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- PDB-3o3z: Complex of a chimeric alpha/beta-peptide based on the gp41 CHR do... -

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Basic information

Entry
Database: PDB / ID: 3o3z
TitleComplex of a chimeric alpha/beta-peptide based on the gp41 CHR domain bound to a gp41 NHR domain peptide
Components
  • Envelope glycoprotein gp160
  • chimeric alpha/beta peptide based on gp41 CHR domain sequence
KeywordsVIRAL PROTEIN / HIV fusion inhibitor / mixed alpha-peptide/beta-peptide backbone
Function / homology
Function and homology information


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 ...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: 2.6 Å
AuthorsHorne, W.S. / Johnson, L.M. / Gellman, S.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Broad Distribution of Energetically Important Contacts across an Extended Protein Interface.
Authors: Johnson, L.M. / Horne, W.S. / Gellman, S.H.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Structure summary
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_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_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_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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _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_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/beta peptide based on gp41 CHR domain sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8384
Polymers8,6542
Non-polymers1842
Water30617
1
A: Envelope glycoprotein gp160
B: chimeric alpha/beta peptide based on gp41 CHR domain sequence
hetero molecules

A: Envelope glycoprotein gp160
B: chimeric alpha/beta peptide based on gp41 CHR domain sequence
hetero molecules

A: Envelope glycoprotein gp160
B: chimeric alpha/beta peptide based on gp41 CHR domain sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,51412
Polymers25,9626
Non-polymers5536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9770 Å2
ΔGint-64 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.804, 85.804, 85.804
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


Mass: 4150.851 Da / Num. of mol.: 1 / Fragment: UNP residues 554 to 589 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: Q9YP39
#2: Protein/peptide chimeric alpha/beta peptide based on gp41 CHR domain sequence


Mass: 4503.033 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.04 Å3/Da / Density % sol: 59.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.17 M NaOAc, 0.085 M Tris pH 8.5, 25% w/v PEG 4000, 15% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2008
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 3662 / % possible obs: 99.8 % / Redundancy: 39 % / Rsym value: 0.077 / Net I/σ(I): 74.9

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Processing

Software
NameVersionClassification
MD2diffractometer softwaredata collection
PHASERphasing
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F50

3f50


Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.862 / SU B: 10.795 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30242 157 4.3 %RANDOM
Rwork0.2412 ---
obs0.24395 3469 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.432 Å2
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms527 0 12 17 556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021544
X-RAY DIFFRACTIONr_bond_other_d0.0010.02365
X-RAY DIFFRACTIONr_angle_refined_deg1.5522.041736
X-RAY DIFFRACTIONr_angle_other_deg1.0073900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.838554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27626.53826
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.631582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.351153
X-RAY DIFFRACTIONr_chiral_restr0.0760.288
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.018561
X-RAY DIFFRACTIONr_gen_planes_other0.0010.01889
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_it1.581.5344
X-RAY DIFFRACTIONr_mcbond_other0.3391.5139
X-RAY DIFFRACTIONr_mcangle_it2.9452540
X-RAY DIFFRACTIONr_scbond_it4.6973200
X-RAY DIFFRACTIONr_scangle_it8.394.5196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 11 -
Rwork0.267 244 -
obs--100 %

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