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- PDB-8gdj: 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: 8gdj
TitleCrystal Structure of HIV-1 LM/HT CLADE A/E CRF01 GP120 Core in Complex with TFH-II-128
ComponentsHIV-1 LM/HT Clade A/E CRF01 gp120 core
KeywordsVIRAL PROTEIN/INHIBITOR / HIV-1 GP120 / CLADE A/E CF01 / VIRAL PROTEIN-INHIBITOR complex
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / : / clade A/E 93TH057 HIV-1 gp120 core
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsNguyen, D.N. / Tolbert, W.D. / 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: To Be Published
Title: Crystal Structure of HIV-1 LM/HT CLADE A/E CRF01 GP120 Core in Complex with TFH-II-128
Authors: Nguyen, D.N. / Tolbert, W.D. / Pazgier, M.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: 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/HT Clade A/E CRF01 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,77215
Polymers39,4671
Non-polymers3,30614
Water57632
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)62.180, 66.115, 91.173
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/HT Clade A/E CRF01 gp120 core


Mass: 39466.750 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
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-Z6F / (3S,5R)-N-(4-chloro-3-fluorophenyl)-5-(hydroxymethyl)-1-(4-methylpiperazine-1-carbonyl)piperidine-3-carboxamide


Mass: 412.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26ClFN4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.19 %
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 PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2021
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 13866 / % possible obs: 82.3 % / Redundancy: 3.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.08 / Net I/σ(I): 13.4
Reflection shellResolution: 2.42→2.48 Å / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 677 / CC1/2: 0.63 / Rpim(I) all: 0.489 / % possible all: 69.8

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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: 2.42→45.3 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2864 667 4.82 %
Rwork0.2277 --
obs0.2305 13836 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 211 32 2918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072945
X-RAY DIFFRACTIONf_angle_d1.1274000
X-RAY DIFFRACTIONf_dihedral_angle_d11.402446
X-RAY DIFFRACTIONf_chiral_restr0.095480
X-RAY DIFFRACTIONf_plane_restr0.007496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.610.35561180.32342060X-RAY DIFFRACTION74
2.61-2.870.37121090.31352619X-RAY DIFFRACTION93
2.87-3.280.35311320.27152788X-RAY DIFFRACTION99
3.28-4.140.30431630.22112793X-RAY DIFFRACTION99
4.14-45.30.23561450.18992909X-RAY DIFFRACTION98

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