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- PDB-7uel: Genetic and structural basis for the human anti-alpha-galactosyl ... -

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Basic information

Entry
Database: PDB / ID: 7uel
TitleGenetic and structural basis for the human anti-alpha-galactosyl antibody response
Components
  • Heavy chain Fab of antibody JEC1
  • Light chain Fab of antibody JEC1
KeywordsIMMUNE SYSTEM / alpha-galactosyl / antibody / anti-alpha-gal / immune response / M86
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLangley, D.B. / Christ, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Genetic and structural basis of the human anti-alpha-galactosyl antibody response.
Authors: Langley, D.B. / Schofield, P. / Nevoltris, D. / Jackson, J. / Jackson, K.J.L. / Peters, T.J. / Burk, M. / Matthews, J.M. / Basten, A. / Goodnow, C.C. / van Nunen, S. / Reed, J.H. / Christ, D.
History
DepositionMar 22, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionJun 29, 2022ID: 6NUZ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 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

Downloads & links

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Assembly

Deposited unit
H: Heavy chain Fab of antibody JEC1
L: Light chain Fab of antibody JEC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,62310
Polymers47,2632
Non-polymers3598
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The complex of heavy and light chain held together over gel filtration chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-81 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.540, 71.370, 95.821
Angle α, β, γ (deg.)90.000, 104.940, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11L-595-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Heavy chain Fab of antibody JEC1


Mass: 24708.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Light chain Fab of antibody JEC1


Mass: 22554.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 330 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.57 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Equal volumes of protein (in 25 mM Tris (pH 8.0) and 100 mM NaCl) and well solution (100 mM HEPES (pH 7.4), 65% (v/v) 2-methyl-2,4-pentanediol (MPD)) were combined.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→37.68 Å / Num. obs: 37838 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 25.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.033 / Rrim(I) all: 0.09 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.9470.8491705224250.7630.3430.9172.2100
9.11-37.686.20.02422583620.9990.010.02648.398.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.59 Å37.68 Å
Translation5.59 Å37.68 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
PHENIX1.11.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: generic Fab

Resolution: 1.9→37.68 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 1907 5.04 %
Rwork0.1691 35928 -
obs0.1714 37835 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.82 Å2 / Biso mean: 38.023 Å2 / Biso min: 13.77 Å2
Refinement stepCycle: final / Resolution: 1.9→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 15 322 3566
Biso mean--64.65 42.57 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133365
X-RAY DIFFRACTIONf_angle_d1.3114602
X-RAY DIFFRACTIONf_chiral_restr0.081511
X-RAY DIFFRACTIONf_plane_restr0.009591
X-RAY DIFFRACTIONf_dihedral_angle_d3.5492678
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9-1.94750.32751210.25042543
1.9475-2.00020.27331370.23022566
2.0002-2.0590.23451590.20792543
2.059-2.12550.24111340.19672544
2.1255-2.20140.27571390.19082543
2.2014-2.28960.21271330.19132569
2.2896-2.39380.22761350.18132559
2.3938-2.51990.23011360.17892558
2.5199-2.67780.22711420.18272536
2.6778-2.88450.21881310.1772581
2.8845-3.17460.21291160.16842610
3.1746-3.63370.21641410.1522554
3.6337-4.57680.16671270.13282602
4.5768-37.680.20411560.15972620
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3382-0.00490.92910.92690.33112.162-0.1816-0.25320.0551-0.0438-0.01380.2246-0.2959-0.45430.13230.1850.0617-0.01390.1904-0.02130.245-67.63510.63939.376
20.7999-0.28820.66620.5780.44222.93990.0979-0.1884-0.12990.0208-0.0340.17680.5867-0.8755-0.01220.2355-0.1590.00090.30750.03380.3229-66.526-5.56442.559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN L AND RESID 4:212 )L4 - 212
2X-RAY DIFFRACTION2( CHAIN H AND RESID 1:216 )H1 - 216

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