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- PDB-7ekb: Crystal structure of 4E10 modified with pyrene acetamide -

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Basic information

Entry
Database: PDB / ID: 7ekb
TitleCrystal structure of 4E10 modified with pyrene acetamide
Components
  • (Fab region of the ...) x 2
  • MPER region of the HIV-1 envelope glycoprotein protein gp41
KeywordsIMMUNE SYSTEM / IgG / Fab / Chemical modification
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
Revision 1.3Nov 20, 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
H: Fab region of the heavy chain of broadly neutralizing antibody anti-HIV-1 4E10
L: Fab region of the light chain of the broadly neutralizing anti-HIV-1 antibody 4E10
P: MPER region of the HIV-1 envelope glycoprotein protein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,99910
Polymers49,3873
Non-polymers6127
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-35 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.109, 44.890, 86.041
Angle α, β, γ (deg.)90.000, 113.680, 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 HIV-1 envelope glycoprotein protein gp41


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 Fab region of the heavy chain of broadly neutralizing antibody anti-HIV-1 4E10


Mass: 23906.961 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)
#2: Antibody Fab region of the light chain of the broadly neutralizing anti-HIV-1 antibody 4E10


Mass: 23292.705 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 , 3 types, 479 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.83 Å3/Da / Density % sol: 56.55 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 12% PEG 4,000; 200 mM Ammonium sulfate; 100 mM sodium acetate

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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: 1.45→34.5 Å / Num. obs: 96390 / % possible obs: 98.1 % / Redundancy: 5.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.04 / Net I/σ(I): 11.2
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 3 / Num. unique obs: 12753 / CC1/2: 0.454 / Rpim(I) all: 0.464 / % possible all: 89.9

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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: 4WY7

4wy7


Resolution: 1.45→34.44 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.541 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1505 2919 3 %RANDOM
Rwork0.1199 ---
obs0.1208 93433 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.65 Å2 / Biso mean: 20.482 Å2 / Biso min: 9.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20.01 Å2
2--0.06 Å20 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 1.45→34.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 0 40 480 3890
Biso mean--26.17 31.84 -
Num. residues----443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133576
X-RAY DIFFRACTIONr_bond_other_d0.0050.0173263
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.6484874
X-RAY DIFFRACTIONr_angle_other_deg1.4561.5737626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg26.2645.559492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.59722.387155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33915555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8461519
X-RAY DIFFRACTIONr_chiral_restr0.0860.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024503
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02730
X-RAY DIFFRACTIONr_rigid_bond_restr2.83636838
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 188 -
Rwork0.192 5869 -
all-6057 -
obs--83.97 %

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