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- PDB-9bxd: 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: 9bxd
TitleCRYSTAL STRUCTURE OF HIV-1 LM/HS CLADE A/E CRF01 GP120 CORE IN COMPLEX WITH HZ-IV-188
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: 1.85 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

Downloads & links

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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)42,32513
Polymers39,4531
Non-polymers2,87212
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.013, 65.837, 90.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 10 molecules A

#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

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Non-polymers , 4 types, 183 molecules

#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-A1ATK / (3S)-1-(4-L-arginylpiperazine-1-carbonyl)-N-(4-chloro-3-fluorophenyl)piperidine-3-carboxamide


Mass: 525.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H34ClFN8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.62 %
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: 0.95369 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 25, 2023
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 29237 / % possible obs: 92.4 % / Redundancy: 2.8 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.043 / Net I/σ(I): 23.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1143 / CC1/2: 0.5 / Rpim(I) all: 0.526 / % possible all: 74.2

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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: 1.85→27.43 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 1457 4.99 %
Rwork0.2297 --
obs0.2311 29202 92.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 185 180 3024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052901
X-RAY DIFFRACTIONf_angle_d0.9973939
X-RAY DIFFRACTIONf_dihedral_angle_d13.326433
X-RAY DIFFRACTIONf_chiral_restr0.054462
X-RAY DIFFRACTIONf_plane_restr0.005493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.33021200.35522270X-RAY DIFFRACTION77
1.92-20.35321320.31732512X-RAY DIFFRACTION85
2-2.090.35851250.29872554X-RAY DIFFRACTION86
2.09-2.20.30871420.28522899X-RAY DIFFRACTION97
2.2-2.330.2951720.27832919X-RAY DIFFRACTION99
2.34-2.520.2731810.26742923X-RAY DIFFRACTION99
2.52-2.770.31161420.25592943X-RAY DIFFRACTION98
2.77-3.170.23481240.23932890X-RAY DIFFRACTION95
3.17-3.990.25521670.20852937X-RAY DIFFRACTION97
3.99-27.430.21711520.18972898X-RAY DIFFRACTION91

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