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- PDB-3w19: Potent HIV fusion inhibitor CP32M-2 -

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Basic information

Entry
Database: PDB / ID: 3w19
TitlePotent HIV fusion inhibitor CP32M-2
Components
  • Transmembrane protein gp41
  • fusion inhibitor CP32M-2
KeywordsMEMBRANE PROTEIN/INHIBITOR / 6-helix-bundle / MT-hook / inhibit HIV membrane fusion / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / host cell perinuclear region of cytoplasm / viral protein processing ...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 / 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 / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / 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: 1.278 Å
AuthorsYao, X. / Waltersperger, S. / Wang, M.T. / Cui, S.
CitationJournal: To be Published
Title: Optimization of novel anti-HIV fusion inhibitor
Authors: Yao, X. / Waltersperger, S. / Wang, M.T. / Cui, S.
History
DepositionNov 13, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Transmembrane protein gp41
D: fusion inhibitor CP32M-2


Theoretical massNumber of molelcules
Total (without water)8,3412
Polymers8,3412
Non-polymers00
Water1,35175
1
C: Transmembrane protein gp41
D: fusion inhibitor CP32M-2

C: Transmembrane protein gp41
D: fusion inhibitor CP32M-2

C: Transmembrane protein gp41
D: fusion inhibitor CP32M-2


Theoretical massNumber of molelcules
Total (without water)25,0226
Polymers25,0226
Non-polymers00
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 area11220 Å2
ΔGint-87 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.488, 44.488, 208.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-601-

HOH

21C-613-

HOH

31C-646-

HOH

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Components

#1: Protein/peptide Transmembrane protein gp41 / TM / Glycoprotein 41 / Glycoprotein 120 / gp120


Mass: 4515.291 Da / Num. of mol.: 1 / Fragment: N-peptide T21, UNP RESIDIES 552-589 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN HIV-1 VIRUS / Source: (synth.) Human immunodeficiency virus type 1 / References: UniProt: P03375
#2: Protein/peptide fusion inhibitor CP32M-2


Mass: 3825.257 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS SEQUENCE DOES NOT OCCUR NATURALLY IN HIV-1, BUT DESIGNED BASED ON SEQUENCE OF HIV-1 GP41 CHR AND ITS PARENTAL PEPTIDE CP32M
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Ammonium sulfate, 0.1 M HEPES, 16%(w/v) PEG 4000, 10%(w/v) isopropanol, 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: X10SA / Wavelength: 0.82656 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2011
RadiationMonochromator: Bartels Monochromator Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 1.278→36.144 Å / Num. all: 21170 / Num. obs: 21170 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 27.92
Reflection shellResolution: 1.28→1.35 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 3.49 / Num. unique all: 3334 / % possible all: 98.4

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERfor MRphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3VGX

3vgx


Resolution: 1.278→36.14 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 14.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1724 1059 5.01 %RANDOM
Rwork0.1553 ---
obs0.1561 21146 99.52 %-
all-21170 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.505 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.932 Å2-0 Å2-0 Å2
2--0.932 Å2-0 Å2
3----1.8641 Å2
Refinement stepCycle: LAST / Resolution: 1.278→36.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms588 0 0 75 663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005649
X-RAY DIFFRACTIONf_angle_d0.794886
X-RAY DIFFRACTIONf_dihedral_angle_d14.32260
X-RAY DIFFRACTIONf_chiral_restr0.04695
X-RAY DIFFRACTIONf_plane_restr0.003112
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2781-1.33630.26191280.2039242698
1.3363-1.40670.23731300.17512473100
1.4067-1.49490.18061310.1401247399
1.4949-1.61030.13711310.1118248699
1.6103-1.77230.1461320.11082500100
1.7723-2.02880.19531330.13332538100
2.0288-2.5560.14351330.13182527100
2.556-36.15820.17941410.1838266499

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