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- PDB-8gdk: 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: 8gdk
TitleCrystal Structure of HIV-1 LM/HT CLADE A/E CRF01 GP120 Core in Complex with TFH-II-151
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 / 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
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: 2.65 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: To Be Published
Title: Crystal Structure of HIV-1 LM/HT CLADE A/E CRF01 GP120 Core in Complex with TFH-II-151
Authors: Tolbert, W.D. / Nguyen, D.N. / Pazgier, M.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: 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/HT Clade A/E CRF01 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,12819
Polymers39,4671
Non-polymers3,66118
Water543
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)61.418, 65.997, 90.826
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, 14 molecules A

#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 13
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, 8 molecules

#3: Chemical ChemComp-Z7N / (3S,5R)-N-(4-chloro-3-fluorophenyl)-5-(hydroxymethyl)-1-[(3R,5S)-3,4,5-trimethylpiperazine-1-carbonyl]piperidine-3-carboxamide


Mass: 440.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30ClFN4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 3350 5% PEG 400 0.1M 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: 2.6→50 Å / Num. obs: 11456 / % possible obs: 68.1 % / Redundancy: 4 % / CC1/2: 0.98 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.035 / Net I/σ(I): 40.3
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 609 / CC1/2: 0.95 / Rpim(I) all: 0.149 / % possible all: 61.3

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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: 2.65→40.29 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2836 494 4.7 %
Rwork0.2378 --
obs0.2399 10508 93.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 230 3 2908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032961
X-RAY DIFFRACTIONf_angle_d0.7514023
X-RAY DIFFRACTIONf_dihedral_angle_d11.657448
X-RAY DIFFRACTIONf_chiral_restr0.06487
X-RAY DIFFRACTIONf_plane_restr0.004497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.920.4131940.33772235X-RAY DIFFRACTION85
2.92-3.340.36131230.30322540X-RAY DIFFRACTION97
3.34-4.210.35071420.25162569X-RAY DIFFRACTION97
4.21-40.290.22741350.20372670X-RAY DIFFRACTION96

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