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- PDB-8aci: Structure of ARG-117 Fab in complex with a fragment of complement... -

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Basic information

Entry
Database: PDB / ID: 8aci
TitleStructure of ARG-117 Fab in complex with a fragment of complement C2, neutral pH
Components
  • (ARGX-117 Fab ...) x 2
  • Complement C2b fragment
  • nanobody specific for kappa light chain of Fab
KeywordsIMMUNE SYSTEM / innate immune system / antibody / complement
Function / homology
Function and homology information


classical-complement-pathway C3/C5 convertase / positive regulation of apoptotic cell clearance / response to thyroid hormone / Activation of C3 and C5 / complement activation / Initial triggering of complement / complement activation, classical pathway / response to nutrient / Regulation of Complement cascade / response to bacterium ...classical-complement-pathway C3/C5 convertase / positive regulation of apoptotic cell clearance / response to thyroid hormone / Activation of C3 and C5 / complement activation / Initial triggering of complement / complement activation, classical pathway / response to nutrient / Regulation of Complement cascade / response to bacterium / response to lipopolysaccharide / serine-type endopeptidase activity / innate immune response / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding
Similarity search - Function
Complement B/C2 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A ...Complement B/C2 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsOlesen, H.G. / Andersen, G.R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Other privateNot applicable Belgium
CitationJournal: To be published
Title: Structure-function analysis of ARGX-117, a calcium- and pH-dependent clinical phase complement C2 blocking antibody
Authors: Olesen, H.G. / Andersen, G.R.
History
DepositionJul 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: Complement C2b fragment
H: ARGX-117 Fab heavy chain
K: nanobody specific for kappa light chain of Fab
L: ARGX-117 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1658
Polymers82,6044
Non-polymers5614
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-50 kcal/mol
Surface area30600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.590, 88.760, 144.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Antibody , 3 types, 3 molecules HKL

#2: Antibody ARGX-117 Fab heavy chain


Mass: 23450.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody nanobody specific for kappa light chain of Fab


Mass: 14204.509 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#4: Antibody ARGX-117 Fab light chain


Mass: 23957.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Complement C2b fragment


Mass: 20991.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P06681
#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 288 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: The reservoirs contained 50-70% MPD, 100 mM Hepes pH 7.0-7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→44.16 Å / Num. obs: 79409 / % possible obs: 99.98 % / Redundancy: 52.1 % / Biso Wilson estimate: 42.17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1386 / Net I/σ(I): 19.68
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 44.1 % / Rmerge(I) obs: 4.45 / Num. unique obs: 7809 / CC1/2: 0.562 / % possible all: 99.99

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ANI

6ani


Resolution: 1.85→44.16 Å / SU ML: 0.2502 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.1844
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1994 3977 5.01 %
Rwork0.1871 75427 -
obs0.1877 79404 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.13 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5330 0 34 285 5649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01055485
X-RAY DIFFRACTIONf_angle_d0.97527446
X-RAY DIFFRACTIONf_chiral_restr0.0644812
X-RAY DIFFRACTIONf_plane_restr0.0081970
X-RAY DIFFRACTIONf_dihedral_angle_d13.1581987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.44681380.41382631X-RAY DIFFRACTION99.96
1.87-1.90.36051410.36592671X-RAY DIFFRACTION100
1.9-1.920.32021400.30082658X-RAY DIFFRACTION100
1.92-1.950.31241400.27042654X-RAY DIFFRACTION100
1.95-1.980.26831410.24482670X-RAY DIFFRACTION100
1.98-20.2561400.2252658X-RAY DIFFRACTION99.96
2-2.040.23151530.21922663X-RAY DIFFRACTION100
2.04-2.070.23591280.21512699X-RAY DIFFRACTION100
2.07-2.110.23571360.21362665X-RAY DIFFRACTION100
2.11-2.140.251460.21422643X-RAY DIFFRACTION100
2.14-2.180.22791300.20542671X-RAY DIFFRACTION100
2.18-2.230.20571320.21132690X-RAY DIFFRACTION100
2.23-2.280.20651580.20612669X-RAY DIFFRACTION100
2.28-2.330.21361260.20252683X-RAY DIFFRACTION100
2.33-2.390.22341470.19912662X-RAY DIFFRACTION100
2.39-2.450.23041360.19132695X-RAY DIFFRACTION100
2.45-2.530.23851380.19422694X-RAY DIFFRACTION100
2.53-2.610.25031470.18772683X-RAY DIFFRACTION100
2.61-2.70.21081470.2072666X-RAY DIFFRACTION100
2.7-2.810.22451390.2032690X-RAY DIFFRACTION100
2.81-2.940.23231190.21552745X-RAY DIFFRACTION100
2.94-3.090.20751550.20732685X-RAY DIFFRACTION100
3.09-3.280.19941550.18682707X-RAY DIFFRACTION99.97
3.28-3.540.20051420.17962710X-RAY DIFFRACTION100
3.54-3.890.17421430.16782728X-RAY DIFFRACTION100
3.89-4.460.14451400.14952763X-RAY DIFFRACTION100
4.46-5.610.14181560.14682772X-RAY DIFFRACTION100
5.61-44.160.22951640.20112902X-RAY DIFFRACTION99.93
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)
12.99746142975-0.7964797235480.6358174165464.543717604550.2040237624413.97447435895-0.146954682194-0.499393365856-0.3363669569881.037839899890.117928418531-0.08705535369860.5703198684750.230481285721-0.01461528987920.6458830362580.00895937199238-0.08481939886540.419397984327-0.00666090655730.39550673674439.984203359825.033687075855.4873403334
21.70970796610.6817909189621.438152322021.346731697811.043650352592.182634438840.160272607771-0.00112525831833-0.1146871684810.179386983935-0.00527130124395-0.05602113535690.14126407363-0.0375456238801-0.1506975800810.3571596224550.0209638859869-0.01391929110590.3506416745740.04796386530810.38054938032521.04996847575.3934963214623.1026143942
32.130153318130.6991817324661.232608980890.78903449810.4703961599861.266005292570.007212756606630.0501500221430.08715188668350.06161729295780.03915291433350.104306465438-0.0192391152562-0.0259400881405-0.0379709279990.3163380425930.01750547861950.01044348870460.300631339150.04514567918880.33233887532214.480779280319.551570622914.2216697325
42.60978381542-0.6548951947040.3570438443213.94505893605-1.892834839443.709864231830.04601923379350.04500341802460.1540796292890.0861041526764-0.05956169027530.114015723905-0.166623742608-0.04158842806720.01529515502650.331041135406-0.037511593775-0.02260590773280.3447881234840.02012352734310.3487162422174.6282178117838.5595736116-2.56898113281
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA51 - 2091 - 138
22chain HHB1 - 2191 - 219
33chain LLD1 - 2181 - 218
44chain KKC3 - 1271 - 125

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