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- PDB-5idl: Crystal structure of the germline-targeting HIV-1 gp120 engineere... -

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Basic information

Entry
Database: PDB / ID: 5idl
TitleCrystal structure of the germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT8
ComponentsGermline-targeting HIV-1 gp120 engineered outer domain, eOD-GT8
KeywordsVIRAL PROTEIN / HIV Env / germline-targeting immunogen
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJulien, J.P. / Ereno-Orbea, J. / Jardine, J.G. / Schief, W.R. / Wilson, I.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI82362 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)CHAVI-ID 1UM1AI100663 United States
CAVDIAVI NAC Center United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI084817 United States
CitationJournal: Science / Year: 2016
Title: HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen.
Authors: Jardine, J.G. / Kulp, D.W. / Havenar-Daughton, C. / Sarkar, A. / Briney, B. / Sok, D. / Sesterhenn, F. / Ereno-Orbea, J. / Kalyuzhniy, O. / Deresa, I. / Hu, X. / Spencer, S. / Jones, M. / ...Authors: Jardine, J.G. / Kulp, D.W. / Havenar-Daughton, C. / Sarkar, A. / Briney, B. / Sok, D. / Sesterhenn, F. / Ereno-Orbea, J. / Kalyuzhniy, O. / Deresa, I. / Hu, X. / Spencer, S. / Jones, M. / Georgeson, E. / Adachi, Y. / Kubitz, M. / deCamp, A.C. / Julien, J.P. / Wilson, I.A. / Burton, D.R. / Crotty, S. / Schief, W.R.
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1743
Polymers19,7311
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.330, 53.060, 77.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT8


Mass: 19731.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#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.: 2
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2% (v/v) PEG 400, 2M ammonium sulfate, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.84→40 Å / Num. obs: 3333 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 62.61 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.131 / Net I/σ(I): 6.93
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.84-2.920.7791.4198.9
2.92-30.5641.79199.8
3-3.080.5812.02199.3
3.08-3.180.4572.451100
3.18-3.280.2963.43199.8
3.28-3.40.2943.33198.8
3.4-3.530.2494.02199.2
3.53-3.670.1945.511100
3.67-3.830.1676.52199.7
3.83-4.020.1267.48198.3
4.02-4.240.119.31198.8
4.24-4.50.110.281100
4.5-4.810.07712.62199.7
4.81-5.190.07113.841100
5.19-5.690.07612.31100
5.69-6.360.08711.41199.1
6.36-7.340.086111100
7.34-8.990.04618.18199.4
8.99-12.710.04822.38199.3
12.710.03324.59195.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JPJ

4jpj


Resolution: 2.9→31.422 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / Phase error: 28.96
RfactorNum. reflection% reflection
Rfree0.2971 243 10.02 %
Rwork0.2531 --
obs0.2575 3332 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.09 Å2 / Biso mean: 52.3497 Å2 / Biso min: 33.99 Å2
Refinement stepCycle: final / Resolution: 2.9→31.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 28 0 1245
Biso mean--58.83 --
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021278
X-RAY DIFFRACTIONf_angle_d0.4551745
X-RAY DIFFRACTIONf_chiral_restr0.042206
X-RAY DIFFRACTIONf_plane_restr0.003220
X-RAY DIFFRACTIONf_dihedral_angle_d13.888756
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9004-3.65330.3498157141395
3.65330.27621770.2357158599

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