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- PDB-7ekk: Anti-HIV-1 broadly neutralizing antibody delta-loop 4E10 modified... -

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Entry
Database: PDB / ID: 7ekk
TitleAnti-HIV-1 broadly neutralizing antibody delta-loop 4E10 modified with pyrene acetamide
Components
  • Heavy chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide
  • Light chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide
  • MPER region of the envelope glycoprotein gp41 from HIV-1
KeywordsIMMUNE SYSTEM / IgG / Fab / Chemical modification
Function / homologyAMMONIUM ION
Function and homology information
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCaaveiro, J.M.M. / Rujas, E. / Nieva, J.L.
CitationJournal: Iscience / Year: 2021
Title: Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile.
Authors: Rujas, E. / Leaman, D.P. / Insausti, S. / Carravilla, P. / Garcia-Porras, M. / Largo, E. / Morillo, I. / Sanchez-Eugenia, R. / Zhang, L. / Cui, H. / Iloro, I. / Elortza, F. / Julien, J.P. / ...Authors: Rujas, E. / Leaman, D.P. / Insausti, S. / Carravilla, P. / Garcia-Porras, M. / Largo, E. / Morillo, I. / Sanchez-Eugenia, R. / Zhang, L. / Cui, H. / Iloro, I. / Elortza, F. / Julien, J.P. / Eggeling, C. / Zwick, M.B. / Caaveiro, J.M.M. / Nieva, J.L.
History
DepositionApr 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide
L: Light chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide
P: MPER region of the envelope glycoprotein gp41 from HIV-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,16210
Polymers48,6443
Non-polymers5187
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-55 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.981, 44.800, 85.949
Angle α, β, γ (deg.)90.000, 113.630, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide MPER region of the envelope glycoprotein gp41 from HIV-1


Mass: 2187.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1

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Antibody , 2 types, 2 molecules HL

#1: Antibody Heavy chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide


Mass: 23350.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: immunoglobin / Production host: Escherichia coli BL21 (bacteria)
#2: Antibody Light chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide


Mass: 23106.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: immunoglobulin / Production host: Escherichia coli BL21 (bacteria)

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Non-polymers , 5 types, 509 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.86 Å3/Da / Density % sol: 57.06 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4,000 30% Ammonium sulphate 200 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97953 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 1.7→34.4 Å / Num. obs: 57219 / % possible obs: 94.2 % / Redundancy: 2.5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.8
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6629 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CIN

5cin


Resolution: 1.7→34.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.876 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1915 2324 4.1 %RANDOM
Rwork0.1584 ---
obs0.1597 54867 93.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.58 Å2 / Biso mean: 16.977 Å2 / Biso min: 7.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20.34 Å2
2---1.11 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.7→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 31 504 3901
Biso mean--26.63 28.57 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133588
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173252
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.6464907
X-RAY DIFFRACTIONr_angle_other_deg1.4261.5717603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.8945.421499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03722.089158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85315552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.61520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02744
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 126 -
Rwork0.258 2869 -
all-2995 -
obs--67.44 %

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