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- PDB-9bxf: CRYSTAL STRUCTURE OF HIV-1 LM/HS CLADE A/E CRF01 GP120 CORE IN CO... -

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Basic information

Entry
Database: PDB / ID: 9bxf
TitleCRYSTAL STRUCTURE OF HIV-1 LM/HS CLADE A/E CRF01 GP120 CORE IN COMPLEX WITH HZ-IV-236
ComponentsHIV-1 LM/HS clade A/E CRF01 gp120 core
KeywordsVIRAL PROTEIN / HIV-1 GP120 / CLADE A/E CF01
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / symbiont entry into host cell / viral envelope / virion attachment to host cell / virion membrane
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
: / clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsNiu, L. / Tolbert, W.D. / Pazgier, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI174908 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI162242 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Optimization of a Piperidine CD4-Mimetic Scaffold Sensitizing HIV-1 Infected Cells to Antibody-Dependent Cellular Cytotoxicity.
Authors: Lee, D. / Niu, L. / Ding, S. / Zhu, H. / Tolbert, W.D. / Medjahed, H. / Beaudoin-Bussieres, G. / Abrams, C. / Finzi, A. / Pazgier, M. / Smith 3rd, A.B.
History
DepositionMay 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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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)42,13612
Polymers39,4531
Non-polymers2,68311
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.479, 66.191, 90.873
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 H375S N474D I475M K476R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell line (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.: 9
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-A1AS8 / (3S)-1-[4-(2-carbamimidamidoethyl)piperazine-1-carbonyl]-N-(4-chloro-3-fluorophenyl)piperidine-3-carboxamide


Mass: 453.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29ClFN7O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
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: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 2, 2024
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 11946 / % possible obs: 91 % / Redundancy: 3.3 % / CC1/2: 0.97 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.067 / Net I/σ(I): 13.7
Reflection shellResolution: 2.69→2.75 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 630 / CC1/2: 0.73 / Rpim(I) all: 0.772 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→45.05 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2706 470 4.63 %
Rwork0.2248 --
obs0.227 10156 94.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 172 8 2839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052889
X-RAY DIFFRACTIONf_angle_d0.8593922
X-RAY DIFFRACTIONf_dihedral_angle_d12.626431
X-RAY DIFFRACTIONf_chiral_restr0.051460
X-RAY DIFFRACTIONf_plane_restr0.007492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-3.080.39121320.32673249X-RAY DIFFRACTION96
3.08-3.880.31651840.25723172X-RAY DIFFRACTION94
3.88-45.050.22981540.19363265X-RAY DIFFRACTION92

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