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- PDB-8f3b: HIV-1 gp41 coiled-coil pocket IQN22 -

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Basic information

Entry
Database: PDB / ID: 8f3b
TitleHIV-1 gp41 coiled-coil pocket IQN22
ComponentsIQN22
KeywordsVIRAL PROTEIN / HIV-1 / gp41 / coiled-coil / pocket
Biological speciesHIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBruun, T.U.J. / Tang, S. / Fernandez, D. / Kim, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DP1 AI158125 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structure-guided stabilization improves the ability of the HIV-1 gp41 hydrophobic pocket to elicit neutralizing antibodies.
Authors: Bruun, T.U.J. / Tang, S. / Erwin, G. / Deis, L. / Fernandez, D. / Kim, P.S.
History
DepositionNov 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IQN22
B: IQN22
C: IQN22


Theoretical massNumber of molelcules
Total (without water)18,3073
Polymers18,3073
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-52 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.359, 38.217, 151.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein IQN22


Mass: 6102.262 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) HIV-1 M:B_HXB2R (virus)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M di-ammonium phosphate and 40 % MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→37.05 Å / Num. obs: 11287 / % possible obs: 90.77 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.064 / Net I/σ(I): 26.4
Reflection shellResolution: 1.98→2.05 Å / Rmerge(I) obs: 0.064 / Num. unique obs: 1108 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
XDSdata scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8F3A

8f3a


Resolution: 2→30.48 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 581 5.16 %
Rwork0.232 --
obs0.2339 11255 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→30.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 0 69 1310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071252
X-RAY DIFFRACTIONf_angle_d0.8281670
X-RAY DIFFRACTIONf_dihedral_angle_d14.049516
X-RAY DIFFRACTIONf_chiral_restr0.047195
X-RAY DIFFRACTIONf_plane_restr0.005211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20.35591460.25342573X-RAY DIFFRACTION98
2.2-2.520.2971440.23542629X-RAY DIFFRACTION98
2.52-3.170.26621410.25242655X-RAY DIFFRACTION99
3.17-30.480.2461500.21982817X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.2213 Å / Origin y: 0.6165 Å / Origin z: 21.5992 Å
111213212223313233
T0.1324 Å20.0134 Å2-0.0133 Å2-0.2251 Å2-0.0103 Å2--0.2579 Å2
L1.3191 °2-0.0665 °2-1.1216 °2-1.1712 °21.0665 °2--7.1264 °2
S0.0673 Å °0.1251 Å °-0.0678 Å °0.0519 Å °-0.0786 Å °0.0058 Å °0.0003 Å °-0.0615 Å °-0.0089 Å °
Refinement TLS groupSelection details: all

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