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- PDB-9ggp: Alpha-1-antitrypsin in complex with the Fab fragment of an anti-p... -

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Basic information

Entry
Database: PDB / ID: 9ggp
TitleAlpha-1-antitrypsin in complex with the Fab fragment of an anti-polymer antibody
Components
  • Alpha-1-antitrypsin
  • Fab fragment heavy chain of 2C1 monoclonal antibody
  • Fab fragment light chain of 2C1 monoclonal antibody
KeywordsPROTEIN BINDING / Serpin / Fab fragment / monoclonal antibody / selective binding / epitope
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 / 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
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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsLowen, S.M. / Laffranchi, M. / Lomas, D.A. / Irving, J.A.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V034243/1 United Kingdom
Other private1036784 United States
Citation
Journal: Sci Adv / Year: 2025
Title: High-resolution characterization of ex vivo AAT polymers by solution-state NMR spectroscopy.
Authors: Lowen, S.M. / Waudby, C.A. / Jagger, A.M. / Aldobiyan, I. / Laffranchi, M. / Fra, A. / Christodoulou, J. / Irving, J.A. / Lomas, D.A.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2013
Title: How good are my data and what is the resolution?
Authors: Evans, P.R. / Murshudov, G.N.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: Integration, scaling, space-group assignment and post-refinement.
Authors: Kabsch, W.
History
DepositionAug 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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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 fragment heavy chain of 2C1 monoclonal antibody
L: Fab fragment light chain of 2C1 monoclonal antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,7797
Polymers138,5934
Non-polymers1863
Water10,989610
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10980 Å2
ΔGint-62 kcal/mol
Surface area32670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.946, 75.554, 87.146
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-393-

GLN

21A-703-

HOH

31H-459-

HOH

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Components

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


Mass: 45611.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Reactive centre loop cleaved / Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Plasmid: pQE30 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1-Blue / References: UniProt: P01009
#2: Antibody Fab fragment heavy chain of 2C1 monoclonal antibody


Mass: 23874.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: Spleen / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody Fab fragment light chain of 2C1 monoclonal antibody


Mass: 23494.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: Spleen / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDescription: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 0.2 M Ammonium citrate dibasic 20% w/v Polyethylene glycol 3,350 pH 5.1

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 20, 2021 / Details: KB mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.84→44.36 Å / Num. obs: 81380 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 29.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.051 / Rrim(I) all: 0.184 / Χ2: 0.98 / Net I/σ(I): 10.3 / Num. measured all: 1060725
Reflection shellResolution: 1.84→1.9 Å / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 2.869 / Num. measured all: 106307 / Num. unique obs: 7899 / CC1/2: 0.564 / Rpim(I) all: 0.805 / Rrim(I) all: 2.981 / Χ2: 0.83 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→39.9 Å / SU ML: 0.2391 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2059 2000 2.46 %
Rwork0.1728 79305 -
obs0.1737 81305 99.89 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39 Å2
Refinement stepCycle: LAST / Resolution: 1.84→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6120 0 12 610 6742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726396
X-RAY DIFFRACTIONf_angle_d0.85118716
X-RAY DIFFRACTIONf_chiral_restr0.0573996
X-RAY DIFFRACTIONf_plane_restr0.00671116
X-RAY DIFFRACTIONf_dihedral_angle_d12.94712309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.890.37161400.35125586X-RAY DIFFRACTION99.98
1.89-1.940.35691430.28885623X-RAY DIFFRACTION99.93
1.94-1.990.26941400.24445576X-RAY DIFFRACTION99.97
1.99-2.060.27031420.22425608X-RAY DIFFRACTION99.97
2.06-2.130.24081410.20985617X-RAY DIFFRACTION99.97
2.13-2.220.2221420.19075619X-RAY DIFFRACTION99.98
2.22-2.320.26221420.1835624X-RAY DIFFRACTION99.97
2.32-2.440.2371420.17745646X-RAY DIFFRACTION100
2.44-2.590.20641420.18075633X-RAY DIFFRACTION100
2.59-2.790.26151430.18565680X-RAY DIFFRACTION99.98
2.79-3.070.21311440.17665693X-RAY DIFFRACTION100
3.07-3.520.19011440.16185705X-RAY DIFFRACTION100
3.52-4.430.15621460.13565770X-RAY DIFFRACTION99.88
4.43-39.90.1641490.14895925X-RAY DIFFRACTION98.93

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