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

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Basic information

Entry
Database: PDB / ID: 6tvu
TitleStructure of native gp41 derived peptide fusion inhibitor
Components
  • Env polyprotein (Fragment)
  • Transmembrane protein gp41Transmembrane protein
KeywordsVIRAL PROTEIN / Inhibitor / helix bundle / HIV
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 / 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: 1.25 Å
AuthorsHuhmann, S. / Nyakatura, E.K. / Rohrhofer, A. / Schmidt, B. / Eichler, J. / Moschner, J. / Roth, C. / Koksch, B.
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 / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Jul 19, 2023Group: Advisory / Atomic model ...Advisory / 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_name_com / entity_poly / entity_poly_seq / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _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
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact
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 / _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.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _pdbx_validate_close_contact.auth_atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AaA: Env polyprotein (Fragment)
BBB: Transmembrane protein gp41


Theoretical massNumber of molelcules
Total (without water)8,3072
Polymers8,3072
Non-polymers00
Water1,56787
1
AaA: Env polyprotein (Fragment)
BBB: Transmembrane protein gp41

AaA: Env polyprotein (Fragment)
BBB: Transmembrane protein gp41

AaA: Env polyprotein (Fragment)
BBB: Transmembrane protein gp41


Theoretical massNumber of molelcules
Total (without water)24,9226
Polymers24,9226
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
Unit cell
Length a, b, c (Å)44.963, 44.963, 209.010
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-702-

HOH

21AaA-710-

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 Transmembrane protein gp41 / Transmembrane protein / TM / Glycoprotein 41 / gp41


Mass: 3792.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04582
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 5.6 / Details: PEG 4000, 2-Propanol, Citrate

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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: 1.25→38.3 Å / Num. obs: 23184 / % possible obs: 100 % / Redundancy: 14.5 % / CC1/2: 0.997 / Rpim(I) all: 0.083 / Net I/σ(I): 7.5
Reflection shellResolution: 1.25→1.27 Å / Num. unique obs: 1119 / CC1/2: 0.396

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
ACORNphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.25→38.28 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.238 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.048
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2104 1114 4.805 %
Rwork0.162 --
all0.164 --
obs-23183 99.97 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.651 Å2
Baniso -1Baniso -2Baniso -3
1-0.862 Å20.431 Å20 Å2
2--0.862 Å20 Å2
3----2.795 Å2
Refinement stepCycle: LAST / Resolution: 1.25→38.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms564 0 12 87 663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013638
X-RAY DIFFRACTIONr_bond_other_d0.0010.017582
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.63870
X-RAY DIFFRACTIONr_angle_other_deg1.5891.5771354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.74575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07922.25831
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67515106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.075154
X-RAY DIFFRACTIONr_chiral_restr0.0920.283
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02720
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02133
X-RAY DIFFRACTIONr_nbd_refined0.3320.2175
X-RAY DIFFRACTIONr_symmetry_nbd_other0.240.2498
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2311
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2258
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.247
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.217
X-RAY DIFFRACTIONr_nbd_other0.1940.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.216
X-RAY DIFFRACTIONr_mcbond_it2.5481.877294
X-RAY DIFFRACTIONr_mcbond_other2.5471.889295
X-RAY DIFFRACTIONr_mcangle_it3.3132.778371
X-RAY DIFFRACTIONr_mcangle_other3.3392.794372
X-RAY DIFFRACTIONr_scbond_it4.3152.434344
X-RAY DIFFRACTIONr_scbond_other4.3122.446345
X-RAY DIFFRACTIONr_scangle_it5.363.453499
X-RAY DIFFRACTIONr_scangle_other5.3553.465500
X-RAY DIFFRACTIONr_lrange_it5.64625.031812
X-RAY DIFFRACTIONr_lrange_other5.35924.357787
X-RAY DIFFRACTIONr_rigid_bond_restr5.35331218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.2820.323790.3251607X-RAY DIFFRACTION99.9407
1.282-1.3180.272920.3021544X-RAY DIFFRACTION100
1.318-1.3560.296740.2671511X-RAY DIFFRACTION100
1.356-1.3970.289660.2391507X-RAY DIFFRACTION100
1.397-1.4430.249760.2331420X-RAY DIFFRACTION100
1.443-1.4940.218790.1771393X-RAY DIFFRACTION100
1.494-1.550.225600.1361359X-RAY DIFFRACTION100
1.55-1.6140.153740.121269X-RAY DIFFRACTION100
1.614-1.6850.162750.1141233X-RAY DIFFRACTION100
1.685-1.7670.189530.1211207X-RAY DIFFRACTION100
1.767-1.8630.207580.1281144X-RAY DIFFRACTION100
1.863-1.9760.208490.1361073X-RAY DIFFRACTION99.9109
1.976-2.1120.2500.1281019X-RAY DIFFRACTION100
2.112-2.2810.162440.116957X-RAY DIFFRACTION100
2.281-2.4990.15440.115893X-RAY DIFFRACTION99.8934
2.499-2.7930.175360.132803X-RAY DIFFRACTION100
2.793-3.2250.193310.148726X-RAY DIFFRACTION100
3.225-3.9470.186330.163609X-RAY DIFFRACTION100
3.947-5.5730.265280.162493X-RAY DIFFRACTION100
5.573-38.20.318130.279302X-RAY DIFFRACTION99.6835

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