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- PDB-8acf: Structure of the argX-117 in complex with a complement C2 fragmen... -

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Basic information

Entry
Database: PDB / ID: 8acf
TitleStructure of the argX-117 in complex with a complement C2 fragment at low pH
Components
  • Complement C2b fragment
  • Heavy chain of mAb ARGX-117 Fab
  • Light chain of mAb ARGX-117 Fab
  • Nanobody specific for the kappa-light chain
KeywordsIMMUNE SYSTEM / Innate immune system / complement / antibody
Function / homology
Function and homology information


classical-complement-pathway C3/C5 convertase / response to thyroid hormone / positive regulation of apoptotic cell clearance / 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 / response to thyroid hormone / positive regulation of apoptotic cell clearance / 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 / innate immune response / serine-type endopeptidase activity / 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) / von Willebrand factor type A domain / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / VWFA domain profile. / von Willebrand factor (vWF) type A domain / 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) / von Willebrand factor type A domain / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / VWFA domain profile. / von Willebrand factor (vWF) type A domain / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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: 1.8 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 1.1Nov 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
A: Complement C2b fragment
H: Heavy chain of mAb ARGX-117 Fab
K: Nanobody specific for the kappa-light chain
L: Light chain of mAb ARGX-117 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,94010
Polymers82,6044
Non-polymers1,3366
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-41 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.830, 89.140, 146.490
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 Heavy chain of mAb ARGX-117 Fab


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 the kappa-light chain


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 Light chain of mAb ARGX-117 Fab


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-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 333 molecules

#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 50% MPD, 100 mM Hepes pH 5.5-6.0

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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: 1.8→44.57 Å / Num. obs: 87785 / % possible obs: 99.97 % / Redundancy: 13.4 % / Biso Wilson estimate: 38.51 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.2
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 13.6 % / Rmerge(I) obs: 2.457 / Num. unique obs: 8651 / CC1/2: 0.472 / % possible all: 99.98

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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: 1.8→44.57 Å / SU ML: 0.2567 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5515
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1985 4399 5.01 %
Rwork0.1777 83378 -
obs0.1788 87777 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.99 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5311 0 83 328 5722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01375515
X-RAY DIFFRACTIONf_angle_d1.11187486
X-RAY DIFFRACTIONf_chiral_restr0.075819
X-RAY DIFFRACTIONf_plane_restr0.0099967
X-RAY DIFFRACTIONf_dihedral_angle_d12.81612005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.40691460.40362735X-RAY DIFFRACTION99.93
1.82-1.840.33881470.36452748X-RAY DIFFRACTION100
1.84-1.860.35971400.32382735X-RAY DIFFRACTION100
1.86-1.890.30131540.30162741X-RAY DIFFRACTION100
1.89-1.910.29891400.27782756X-RAY DIFFRACTION100
1.91-1.940.25131500.24562772X-RAY DIFFRACTION99.97
1.94-1.970.27551310.21992732X-RAY DIFFRACTION100
1.97-20.23681530.20772771X-RAY DIFFRACTION100
2-2.030.21571410.19672724X-RAY DIFFRACTION100
2.03-2.060.21121490.1952747X-RAY DIFFRACTION100
2.06-2.10.24651340.20222758X-RAY DIFFRACTION100
2.1-2.130.21461520.19982758X-RAY DIFFRACTION100
2.13-2.180.26891400.19382776X-RAY DIFFRACTION100
2.18-2.220.22691380.19572764X-RAY DIFFRACTION100
2.22-2.270.21041460.19572736X-RAY DIFFRACTION100
2.27-2.320.20271510.17972785X-RAY DIFFRACTION100
2.32-2.380.1981420.18072756X-RAY DIFFRACTION100
2.38-2.440.22491540.18292757X-RAY DIFFRACTION100
2.44-2.510.23691320.18162780X-RAY DIFFRACTION100
2.51-2.60.21541510.17982782X-RAY DIFFRACTION100
2.6-2.690.20071530.18432777X-RAY DIFFRACTION100
2.69-2.80.19811470.18442777X-RAY DIFFRACTION100
2.8-2.920.23541240.19552798X-RAY DIFFRACTION100
2.92-3.080.18941530.19672799X-RAY DIFFRACTION100
3.08-3.270.20251590.1782802X-RAY DIFFRACTION100
3.27-3.520.21291540.16982783X-RAY DIFFRACTION100
3.52-3.880.17541360.15732846X-RAY DIFFRACTION100
3.88-4.440.16041520.13772839X-RAY DIFFRACTION100
4.44-5.590.12981590.13872862X-RAY DIFFRACTION100
5.59-44.570.22741710.1952982X-RAY DIFFRACTION99.65
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)
13.14745427163-0.820298786599-0.3291630286383.801444357490.4718675794044.87713448453-0.000447029851955-0.406919594285-0.2835473765720.7055464508460.0691781728088-0.1190920130170.552363074390.317317776459-0.05741830399660.50267927407-0.0151223813249-0.09593274393090.329750026988-0.03601821549550.37204262877539.965501141125.679915926355.5540909864
21.348950362510.4817813434561.188143893280.9730820922360.7745460756371.876550721960.1429706217210.00510885999184-0.1129042518730.1057672636450.000303496870543-0.02660309524090.16737160457-0.0281427067623-0.1436593148280.2967997664110.0120220912511-0.01951386479920.2784050147520.04123634022110.32385376823121.03379074585.8945356587723.5109038191
31.262990411080.4326947186860.7888483291090.7704908684830.3958197266890.853749587962-0.02029309847090.04038248952930.0772050641667-0.002141602173130.04278418555610.112646370607-0.0202957338304-0.0292512266288-0.009047625243580.2763351408270.008738436031620.006397792783870.2811340502890.0289281687430.29574733864614.865447352320.158997164214.5718172545
42.32169069065-0.1239172039020.2120536107653.81083180394-1.879993205354.44188315450.0394550384543-0.0004493431473280.1503874232370.0833163700483-0.03788226802990.115431284518-0.193870091938-0.0693615137313-0.02136682872530.30301625166-0.0258983631242-0.01247719585740.3134764666670.0201924252810.3204667700684.7589605258838.5175536948-2.9740447567
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 - 2151 - 215
44chain KKC3 - 1271 - 125

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