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- PDB-2r5b: Structure of the gp41 N-trimer in complex with the HIV entry inhi... -

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Basic information

Entry
Database: PDB / ID: 2r5b
TitleStructure of the gp41 N-trimer in complex with the HIV entry inhibitor PIE7
Components
  • HIV entry inhibitor PIE7
  • gp41 N-peptide
KeywordsVIRAL PROTEIN/inhibitor / HIV / viral entry / PIE / VIRAL PROTEIN-inhibitor complex
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / HIV ENTRY INHIBITOR PIE7 / polypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsVanDemark, A.P. / Welch, B. / Heroux, A. / Hill, C.P. / Kay, M.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Potent D-peptide inhibitors of HIV-1 entry
Authors: Welch, B.D. / Vandemark, A.P. / Heroux, A. / Hill, C.P. / Kay, M.S.
History
DepositionSep 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Oct 25, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: gp41 N-peptide
B: gp41 N-peptide
C: gp41 N-peptide
H: HIV entry inhibitor PIE7
K: HIV entry inhibitor PIE7
L: HIV entry inhibitor PIE7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9839
Polymers21,6956
Non-polymers2883
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-108 kcal/mol
Surface area10840 Å2
MethodPISA
2
A: gp41 N-peptide
B: gp41 N-peptide
C: gp41 N-peptide
H: HIV entry inhibitor PIE7
K: HIV entry inhibitor PIE7
L: HIV entry inhibitor PIE7
hetero molecules

A: gp41 N-peptide
B: gp41 N-peptide
C: gp41 N-peptide
H: HIV entry inhibitor PIE7
K: HIV entry inhibitor PIE7
L: HIV entry inhibitor PIE7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,96618
Polymers43,38912
Non-polymers5766
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area21110 Å2
ΔGint-214 kcal/mol
Surface area21230 Å2
MethodPISA
3
A: gp41 N-peptide
B: gp41 N-peptide
C: gp41 N-peptide
H: HIV entry inhibitor PIE7
K: HIV entry inhibitor PIE7
L: HIV entry inhibitor PIE7
hetero molecules

A: gp41 N-peptide
B: gp41 N-peptide
C: gp41 N-peptide
H: HIV entry inhibitor PIE7
K: HIV entry inhibitor PIE7
L: HIV entry inhibitor PIE7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,96618
Polymers43,38912
Non-polymers5766
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area21610 Å2
ΔGint-223 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.024, 106.201, 76.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein/peptide gp41 N-peptide


Mass: 5466.574 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: peptide synthesis / Source: (synth.) synthetic construct (others)
#2: Polypeptide(D) HIV entry inhibitor PIE7


Type: Peptide-like / Class: Inhibitor / Mass: 1765.001 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: peptide synthesis / Source: (synth.) synthetic construct (others) / References: HIV ENTRY INHIBITOR PIE7
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M MES, 0.2M NaCl, 10 mM zinc sulfate, 25% PEG 550 MME, pH 6.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 14410 / Num. obs: 14381 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.076 / Χ2: 1.054 / Net I/σ(I): 11.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.559 / Num. unique all: 1393 / Χ2: 0.915 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→26.54 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.276 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1027 7.7 %RANDOM, TOTAL REFLECTIONS OVER 1000 in RFREE SET
Rwork0.203 ---
obs0.209 13329 99.85 %-
all-14378 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.962 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--1.44 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 2→26.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 15 132 1671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221556
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9852078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3375174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.71825.88251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.3615294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.147159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021083
X-RAY DIFFRACTIONr_nbd_refined0.1910.2756
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21058
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.212
X-RAY DIFFRACTIONr_mcbond_it1.2261.5961
X-RAY DIFFRACTIONr_mcangle_it1.89121460
X-RAY DIFFRACTIONr_scbond_it3.1663721
X-RAY DIFFRACTIONr_scangle_it4.6784.5618
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 75 -
Rwork0.195 896 -
all-971 -
obs--99.9 %

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