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- PDB-3vgy: Structure of HIV-1 gp41 NHR/fusion inhibitor complex P321 -

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Basic information

Entry
Database: PDB / ID: 3vgy
TitleStructure of HIV-1 gp41 NHR/fusion inhibitor complex P321
Components
  • CP32M
  • Envelope glycoprotein gp160
KeywordsMEMBRANE PROTEIN/INHIBITOR / 6-helix bundle / membrane fusion inhibition / MEMBRANE PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


host cell periphery / CD4 receptor binding / 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 / host cell perinuclear region of cytoplasm ...host cell periphery / CD4 receptor binding / 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 / host cell perinuclear region of cytoplasm / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / 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
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.034 Å
AuthorsYao, X. / Waltersperger, S. / Wang, M.T. / Cui, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis of potent and broad HIV-1 fusion inhibitor CP32M
Authors: Yao, X. / Chong, H. / Zhang, C. / Qiu, Z. / Qin, B. / Han, R. / Waltersperger, S. / Wang, M.T. / He, Y. / Cui, S.
History
DepositionAug 22, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_special_symmetry / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Envelope glycoprotein gp160
D: CP32M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8053
Polymers10,7092
Non-polymers961
Water39622
1
C: Envelope glycoprotein gp160
D: CP32M
hetero molecules

C: Envelope glycoprotein gp160
D: CP32M
hetero molecules

C: Envelope glycoprotein gp160
D: CP32M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4159
Polymers32,1276
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area11740 Å2
ΔGint-93 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.094, 45.094, 73.027
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11C-601-

SO4

21C-713-

HOH

31D-707-

HOH

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Components

#1: Protein Envelope glycoprotein gp160 / Env polyprotein / Surface protein gp120 / SU / Glycoprotein 120 / gp120 / Transmembrane protein ...Env polyprotein / Surface protein gp120 / SU / Glycoprotein 120 / gp120 / Transmembrane protein gp41 / TM / Glycoprotein 41 / gp41


Mass: 6413.350 Da / Num. of mol.: 1 / Fragment: NHR (UNP RESIDUES 546-588) / Source method: obtained synthetically / Details: This sequence occurs naturally. / Source: (synth.) Human immunodeficiency virus type 1 / References: UniProt: P03375
#2: Protein/peptide CP32M


Mass: 4295.733 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence does not occur naturally, but designed based on sequence of HIV-1 gp41 CHR 621-652.
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M AMMONIUM SULFATE, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 29, 2011
RadiationMonochromator: Bartels Monochromator Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.034→39.053 Å / Num. obs: 5850 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.77 % / Rmerge(I) obs: 0.079 / Rsym value: 0.08 / Net I/σ(I): 16.42
Reflection shellResolution: 2.05→2.17 Å / Redundancy: 5.61 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.89 / Num. unique all: 1644 / Rsym value: 0.63 / % possible all: 98.8

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3F4Y

3f4y


Resolution: 2.034→34.438 Å / SU ML: 0.12 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.259 526 4.96 %RANDOM
Rwork0.1969 ---
obs0.2002 5842 99.01 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.008 Å2 / ksol: 0.393 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.1153 Å2-0 Å2-0 Å2
2--5.1153 Å2-0 Å2
3----10.2306 Å2
Refinement stepCycle: LAST / Resolution: 2.034→34.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 0 5 22 697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014698
X-RAY DIFFRACTIONf_angle_d1.359946
X-RAY DIFFRACTIONf_dihedral_angle_d17.476263
X-RAY DIFFRACTIONf_chiral_restr0.075102
X-RAY DIFFRACTIONf_plane_restr0.005120
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0342-2.23890.23861290.1912247097
2.2389-2.56280.27731280.17562518100
2.5628-3.22860.27081330.18432566100
3.2286-39.05970.25361360.2122535100

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