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- PDB-5f6i: Crystal Structure of Tier 2 Neutralizing Antibody DH428 from a Rh... -

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Basic information

Entry
Database: PDB / ID: 5f6i
TitleCrystal Structure of Tier 2 Neutralizing Antibody DH428 from a Rhesus Macaque
Components
  • DH428 Antibody Heavy Chain
  • DH428 Antibody Light Chain
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / HIV-1 / ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsFera, D. / Harrison, S.C.
CitationJournal: Cell Rep / Year: 2016
Title: Structural Constraints of Vaccine-Induced Tier-2 Autologous HIV Neutralizing Antibodies Targeting the Receptor-Binding Site.
Authors: Bradley, T. / Fera, D. / Bhiman, J. / Eslamizar, L. / Lu, X. / Anasti, K. / Zhang, R. / Sutherland, L.L. / Scearce, R.M. / Bowman, C.M. / Stolarchuk, C. / Lloyd, K.E. / Parks, R. / Eaton, A. ...Authors: Bradley, T. / Fera, D. / Bhiman, J. / Eslamizar, L. / Lu, X. / Anasti, K. / Zhang, R. / Sutherland, L.L. / Scearce, R.M. / Bowman, C.M. / Stolarchuk, C. / Lloyd, K.E. / Parks, R. / Eaton, A. / Foulger, A. / Nie, X. / Karim, S.S. / Barnett, S. / Kelsoe, G. / Kepler, T.B. / Alam, S.M. / Montefiori, D.C. / Moody, M.A. / Liao, H.X. / Morris, L. / Santra, S. / Harrison, S.C. / Haynes, B.F.
History
DepositionDec 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jul 5, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Sep 27, 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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DH428 Antibody Heavy Chain
C: DH428 Antibody Light Chain


Theoretical massNumber of molelcules
Total (without water)47,2192
Polymers47,2192
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-26 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.106, 74.628, 102.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Antibody DH428 Antibody Heavy Chain


Mass: 24293.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#2: Antibody DH428 Antibody Light Chain


Mass: 22926.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 40% PEG 400 and 100 mM sodium citrate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97916 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.32→60.36 Å / Num. obs: 22905 / % possible obs: 91.72 % / Redundancy: 4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.43
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.2 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: separated Fv and Fc regions of I3.2 Fab from PDB Entry 4QHL

4qhl


Resolution: 2.32→60.356 Å / FOM work R set: 0.8008 / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2646 1213 5.3 %
Rwork0.2181 21679 -
obs0.2204 22892 91.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.72 Å2 / Biso mean: 48.6 Å2 / Biso min: 23.45 Å2
Refinement stepCycle: final / Resolution: 2.32→60.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 0 83 3225
Biso mean---48.86 -
Num. residues----420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093230
X-RAY DIFFRACTIONf_angle_d1.2784398
X-RAY DIFFRACTIONf_chiral_restr0.082499
X-RAY DIFFRACTIONf_plane_restr0.006560
X-RAY DIFFRACTIONf_dihedral_angle_d14.4971135
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.32-2.41290.28221420.25182431257395
2.4129-2.52270.34271350.26372440257594
2.5227-2.65570.28591490.25992394254393
2.6557-2.82210.30161270.23062417254493
2.8221-3.040.27411270.2372391251892
3.04-3.34590.29041420.22472359250191
3.3459-3.830.26211450.21182372251790
3.83-4.82510.24271110.18952408251990
4.8251-60.37610.241350.22182467260288
Refinement TLS params.Method: refined / Origin x: 3.0516 Å / Origin y: -18.8539 Å / Origin z: -21.5289 Å
111213212223313233
T0.3518 Å20.0394 Å20.0382 Å2-0.3719 Å2-0.0219 Å2--0.277 Å2
L1.3966 °2-0.0093 °20.2045 °2-1.0652 °2-0.3205 °2--0.4446 °2
S0.0306 Å °-0.0068 Å °0.3389 Å °-0.005 Å °-0.0551 Å °0.0285 Å °-0.1128 Å °-0.0265 Å °0.0273 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 90
2X-RAY DIFFRACTION1allB2 - 219
3X-RAY DIFFRACTION1allC1 - 212

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