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- PDB-7uem: Genomic and structural basis for the human anti-alpha-galactosyl ... -

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Basic information

Entry
Database: PDB / ID: 7uem
TitleGenomic and structural basis for the human anti-alpha-galactosyl antibody response
Components
  • Heavy chain Fab arm of antibody HKB7
  • Light chain Fab of antibody HKB7
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: 2.314 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: 6NV0
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 1.4Oct 23, 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
C: Light chain Fab of antibody HKB7
D: Heavy chain Fab arm of antibody HKB7
H: Heavy chain Fab arm of antibody HKB7
L: Light chain Fab of antibody HKB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,15421
Polymers96,9384
Non-polymers1,21617
Water5,765320
1
C: Light chain Fab of antibody HKB7
D: Heavy chain Fab arm of antibody HKB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,05910
Polymers48,4692
Non-polymers5908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-79 kcal/mol
Surface area18880 Å2
MethodPISA
2
H: Heavy chain Fab arm of antibody HKB7
L: Light chain Fab of antibody HKB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,09511
Polymers48,4692
Non-polymers6269
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-88 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.937, 65.931, 151.513
Angle α, β, γ (deg.)90.000, 90.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-489-

HOH

21D-401-

HOH

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Components

#1: Antibody Light chain Fab of antibody HKB7


Mass: 23999.592 Da / Num. of mol.: 2
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 Heavy chain Fab arm of antibody HKB7


Mass: 24469.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Polysaccharide alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2112h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.24 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Equal volumes of protein (in 25 mM Tris, 100 mM NaCl) were combined with well solution (1 M LiCl2, 100 mM citrate (pH 4.0), 20% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.31→43.46 Å / Num. obs: 37114 / % possible obs: 98.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 33.28 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.05 / Rrim(I) all: 0.123 / Net I/σ(I): 10 / Num. measured all: 215453 / Scaling rejects: 24
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
2.31-2.45.40.5191853734340.8570.2390.574392.9
8.96-43.465.90.06440056740.9940.0290.07124.698.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.21 Å43.36 Å
Translation3.21 Å43.36 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: generic Fab

Resolution: 2.314→42.974 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 1810 4.88 %
Rwork0.1889 35283 -
obs0.191 37093 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.32 Å2 / Biso mean: 37.0057 Å2 / Biso min: 20.13 Å2
Refinement stepCycle: final / Resolution: 2.314→42.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6581 0 61 320 6962
Biso mean--42.79 37.77 -
Num. residues----869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066800
X-RAY DIFFRACTIONf_angle_d0.8049265
X-RAY DIFFRACTIONf_chiral_restr0.0511044
X-RAY DIFFRACTIONf_plane_restr0.0051192
X-RAY DIFFRACTIONf_dihedral_angle_d3.1654415
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.314-2.37650.33441340.2756250791
2.3765-2.44640.34241410.2541270699
2.4464-2.52540.28771300.2419271099
2.5254-2.61560.27321300.234275499
2.6156-2.72040.29291200.2318273199
2.7204-2.84410.24541260.2263269199
2.8441-2.9940.3111610.2351271199
2.994-3.18160.28731460.2172270299
3.1816-3.42710.24641530.1947271399
3.4271-3.77180.20711420.1685272999
3.7718-4.31720.18141380.1522273698
4.3172-5.43750.15411380.1397279099
5.4375-42.9740.20571510.1666280399
Refinement TLS params.Method: refined / Origin x: 21.264 Å / Origin y: 16.8824 Å / Origin z: 38.0035 Å
111213212223313233
T0.2409 Å20.0032 Å2-0.0172 Å2-0.2098 Å2-0.0014 Å2--0.221 Å2
L0.0057 °20.0125 °2-0.0122 °2-0.1076 °20.2202 °2--0.7424 °2
S0.0305 Å °-0.0018 Å °-0.0087 Å °0.002 Å °0.0166 Å °-0.0438 Å °0.0067 Å °-0.0438 Å °-0.0414 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allC1 - 211
2X-RAY DIFFRACTION1allD1 - 213
3X-RAY DIFFRACTION1allH1 - 214
4X-RAY DIFFRACTION1allL1 - 211
5X-RAY DIFFRACTION1allA1 - 2
6X-RAY DIFFRACTION1allB1 - 2
7X-RAY DIFFRACTION1allS1 - 337
8X-RAY DIFFRACTION1allE1 - 15

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