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- PDB-3f4y: HIV gp41 six-helix bundle containing a mutant CHR alpha-peptide s... -

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Basic information

Entry
Database: PDB / ID: 3f4y
TitleHIV gp41 six-helix bundle containing a mutant CHR alpha-peptide sequence
Components
  • Envelope glycoprotein gp160
  • Mutant peptide derived from HIV gp41 CHR domain
KeywordsVIRAL PROTEIN / helix bundle / AIDS / Apoptosis / Cell membrane / Cleavage on pair of basic residues / Coiled coil / 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 / 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
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 / Resolution: 2 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: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
C: Envelope glycoprotein gp160
D: Mutant peptide derived from HIV gp41 CHR domain
E: Mutant peptide derived from HIV gp41 CHR domain
F: Mutant peptide derived from HIV gp41 CHR domain


Theoretical massNumber of molelcules
Total (without water)25,7876
Polymers25,7876
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-101 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.611, 179.038, 33.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-151-

HOH

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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.: 3 / Fragment: HIV gp41 NHR domain / Source method: obtained synthetically
Details: The peptide is chemically synthesized. It occurs naturally in HIV.
References: UniProt: P04580
#2: Protein/peptide Mutant peptide derived from HIV gp41 CHR domain


Mass: 4444.915 Da / Num. of mol.: 3 / Fragment: HIV gp41 CHR domain mutant
Mutation: M1T, M4E, E5A, E9A, N11A, N12E, T14A, S15A, L16R, H18E, S19A, N21E, Q33A, E34A, L36R
Source method: obtained synthetically
Details: The peptide is chemically synthesized. It is a sequence mutant to a sequence that occurs naturally in HIV.
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 1 M ammonium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Nov 5, 2007 / Details: confocal mirrors
RadiationMonochromator: gobel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→44.8 Å / Num. all: 15956 / Num. obs: 15938 / % possible obs: 99.9 % / Redundancy: 8.6 % / Rsym value: 0.05 / Net I/σ(I): 28
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.262 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0037refinement
PDB_EXTRACT3.006data extraction
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
PHASERphasing
RefinementResolution: 2→25 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 0 / SU B: 5.203 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 758 4.8 %RANDOM
Rwork0.209 ---
obs0.212 15881 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.36 Å2 / Biso mean: 24.219 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.55 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3769 0 0 456 4225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221887
X-RAY DIFFRACTIONr_bond_other_d0.0010.021268
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9352562
X-RAY DIFFRACTIONr_angle_other_deg0.933084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7295227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91125.094106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30915351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5191518
X-RAY DIFFRACTIONr_chiral_restr0.0660.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022094
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02371
X-RAY DIFFRACTIONr_nbd_refined0.2050.2506
X-RAY DIFFRACTIONr_nbd_other0.1760.21354
X-RAY DIFFRACTIONr_nbtor_refined0.170.2890
X-RAY DIFFRACTIONr_nbtor_other0.090.21035
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2104
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.211
X-RAY DIFFRACTIONr_mcbond_it1.5251.51536
X-RAY DIFFRACTIONr_mcbond_other0.1451.5468
X-RAY DIFFRACTIONr_mcangle_it1.24721809
X-RAY DIFFRACTIONr_scbond_it2.7923998
X-RAY DIFFRACTIONr_scangle_it3.1974.5747
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 49 -
Rwork0.248 1079 -
all-1128 -
obs--99.91 %

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