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- PDB-6tvq: Structure of native gp41 derived peptide fusion inhibitor -

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Basic information

Entry
Database: PDB / ID: 6tvq
TitleStructure of native gp41 derived peptide fusion inhibitor
Components
  • Env polyprotein (Fragment)
  • Envelope glycoprotein gp160
KeywordsVIRAL PROTEIN / Inhibitor / helix bundle / HIV
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane ...virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 / plasma 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
Env polyprotein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.45 Å
AuthorsHuhmann, S. / Nyakatura, E.K. / Rohrhofer, A. / Schmidt, B. / Eichler, J. / Moschner, J. / Roth, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Chembiochem / Year: 2021
Title: Systematic Evaluation of Fluorination as Modification for Peptide-Based Fusion Inhibitors against HIV-1 Infection.
Authors: Huhmann, S. / Nyakatura, E.K. / Rohrhofer, A. / Moschner, J. / Schmidt, B. / Eichler, J. / Roth, C. / Koksch, B.
History
DepositionJan 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Jul 19, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AaA: Env polyprotein (Fragment)
BBB: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)8,4292
Polymers8,4292
Non-polymers00
Water95553
1
AaA: Env polyprotein (Fragment)
BBB: Envelope glycoprotein gp160

AaA: Env polyprotein (Fragment)
BBB: Envelope glycoprotein gp160

AaA: Env polyprotein (Fragment)
BBB: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)25,2866
Polymers25,2866
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area10620 Å2
ΔGint-85 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.875, 44.875, 209.645
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11AaA-705-

HOH

21AaA-716-

HOH

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Components

#1: Protein/peptide Env polyprotein (Fragment)


Mass: 4515.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: C7F3P9
#2: Protein/peptide Envelope glycoprotein gp160 / Env polyprotein


Mass: 3913.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q6TAQ1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Ammonium sulfate, PEG 3350, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.45→38.241 Å / Num. obs: 14982 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.048 / Net I/σ(I): 8
Reflection shellResolution: 1.45→1.48 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 742 / CC1/2: 0.669

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
ACORNphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.45→38.24 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.661 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2426 710 4.74 %
Rwork0.1879 --
all0.19 --
obs-14980 99.953 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.725 Å2
Baniso -1Baniso -2Baniso -3
1-1.856 Å20.928 Å2-0 Å2
2--1.856 Å2-0 Å2
3----6.02 Å2
Refinement stepCycle: LAST / Resolution: 1.45→38.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms535 0 4 53 592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013563
X-RAY DIFFRACTIONr_bond_other_d0.0010.017521
X-RAY DIFFRACTIONr_angle_refined_deg1.711.633765
X-RAY DIFFRACTIONr_angle_other_deg1.5851.5711206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.355565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.12821.48127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9861593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.095154
X-RAY DIFFRACTIONr_chiral_restr0.0860.274
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02628
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02117
X-RAY DIFFRACTIONr_nbd_refined0.2180.2134
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.2421
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2272
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2246
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3110.225
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.215
X-RAY DIFFRACTIONr_nbd_other0.1830.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.25
X-RAY DIFFRACTIONr_mcbond_it4.1382.61260
X-RAY DIFFRACTIONr_mcbond_other4.1322.619261
X-RAY DIFFRACTIONr_mcangle_it5.0233.92325
X-RAY DIFFRACTIONr_mcangle_other5.0163.931326
X-RAY DIFFRACTIONr_scbond_it5.3293.167303
X-RAY DIFFRACTIONr_scbond_other5.3033.154302
X-RAY DIFFRACTIONr_scangle_it6.3624.579440
X-RAY DIFFRACTIONr_scangle_other6.3554.59441
X-RAY DIFFRACTIONr_lrange_it5.61632.464667
X-RAY DIFFRACTIONr_lrange_other5.24732.222657
X-RAY DIFFRACTIONr_rigid_bond_restr4.10931082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.4880.413460.3651042X-RAY DIFFRACTION100
1.488-1.5290.333650.309990X-RAY DIFFRACTION100
1.529-1.5730.312510.267963X-RAY DIFFRACTION99.9015
1.573-1.6210.316540.256963X-RAY DIFFRACTION100
1.621-1.6740.295470.227920X-RAY DIFFRACTION100
1.674-1.7330.238460.194902X-RAY DIFFRACTION100
1.733-1.7980.234380.175869X-RAY DIFFRACTION100
1.798-1.8720.204370.14844X-RAY DIFFRACTION100
1.872-1.9550.263460.165805X-RAY DIFFRACTION100
1.955-2.050.204310.164774X-RAY DIFFRACTION99.8759
2.05-2.1610.194260.135743X-RAY DIFFRACTION100
2.161-2.2920.2250.133705X-RAY DIFFRACTION99.8632
2.292-2.450.205280.149659X-RAY DIFFRACTION100
2.45-2.6460.213370.153623X-RAY DIFFRACTION100
2.646-2.8980.207350.171558X-RAY DIFFRACTION100
2.898-3.240.302240.224532X-RAY DIFFRACTION100
3.24-3.740.274300.19456X-RAY DIFFRACTION100
3.74-4.5770.203180.152400X-RAY DIFFRACTION99.7613
4.577-6.4590.178150.191323X-RAY DIFFRACTION100
6.459-100.266110.247199X-RAY DIFFRACTION100

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