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- PDB-3g7a: HIV gp41 six-helix bundle composed of a chimeric alpha+alpha/beta... -

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Basic information

Entry
Database: PDB / ID: 3g7a
TitleHIV gp41 six-helix bundle composed of a chimeric alpha+alpha/beta-peptide analogue of the CHR domain in complex with an NHR domain alpha-peptide
Components
  • Chimeric alpha+alpha/beta-peptide analogue of the HIV gp41 CHR domain
  • Envelope glycoprotein gp160
KeywordsVIRAL PROTEIN / HIV / viral fusion / gp41 / helix-bundle / alpha/beta-peptide / foldamer / 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 / 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
ACETYL GROUP / Envelope glycoprotein gp160
Similarity search - Component
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHorne, W.S. / Johnson, L.M. / 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
DepositionFeb 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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: Chimeric alpha+alpha/beta-peptide analogue of the HIV gp41 CHR domain
A: ACETYL GROUP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0187
Polymers8,6062
Non-polymers4125
Water21612
1
A: Envelope glycoprotein gp160
B: Chimeric alpha+alpha/beta-peptide analogue of the HIV gp41 CHR domain
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)27,05521
Polymers25,8176
Non-polymers1,23715
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area12450 Å2
ΔGint-103 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.043, 57.043, 186.314
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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: 4126.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P04580
#2: Protein/peptide Chimeric alpha+alpha/beta-peptide analogue of the HIV gp41 CHR domain


Mass: 4478.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#3: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.39 Å3/Da / Density % sol: 63.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.4 M lithium sulfate, 12% w/v PEG 8000, 20% v/v glycerol, pH 7, 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 18, 2008 / 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: 2.8→50 Å / Num. all: 3100 / Num. obs: 3085 / % possible obs: 99.5 % / Redundancy: 5.9 % / Rsym value: 0.058 / Net I/σ(I): 16.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.388 / % possible all: 100

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.5.0070refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3F4Y, 3F50

3f4y

3f50


Resolution: 2.8→25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.898 / SU B: 39.29 / SU ML: 0.329 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.797 / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31083 132 4.3 %RANDOM
Rwork0.25177 ---
obs0.25425 2947 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.413 Å2
Baniso -1Baniso -2Baniso -3
1-3.54 Å21.77 Å20 Å2
2--3.54 Å20 Å2
3----5.31 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms574 0 27 12 613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021608
X-RAY DIFFRACTIONr_bond_other_d0.0050.02417
X-RAY DIFFRACTIONr_angle_refined_deg1.7512.038820
X-RAY DIFFRACTIONr_angle_other_deg0.9731026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.362557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57626.53826
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.4761592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.274152
X-RAY DIFFRACTIONr_chiral_restr0.0810.295
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.018603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.017100
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_it5.4612369
X-RAY DIFFRACTIONr_mcbond_other2.2612150
X-RAY DIFFRACTIONr_mcangle_it7.7093582
X-RAY DIFFRACTIONr_scbond_it4.4222239
X-RAY DIFFRACTIONr_scangle_it7.0953238
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
Rfree0.462 5 -
Rwork0.455 208 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 20.452 Å / Origin y: -17.234 Å / Origin z: 5.576 Å
111213212223313233
T0.0391 Å20.0312 Å2-0.0074 Å2-0.3342 Å20.0181 Å2--0.0104 Å2
L2.682 °20.5016 °2-1.034 °2-2.5328 °2-1.1693 °2--0.8075 °2
S0.0671 Å °-0.1593 Å °-0.1115 Å °0.0284 Å °-0.0662 Å °-0.1297 Å °-0.0705 Å °-0.0345 Å °-0.0009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 36
2X-RAY DIFFRACTION1B2 - 38

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