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- PDB-7q6c: complement C6 FIM1-2 bound to CP010 antibody -

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Basic information

Entry
Database: PDB / ID: 7q6c
Titlecomplement C6 FIM1-2 bound to CP010 antibody
Components
  • CP010 heavy chain
  • CP010 light chain
  • Complement component C6
  • kappa specific nanobody
KeywordsIMMUNE SYSTEM / complement antibody terminal pathway
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / complement activation / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / killing of cells of another organism / in utero embryonic development / innate immune response / extracellular space ...Terminal pathway of complement / membrane attack complex / complement activation / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / killing of cells of another organism / in utero embryonic development / innate immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Complement component C6, KAZAL domain / : / Complement components C8A/B/C6, EGF-like domain / Membrane attack complex component/perforin/complement C9 / Factor I / membrane attack complex / Membrane attack complex component/perforin domain, conserved site / Membrane attack complex/perforin (MACPF) domain signature. / factor I membrane attack complex / membrane-attack complex / perforin ...: / Complement component C6, KAZAL domain / : / Complement components C8A/B/C6, EGF-like domain / Membrane attack complex component/perforin/complement C9 / Factor I / membrane attack complex / Membrane attack complex component/perforin domain, conserved site / Membrane attack complex/perforin (MACPF) domain signature. / factor I membrane attack complex / membrane-attack complex / perforin / MAC/Perforin domain / Membrane attack complex/perforin (MACPF) domain profile. / Membrane attack complex component/perforin (MACPF) domain / Kazal domain / Kazal domain profile. / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / Sushi repeat (SCR repeat) / LDL-receptor class A (LDLRA) domain profile. / 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 / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / EGF-like domain signature 1. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Complement component C6
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29274 Å
AuthorsOlesen, H.G. / Andersen, G.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Innate Immun / Year: 2022
Title: Development, Characterization, and in vivo Validation of a Humanized C6 Monoclonal Antibody that Inhibits the Membrane Attack Complex.
Authors: Gytz Olesen, H. / Michailidou, I. / Zelek, W.M. / Vreijling, J. / Ruizendaal, P. / de Klein, F. / Marquart, J.A. / Kuipers, T.B. / Mei, H. / Zhang, Y. / Ahasan, M. / Johnson, K.K. / Wang, Y. ...Authors: Gytz Olesen, H. / Michailidou, I. / Zelek, W.M. / Vreijling, J. / Ruizendaal, P. / de Klein, F. / Marquart, J.A. / Kuipers, T.B. / Mei, H. / Zhang, Y. / Ahasan, M. / Johnson, K.K. / Wang, Y. / Morgan, B.P. / van Dijk, M. / Fluiter, K. / Andersen, G.R. / Baas, F.
History
DepositionNov 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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 component C6
H: CP010 heavy chain
K: kappa specific nanobody
L: CP010 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2545
Polymers79,1954
Non-polymers591
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.057, 63.527, 128.589
Angle α, β, γ (deg.)90.000, 128.363, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Complement component C6


Mass: 18478.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C6 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P13671

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Antibody , 3 types, 3 molecules HKL

#2: Antibody CP010 heavy chain


Mass: 23490.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody kappa specific nanobody


Mass: 13375.629 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 CP010 light chain


Mass: 23851.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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Non-polymers , 2 types, 129 molecules

#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.4
Details: 112 mM calcium acetate, 56 mM sodium cacodylate pH 6.4, 8.5% PEG8000 and 16% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.29274→100.826 Å / Num. obs: 45105 / % possible obs: 97.2 % / Redundancy: 3.46 % / Biso Wilson estimate: 49.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.075 / Net I/σ(I): 12.08
Reflection shellResolution: 2.29274→2.43 Å / Num. unique obs: 6899 / CC1/2: 0.399

