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- PDB-3vh7: Structure of HIV-1 gp41 NHR/fusion inhibitor complex P21 -

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Basic information

Entry
Database: PDB / ID: 3vh7
TitleStructure of HIV-1 gp41 NHR/fusion inhibitor complex P21
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 / 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
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.019 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 23, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein gp160
B: CP32M
C: Envelope glycoprotein gp160
D: CP32M
E: Envelope glycoprotein gp160
F: CP32M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1527
Polymers32,1276
Non-polymers241
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-108 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.506, 45.504, 55.514
Angle α, β, γ (deg.)90.00, 107.65, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 3 / 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.: 3 / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.89 Å3/Da / Density % sol: 34.99 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M MgCl2, 0.1M Sodium acetate, 25% PEG 400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2011
RadiationMonochromator: Bartels Monochromator Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.019→42.607 Å / Num. obs: 14977 / % possible obs: 90.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 1.97 % / Rmerge(I) obs: 0.084 / Rsym value: 0.085 / Net I/σ(I): 7.8
Reflection shellResolution: 2.02→2.14 Å / Redundancy: 1.24 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 1.18 / Num. unique all: 3185 / Rsym value: 0.764 / % possible all: 63.3

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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: 2.019→42.607 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 28.02 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 748 5.01 %RANDOM
Rwork0.2216 ---
obs0.2241 14944 93.43 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.303 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.4566 Å20 Å2-1.841 Å2
2--0.6326 Å20 Å2
3---12.824 Å2
Refinement stepCycle: LAST / Resolution: 2.019→42.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 1 68 2167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022147
X-RAY DIFFRACTIONf_angle_d0.5452896
X-RAY DIFFRACTIONf_dihedral_angle_d15.726806
X-RAY DIFFRACTIONf_chiral_restr0.035315
X-RAY DIFFRACTIONf_plane_restr0.001366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0188-2.17470.40421150.31922193X-RAY DIFFRACTION72
2.1747-2.39350.30251550.24062941X-RAY DIFFRACTION98
2.3935-2.73980.25551570.2112976X-RAY DIFFRACTION99
2.7398-3.45170.24331590.18663021X-RAY DIFFRACTION99
3.4517-42.61610.26621620.22173065X-RAY DIFFRACTION99

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