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- PDB-3vtp: HIV fusion inhibitor MT-C34 -

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Basic information

Entry
Database: PDB / ID: 3vtp
TitleHIV fusion inhibitor MT-C34
Components(Transmembrane protein gp41) x 2
KeywordsVIRAL PROTEIN/ANTIVIRAL PROTEIN / 6-helix-bundle / M-T hook / fusion inhibitor / membrane fusion / VIRAL PROTEIN-ANTIVIRAL PROTEIN complex
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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / 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 ...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 / 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 / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYao, X. / Waltersperger, S. / Wang, M. / Cui, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The M-T hook structure is critical for design of HIV-1 fusion inhibitors.
Authors: Chong, H. / Yao, X. / Sun, J. / Qiu, Z. / Zhang, M. / Waltersperger, S. / Wang, M. / Cui, S. / He, Y.
History
DepositionJun 2, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: 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_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 1.3Nov 6, 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: Transmembrane protein gp41


Theoretical massNumber of molelcules
Total (without water)9,4082
Polymers9,4082
Non-polymers00
Water1,38777
1
C: Transmembrane protein gp41
D: Transmembrane protein gp41

C: Transmembrane protein gp41
D: Transmembrane protein gp41

C: Transmembrane protein gp41
D: Transmembrane protein gp41


Theoretical massNumber of molelcules
Total (without water)28,2236
Polymers28,2236
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area12120 Å2
ΔGint-86 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.260, 45.260, 209.895
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-615-

HOH

31C-641-

HOH

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Components

#1: Protein/peptide Transmembrane protein gp41 / Glycoprotein 41 / gp41


Mass: 4899.677 Da / Num. of mol.: 1 / Fragment: N-peptide, UNP RESIDUES 555-595 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Human immunodeficiency virus type 1 / References: UniProt: P03377
#2: Protein/peptide Transmembrane protein gp41 / fusion inhibitor MT-C34 / Glycoprotein 41 / gp41


Mass: 4507.922 Da / Num. of mol.: 1 / Fragment: NHR, UNP RESIDUES 631-666 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Human immunodeficiency virus type 1 / References: UniProt: P03377
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1M MES, 12 %(w/v) PEG 10000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 25, 2012
RadiationMonochromator: Osmic VariMax optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→31.403 Å / Num. all: 6812 / Num. obs: 6812 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.64 % / Rmerge(I) obs: 0.053 / Rsym value: 0.059 / Net I/σ(I): 18.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.316 / % possible all: 87.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERMRphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VGX

3vgx


Resolution: 1.9→31.403 Å / SU ML: 0.16 / Cross valid method: RANDOM / σ(F): 1.36 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 321 4.72 %
Rwork0.1953 --
all0.1969 6812 -
obs0.1969 6807 98.34 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 86.888 Å2 / ksol: 0.498 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.6471 Å2-0 Å2-0 Å2
2--3.6471 Å2-0 Å2
3----7.2942 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms581 0 0 77 658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006609
X-RAY DIFFRACTIONf_angle_d0.758830
X-RAY DIFFRACTIONf_dihedral_angle_d13.288234
X-RAY DIFFRACTIONf_chiral_restr0.04893
X-RAY DIFFRACTIONf_plane_restr0.002108
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9001-2.39380.24321610.1934311297
2.3938-31.4070.23061600.19593374100

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