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- PDB-8gd5: Crystal Structure of HIV-1 LM/HT Clade A/E CRF01 GP120 Core in Co... -

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Basic information

Entry
Database: PDB / ID: 8gd5
TitleCrystal Structure of HIV-1 LM/HT Clade A/E CRF01 GP120 Core in Complex with DL-I-102
ComponentsHIV-1 LM/HS clade A/E CRF01 gp120 core
KeywordsVIRAL PROTEIN/INHIBITOR / HIV-1 GP120 / CLADE A/E CF01 / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-Z2O / clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTolbert, W.D. / Nguyen, D.N. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI129769 United States
CitationJournal: Viruses / Year: 2023
Title: Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing HIV-1-Infected Cells to ADCC.
Authors: Ding, S. / Tolbert, W.D. / Zhu, H. / Lee, D. / Marchitto, L. / Higgins, T. / Zhao, X. / Nguyen, D. / Sherburn, R. / Richard, J. / Gendron-Lepage, G. / Medjahed, H. / Mohammadi, M. / Abrams, ...Authors: Ding, S. / Tolbert, W.D. / Zhu, H. / Lee, D. / Marchitto, L. / Higgins, T. / Zhao, X. / Nguyen, D. / Sherburn, R. / Richard, J. / Gendron-Lepage, G. / Medjahed, H. / Mohammadi, M. / Abrams, C. / Pazgier, M. / Smith III, A.B. / Finzi, A.
History
DepositionMar 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 LM/HS clade A/E CRF01 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,36013
Polymers39,4531
Non-polymers2,90712
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.395, 66.792, 92.123
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 HIV-1 LM/HS clade A/E CRF01 gp120 core


Mass: 39452.723 Da / Num. of mol.: 1 / Mutation: H61Y,Q105H,V108I,H375T,N474D,I475M,K476R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-Z2O / {4-[(3S,5R)-3-[(4-chloro-3-fluorophenyl)carbamoyl]-5-(hydroxymethyl)piperidine-1-carbonyl]piperazin-1-yl}acetic acid


Mass: 456.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26ClFN4O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 3350 5% PEG 400 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2022
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 10748 / % possible obs: 86.1 % / Redundancy: 3.7 % / CC1/2: 0.94 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.09 / Net I/σ(I): 17.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.983 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 562 / CC1/2: 0.6 / Rpim(I) all: 0.65 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→32.54 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 37.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 497 4.63 %
Rwork0.2187 --
obs0.2213 10731 85.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→32.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2668 0 186 2 2856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122920
X-RAY DIFFRACTIONf_angle_d1.363964
X-RAY DIFFRACTIONf_dihedral_angle_d12.03436
X-RAY DIFFRACTIONf_chiral_restr0.069468
X-RAY DIFFRACTIONf_plane_restr0.01495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.860.36131250.30282512X-RAY DIFFRACTION86
2.86-3.270.30671080.26272631X-RAY DIFFRACTION88
3.27-4.120.29381450.23462546X-RAY DIFFRACTION86
4.12-32.540.24731190.19182545X-RAY DIFFRACTION81

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