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- PDB-6utb: CRYSTAL STRUCTURE OF UNLIGANDED HIV-1 LM/HT CLADE A/E CRF01 GP120 CORE -

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Basic information

Entry
Database: PDB / ID: 6utb
TitleCRYSTAL STRUCTURE OF UNLIGANDED HIV-1 LM/HT CLADE A/E CRF01 GP120 CORE
ComponentsHIV-1 LM/HT Clade A/E CRF01 gp120 core
KeywordsIMMUNE SYSTEM / HIV-1 GP120 / CLADE A/E CF01 / VIRAL PROTEIN
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
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
clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTolbert, W.D. / Sherburn, R. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI129769 United States
CitationJournal: Mbio / Year: 2020
Title: The HIV-1 Env gp120 Inner Domain Shapes the Phe43 Cavity and the CD4 Binding Site.
Authors: Prevost, J. / Tolbert, W.D. / Medjahed, H. / Sherburn, R.T. / Madani, N. / Zoubchenok, D. / Gendron-Lepage, G. / Gaffney, A.E. / Grenier, M.C. / Kirk, S. / Vergara, N. / Han, C. / Mann, B.T. ...Authors: Prevost, J. / Tolbert, W.D. / Medjahed, H. / Sherburn, R.T. / Madani, N. / Zoubchenok, D. / Gendron-Lepage, G. / Gaffney, A.E. / Grenier, M.C. / Kirk, S. / Vergara, N. / Han, C. / Mann, B.T. / Chenine, A.L. / Ahmed, A. / Chaiken, I. / Kirchhoff, F. / Hahn, B.H. / Haim, H. / Abrams, C.F. / Smith 3rd, A.B. / Sodroski, J. / Pazgier, M. / Finzi, A.
History
DepositionOct 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 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)41,91712
Polymers39,4671
Non-polymers2,45011
Water82946
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.901, 67.687, 86.470
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10 / Source method: obtained synthetically / 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: isolated from a genetically manipulated source
Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 1500, 10% 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: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92007 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 28, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92007 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13726 / % possible obs: 96.7 % / Redundancy: 4 % / CC1/2: 0.98 / Rmerge(I) obs: 0.165 / Net I/σ(I): 6.1
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2025 / CC1/2: 0.7 / % possible all: 62.3

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TGT

3tgt


Resolution: 2.5→28.511 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 35.81
RfactorNum. reflection% reflection
Rfree0.3054 1173 4.69 %
Rwork0.2626 --
obs0.2646 13660 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→28.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 155 46 2875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062886
X-RAY DIFFRACTIONf_angle_d0.9893920
X-RAY DIFFRACTIONf_dihedral_angle_d8.1061715
X-RAY DIFFRACTIONf_chiral_restr0.093469
X-RAY DIFFRACTIONf_plane_restr0.006501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60960.41891210.36442322X-RAY DIFFRACTION74
2.6096-2.74710.28111620.34453058X-RAY DIFFRACTION98
2.7471-2.9190.42991240.33083126X-RAY DIFFRACTION98
2.919-3.14410.38521390.32633124X-RAY DIFFRACTION99
3.1441-3.460.40671760.30923032X-RAY DIFFRACTION98
3.46-3.95960.27451710.26993054X-RAY DIFFRACTION97
3.9596-4.98430.24131320.20533056X-RAY DIFFRACTION97
4.9843-28.5110.25421480.20743085X-RAY DIFFRACTION98

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