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- PDB-8coe: complement C5 in complex with the LCP0195 nanobody -

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Basic information

Entry
Database: PDB / ID: 8coe
Titlecomplement C5 in complex with the LCP0195 nanobody
Components
  • Complement C5 alpha chain
  • Complement C5 beta chain
  • LCP0195
KeywordsIMMUNE SYSTEM / innate immunity / complement / terminal pathway / nanobody / antigen-antibody complex
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production / Peptide ligand-binding receptors / Regulation of Complement cascade / chemotaxis / G alpha (i) signalling events / killing of cells of another organism / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
: / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. ...: / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsAndersen, G.R. / Pedersen, D.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private2018 United States
CitationJournal: Mol.Immunol. / Year: 2023
Title: Characterization of the bispecific VHH antibody gefurulimab (ALXN1720) targeting complement component 5, and designed for low volume subcutaneous administration.
Authors: Jindal, S. / Pedersen, D.V. / Gera, N. / Chandler, J. / Patel, R. / Neill, A. / Cone, J. / Zhang, Y. / Yuan, C.X. / Millman, E.E. / Carlin, D. / Puffer, B. / Sheridan, D. / Andersen, G.R. / Tamburini, P.
History
DepositionFeb 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Complement C5 beta chain
A: Complement C5 alpha chain
B: LCP0195
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,8554
Polymers200,6333
Non-polymers2211
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-52 kcal/mol
Surface area78460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.830, 194.830, 207.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Complement C5 beta chain


Mass: 73361.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: T / Source: (natural) Homo sapiens (human) / References: UniProt: P01031
#2: Protein Complement C5 alpha chain


Mass: 112635.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: T / Source: (natural) Homo sapiens (human) / References: UniProt: P01031
#3: Antibody LCP0195


Mass: 14636.989 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): Expi
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY

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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: 4.91 Å3/Da / Density % sol: 74.94 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.025 M succinic acid pH 7.0 and 3.75% w/v polyethylene glycol 3350.

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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 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 4.2→48.71 Å / Num. obs: 28237 / % possible obs: 99.85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 209.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1286 / Net I/σ(I): 11.94
Reflection shellResolution: 4.2→4.35 Å / Redundancy: 14.2 % / Rmerge(I) obs: 2.421 / Num. unique obs: 2779 / CC1/2: 0.413 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→48.71 Å / SU ML: 0.6131 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 34.7373
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2689 1740 6.17 %
Rwork0.2481 26480 -
obs0.2493 28220 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 242.41 Å2
Refinement stepCycle: LAST / Resolution: 4.2→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13721 0 14 0 13735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007414039
X-RAY DIFFRACTIONf_angle_d1.401619045
X-RAY DIFFRACTIONf_chiral_restr0.11932153
X-RAY DIFFRACTIONf_plane_restr0.00952428
X-RAY DIFFRACTIONf_dihedral_angle_d5.36351890
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.320.40871390.35012206X-RAY DIFFRACTION100
4.32-4.460.3611430.31282197X-RAY DIFFRACTION99.96
4.46-4.620.30551450.29372176X-RAY DIFFRACTION100
4.62-4.810.30331580.27962210X-RAY DIFFRACTION100
4.81-5.030.26071350.27092216X-RAY DIFFRACTION100
5.03-5.290.29531490.26512178X-RAY DIFFRACTION100
5.29-5.620.3061530.27752198X-RAY DIFFRACTION99.96
5.62-6.050.35791170.2982236X-RAY DIFFRACTION100
6.06-6.660.30211540.29682202X-RAY DIFFRACTION100
6.66-7.620.31891450.2972212X-RAY DIFFRACTION100
7.63-9.590.20811500.22842223X-RAY DIFFRACTION100
9.59-48.710.22831520.18952226X-RAY DIFFRACTION99.25
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)
13.267662028891.40345663873-1.109684672761.87997697814-0.8651311047061.59027070874-0.133577202942-0.12111198216-0.4631217846050.04012717372-0.0913602476249-0.392106064824-0.1508955694190.4941186476850.2045219692712.052790875190.241341249045-0.0205932468332.153444036620.2991808194661.73430304134116.6335.752-2.49
26.83533117691-2.7143627819-2.574356069919.328043362622.357323824289.239792070810.650703244291-0.5907003306960.8708468898661.146679275341.00271547912-1.76610182701-1.083626655111.24408272652-1.67784911133.050279874160.08251521888660.07050644710923.71799316339-0.2363828912252.896896993891.39936.58942.158
39.2268116402-1.61276408351-6.557725662836.500240099984.190861647126.018799417760.2202490627510.8964639104321.20626116507-0.864685912289-0.1549118584790.2123340546560.0384293683072-0.155672533972-0.268365080131.739779533810.0457738818125-0.1999002825372.164370331030.5887214522681.758961248188.37838.627-9.092
42.411998357425.31334324305-2.104557742289.81137267006-1.155237930925.47709321775-0.3599440300090.3120328808090.442666394965-1.37589764445-0.5797178947320.656829125981-0.320713386597-0.7776490325030.6030404490982.283325056330.2813746693560.1674603360022.174993060670.3368565925633.2509081716561.50951.8128.687
53.31548321393-1.34248839241-0.3651563284523.531694622380.8410553476063.662999256810.0302256958176-0.373559857239-0.7625298527780.416924337655-0.06261779197321.305643241310.238490646344-0.8970390167910.06959846792151.75099394103-0.1114446410860.2669369647181.462596971430.2417618649122.23778309166.59210.80221.305
62.328046779216.164785959180.9687467289259.133654990092.637997907126.128705438981.05732394338-3.061052170370.4375070866391.83624117743-2.578941257652.519174074650.616137114566-2.471192356021.364736748082.889684601430.02678832114940.7204614115653.66156089027-0.3250614600073.3661186120826.16738.51327.682
78.686660527833.25658498747-0.2751994219889.7777700619-1.565764506417.880956047280.1515673931589.05143683474E-50.3924297474660.346211455751-0.215536865532-0.7419563185780.220766857373-0.3422781419740.2607512609792.33172083935-0.1188179383150.1329068389631.965562445690.2489527527322.00767701162131.75362.845-26.37
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND ( RESID 20:566 OR RESID 613:669 ) )C20 - 566
2X-RAY DIFFRACTION1( CHAIN C AND ( RESID 20:566 OR RESID 613:669 ) )C613 - 669
3X-RAY DIFFRACTION2( CHAIN A AND RESID 680:760 )A680 - 760
4X-RAY DIFFRACTION3( CHAIN A AND RESID 761:820 ) OR ( CHAIN C AND RESID 567:612 )A761 - 820
5X-RAY DIFFRACTION3( CHAIN A AND RESID 761:820 ) OR ( CHAIN C AND RESID 567:612 )C567 - 612
6X-RAY DIFFRACTION4( CHAIN A AND ( RESID 821:931 OR RESID 2000:2000 ) )A821 - 931
7X-RAY DIFFRACTION4( CHAIN A AND ( RESID 821:931 OR RESID 2000:2000 ) )A2000
8X-RAY DIFFRACTION5( CHAIN A AND RESID 932:1511 )A932 - 1511
9X-RAY DIFFRACTION6( CHAIN A AND RESID 1526:1676 )A1526 - 1676
10X-RAY DIFFRACTION7( CHAIN B AND RESID 2:125 )B2 - 125

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