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- PDB-5uxq: Structure of anti-HIV trimer apex antibody PGT143 -

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Basic information

Entry
Database: PDB / ID: 5uxq
TitleStructure of anti-HIV trimer apex antibody PGT143
Components
  • PGT143 Fab Heavy Chain
  • PGT143 Fab Light Chain
KeywordsIMMUNE SYSTEM / Immunology / vaccine
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.415 Å
AuthorsKong, L. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
CitationJournal: Immunity / Year: 2017
Title: A Broadly Neutralizing Antibody Targets the Dynamic HIV Envelope Trimer Apex via a Long, Rigidified, and Anionic Beta-Hairpin Structure
Authors: Lee, J.-H. / Andrabi, R. / Su, C.-Y. / Yasmeen, A. / Julien, J.-P. / Kong, L. / Wu, N.C. / McBride, R. / Sok, D. / Pauthner, M. / Cotrell, C.A. / Nieusma, T. / Blattner, C. / Paulson, J.C. / ...Authors: Lee, J.-H. / Andrabi, R. / Su, C.-Y. / Yasmeen, A. / Julien, J.-P. / Kong, L. / Wu, N.C. / McBride, R. / Sok, D. / Pauthner, M. / Cotrell, C.A. / Nieusma, T. / Blattner, C. / Paulson, J.C. / Klasee, P.J. / Wilson, I.A. / Burton, D.R. / Ward, A.B.
History
DepositionFeb 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PGT143 Fab Heavy Chain
B: PGT143 Fab Light Chain
H: PGT143 Fab Heavy Chain
L: PGT143 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)99,8114
Polymers99,8114
Non-polymers00
Water81145
1
A: PGT143 Fab Heavy Chain
B: PGT143 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)49,9062
Polymers49,9062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-23 kcal/mol
Surface area20570 Å2
MethodPISA
2
H: PGT143 Fab Heavy Chain
L: PGT143 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)49,9062
Polymers49,9062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-25 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.866, 97.643, 126.206
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: Antibody PGT143 Fab Heavy Chain


Mass: 26166.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody PGT143 Fab Light Chain


Mass: 23739.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 65% (v/v) 2-methyl-2,4-pentanediol and 0.1 M Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.4→48.83 Å / Num. obs: 32477 / % possible obs: 95.1 % / Redundancy: 3.5 % / Rsym value: 0.11 / Net I/σ(I): 9.6

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.415→48.822 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.3
RfactorNum. reflection% reflection
Rfree0.2668 1652 5.1 %
Rwork0.2293 --
obs0.2314 32398 94.33 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 2.415→48.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6913 0 0 45 6958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037101
X-RAY DIFFRACTIONf_angle_d0.99633
X-RAY DIFFRACTIONf_dihedral_angle_d16.3562557
X-RAY DIFFRACTIONf_chiral_restr0.0671069
X-RAY DIFFRACTIONf_plane_restr0.0041230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4147-2.48570.41911170.33462124X-RAY DIFFRACTION80
2.4857-2.5660.33851300.31422424X-RAY DIFFRACTION90
2.566-2.65770.4351280.30852406X-RAY DIFFRACTION91
2.6577-2.76410.32161250.2962482X-RAY DIFFRACTION92
2.7641-2.88990.36791470.28992566X-RAY DIFFRACTION95
2.8899-3.04220.2861640.27032594X-RAY DIFFRACTION98
3.0422-3.23280.2681330.24372672X-RAY DIFFRACTION98
3.2328-3.48230.30191520.22752658X-RAY DIFFRACTION99
3.4823-3.83260.24431240.21072687X-RAY DIFFRACTION98
3.8326-4.38690.23071440.19152684X-RAY DIFFRACTION98
4.3869-5.52580.20791520.18662686X-RAY DIFFRACTION97
5.5258-48.83150.24881360.22542763X-RAY DIFFRACTION95

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