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AND

6and


Resolution: 2.29274→44.45 Å / SU ML: 0.3214 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 25.6852
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2329 1988 4.41 %
Rwork0.2081 43113 -
obs0.2092 45101 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.62 Å2
Refinement stepCycle: LAST / Resolution: 2.29274→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5522 0 4 128 5654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00545643
X-RAY DIFFRACTIONf_angle_d0.87657652
X-RAY DIFFRACTIONf_chiral_restr0.0499846
X-RAY DIFFRACTIONf_plane_restr0.0047991
X-RAY DIFFRACTIONf_dihedral_angle_d16.23253407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29274-2.350.33671330.34772826X-RAY DIFFRACTION89.4
2.35-2.410.32211370.32073031X-RAY DIFFRACTION98.51
2.41-2.480.31291400.29033060X-RAY DIFFRACTION97.77
2.48-2.560.28361430.28283088X-RAY DIFFRACTION98.75
2.56-2.660.3211450.26893082X-RAY DIFFRACTION98.53
2.66-2.760.25711420.25823075X-RAY DIFFRACTION98.68
2.76-2.890.29791410.24983110X-RAY DIFFRACTION98.78
2.89-3.040.24981400.23943066X-RAY DIFFRACTION99.01
3.04-3.230.25421460.24863115X-RAY DIFFRACTION99.15
3.23-3.480.25511450.21823115X-RAY DIFFRACTION98.64
3.48-3.830.23531450.2023058X-RAY DIFFRACTION98.31
3.83-4.380.19481400.16873147X-RAY DIFFRACTION99.1
4.38-5.520.18341440.15433136X-RAY DIFFRACTION98.47
5.52-44.450.20891470.18353204X-RAY DIFFRACTION98.21
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)
13.58748961532-0.0990958533858-1.812418881170.510547184798-0.0632572546485.398658655010.0504719410294-0.2101855287080.0325955499330.127198849951-0.111524378443-0.01787654591510.007239594585360.07825886205590.09591965004580.3988583270180.00748906433036-0.04043775983110.3737398430840.02078125230250.41124416145433.925601494923.179860800232.714362382
21.20617057614-0.442103555043-0.01514537969584.23117442903-0.2408477316614.4605650336-0.03799077816320.119254954237-0.155604212809-0.121585990475-0.1189450391850.5290215260880.332602323036-0.1411044404910.07868271945520.3580832061350.04672948291250.03740731925890.1866570526440.02463539148230.2946615593653.8612203643911.195793626843.1356235774
31.956005415850.547525218038-0.447058737215-1.39440595593-0.3445334911891.34760275426-0.04863558199720.2103750425970.1196221675690.173493441620.187889681418-0.313226337612-0.0802105159394-0.44749540906-5.14090077039E-90.3194113899380.04194424366810.04423737736710.4174630322850.07016814919980.34133939334419.630844056131.843659081116.8972666479
41.31936109898-0.4699162389760.714087456809-0.0244708667441-0.1339511066441.12341716115-0.0437070226230.0716594163570.07182514548520.0942603518817-0.1161050427240.1832381477960.1362932290130.07286820338473.48956250281E-90.449592660433-0.02084926203430.0261865018480.3212013573570.02939870822170.408733826697-6.0210367479423.218207736643.3081608855
54.52745685659-0.6218345320030.4790194806771.86159693704-1.127291736253.492000593930.3117338714370.435576275321-0.558425015368-0.232581292247-0.281394431705-0.6000646645550.7964175543620.5159106777480.1150722776330.602999503670.01329677384120.02944650614860.5842454071720.05006664273570.61238315799340.722691370632.6064839259-13.5172556846
63.43294504974-0.7549808784571.068224084442.54772553329-2.317640152063.71337131352-0.302640473652-0.1637171162590.03228555282730.185472722796-0.0425500334905-0.738209564736-0.08386085217090.7218716963640.2043787492540.4121803532030.002912394250980.003881371670420.5960936356120.06753553819480.58205332431447.101888837830.279786690910.6744132317
70.585736780394-1.030630234731.860996122061.4435540137-1.015151271690.950714301730.1059109614760.2960157504010.1123094872720.161879632574-0.3856960117380.0039119972004-0.03358589363490.04318793650211.76163627668E-100.365884060540.03446134601890.009379809170030.456583952610.02469593504610.356012630702-16.73845443236.321041397219.6362216982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain H and resid 1:119
2X-RAY DIFFRACTION2chain H and resid 120:230
3X-RAY DIFFRACTION3chain L and resid 1:113
4X-RAY DIFFRACTION4chain L and resid 114:230
5X-RAY DIFFRACTION5chain A and resid 772:839
6X-RAY DIFFRACTION6chain A and resid 840:950
7X-RAY DIFFRACTION7chain K

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