic residues / Envelope protein / Fusion protein / Glycoprotein / Host-virus interaction / Lipoprotein / Membrane / Palmitate / Transmembrane / Viral immunoevasion / Virion
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
Envelope glycoprotein gp160
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHorne, W.S. / Gellman, S.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural and biological mimicry of protein surface recognition by alpha/beta-peptide foldamers
Authors: Horne, W.S. / Johnson, L.M. / Ketas, T.J. / Klasse, P.J. / Lu, M. / Moore, J.P. / Gellman, S.H.
History
DepositionNov 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 6, 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 / 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.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein gp160
B: alpha/beta-peptide analogue of the HIV gp41 CHR domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7693
Polymers8,6772
Non-polymers921
Water905
1
A: Envelope glycoprotein gp160
B: alpha/beta-peptide analogue of the HIV gp41 CHR domain
hetero molecules

A: Envelope glycoprotein gp160
B: alpha/beta-peptide analogue of the HIV gp41 CHR domain
hetero molecules

A: Envelope glycoprotein gp160
B: alpha/beta-peptide analogue of the HIV gp41 CHR domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3079
Polymers26,0316
Non-polymers2763
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9670 Å2
ΔGint-65 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.945, 84.945, 84.945
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein/peptide Envelope glycoprotein gp160 / Env polyprotein / Surface protein / SU / Glycoprotein 120 / gp120 / Transmembrane protein / TM / ...Env polyprotein / Surface protein / SU / Glycoprotein 120 / gp120 / Transmembrane protein / TM / Glycoprotein 41 / gp41


Mass: 4150.851 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 545 TO 580 / Source method: obtained synthetically
Details: The peptide is chemically synthesized. It is found naturally in HIV.
References: UniProt: P04580
#2: Protein/peptide alpha/beta-peptide analogue of the HIV gp41 CHR domain


Mass: 4526.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide.
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M NaCl, 0.1 M Tris pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2008
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 2893 / % possible obs: 99.8 % / Redundancy: 7.8 % / Rsym value: 0.061 / Net I/σ(I): 31.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.512 / % possible all: 98.2

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Processing

Software
NameVersionClassification
MD2diffractometer softwaredata collection
PHASERphasing
REFMAC5.5.0063refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3F4Y and 3F4Z

3f4y

3f4z


Resolution: 2.8→25 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.884 / SU B: 18.055 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 0.71 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30655 130 4.5 %RANDOM
Rwork0.26645 ---
obs0.26812 2730 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.307 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms514 0 6 5 525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021532
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7432.087723
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.534547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55226.36422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.3271574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.016153
X-RAY DIFFRACTIONr_chiral_restr0.0950.291
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.015397
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9321.5349
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7032550
X-RAY DIFFRACTIONr_scbond_it1.3473183
X-RAY DIFFRACTIONr_scangle_it2.5684.5173
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 12 -
Rwork0.388 184 -
obs--98 %

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