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- PDB-6i3z: Fab fragment of an antibody selective for wild-type alpha-1-antit... -

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Basic information

Entry
Database: PDB / ID: 6i3z
TitleFab fragment of an antibody selective for wild-type alpha-1-antitrypsin in complex with its antigen
Components
  • (Alpha-1-antitrypsinAlpha-1 antitrypsin) x 2
  • Fab 2H2 heavy chain
  • Fab 2H2 light chain
KeywordsPROTEIN BINDING / Antibody fragment / Antitrypsin binding / Diagnostic / Monoclonal / selective / wild-type / Glu342 / E342
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation ...Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / protease binding / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsLaffranchi, M. / Elliston, E.L.K. / Miranda, E. / Perez, J. / Jagger, A.M. / Fra, A. / Lomas, D.A. / Irving, J.A.
Funding support United Kingdom, Italy, United States, 4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N024842/1 United Kingdom
Other privateFondazione Cariplo 2013-0967 Italy
Other privateAlpha-1 Foundation project grant to James Irving United States
Other governmentUCLH/NIHR Biomedical Research Centre United Kingdom
CitationJournal: JCI Insight / Year: 2020
Title: Intrahepatic heteropolymerization of M and Z alpha-1-antitrypsin.
Authors: Laffranchi, M. / Elliston, E.L. / Miranda, E. / Perez, J. / Ronzoni, R. / Jagger, A.M. / Heyer-Chauhan, N. / Brantly, M.L. / Fra, A. / Lomas, D.A. / Irving, J.A.
History
DepositionNov 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1-antitrypsin
B: Alpha-1-antitrypsin
H: Fab 2H2 heavy chain
L: Fab 2H2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8867
Polymers91,7444
Non-polymers1423
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-92 kcal/mol
Surface area32090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.538, 51.930, 105.869
Angle α, β, γ (deg.)84.310, 81.470, 78.950
Int Tables number1
Space group name H-MP1

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Components

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Antibody , 2 types, 2 molecules HL

#3: Antibody Fab 2H2 heavy chain


Mass: 23129.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Organ: Spleen / Variant: BALB/c
#4: Antibody Fab 2H2 light chain


Mass: 23914.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Organ: Spleen / Variant: BALB/c

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Alpha-1-antitrypsin / Alpha-1 antitrypsin / Alpha-1 protease inhibitor / Alpha-1-antiproteinase / Serpin A1


Mass: 40018.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): XL1-Blue / References: UniProt: P01009
#2: Protein/peptide Alpha-1-antitrypsin / Alpha-1 antitrypsin / Alpha-1 protease inhibitor / Alpha-1-antiproteinase / Serpin A1


Mass: 4681.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): XL-1 Blue / References: UniProt: P01009

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Non-polymers , 3 types, 35 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.12 % / Description: Plate
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.1 M ammonium sulfate, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2018 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 3.1→37.82 Å / Num. obs: 13004 / % possible obs: 92.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 51.51 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.127 / Rrim(I) all: 0.226 / Net I/σ(I): 3.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.1-3.183.40.5979890.6590.3820.71195.8
13.86-37.823.60.1171520.9860.070.13795.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.82 Å50.84 Å
Translation4.82 Å50.84 Å

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Processing

Software
NameVersionClassification
XDSJan 26, 2018data reduction
Aimless0.6.2data scaling
PHASER2.8.1phasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IO1,1EZX

6io1

1ezx


Resolution: 3.1→37.82 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 30.66
RfactorNum. reflection% reflection
Rfree0.3073 670 5.28 %
Rwork0.2608 --
obs0.2632 12693 90.43 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 118.54 Å2 / Biso mean: 39.7541 Å2 / Biso min: 2.68 Å2
Refinement stepCycle: final / Resolution: 3.1→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5475 0 7 32 5514
Biso mean--80.03 24.01 -
Num. residues----759
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.33920.33161510.3209251095
3.3392-3.6750.36421140.3213194477
3.675-4.20620.38131420.3218242892
4.2062-5.29710.25191360.1989256996
5.2971-37.820.25451270.2228257297

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