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- PDB-7qiv: Structure of human C3b in complex with the EWE nanobody -

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Basic information

Entry
Database: PDB / ID: 7qiv
TitleStructure of human C3b in complex with the EWE nanobody
Components
  • Complement C3 beta chain
  • Complement C3b alpha' chain
  • Nanobody EWE
KeywordsIMMUNE SYSTEM / complement / alternative pathway / antibody / nanobody / protein engineering
Function / homology
Function and homology information


C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment ...C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of type IIa hypersensitivity / complement receptor mediated signaling pathway / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement activation / complement activation, alternative pathway / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / B cell activation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / fatty acid metabolic process / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of protein phosphorylation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of angiogenesis / azurophil granule lumen / secretory granule lumen / blood microparticle / G alpha (i) signalling events / immune response / receptor ligand activity / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / inflammatory response / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain ...Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPedersen, H. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
Citation
Journal: Front Immunol / Year: 2022
Title: Structure-Guided Engineering of a Complement Component C3-Binding Nanobody Improves Specificity and Adds Cofactor Activity.
Authors: Pedersen, H. / Jensen, R.K. / Hansen, A.G. / Petersen, S.V. / Thiel, S. / Laursen, N.S. / Andersen, G.R.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionDec 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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 C3 beta chain
B: Complement C3b alpha' chain
C: Nanobody EWE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,7005
Polymers190,2583
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-46 kcal/mol
Surface area71410 Å2
Unit cell
Length a, b, c (Å)255.310, 64.880, 144.720
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

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Components

#1: Protein Complement C3 beta chain


Mass: 71393.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#2: Protein Complement C3b alpha' chain


Mass: 104074.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#3: Antibody Nanobody EWE


Mass: 14790.335 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: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / 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
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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 112 mM Sodium Citrate pH 8, 28 mM Sodium Citrate pH 6.0, 12.25 % (w/v) PEG 2000 MME, 70 mM Imidazole pH 7, 60 mM Ammonium acetate, 70 mM TRIS pH 8.5, and 13.5 % (v/v) 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.8→48.31 Å / Num. obs: 60284 / % possible obs: 98.61 % / Redundancy: 13.5 % / Biso Wilson estimate: 83.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.2238 / Rrim(I) all: 0.2326 / Net I/σ(I): 11.74
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 14.1 % / Rmerge(I) obs: 2.725 / Mean I/σ(I) obs: 0.73 / Num. unique obs: 5282 / CC1/2: 0.495 / % possible all: 89.1

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Processing

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

6ehg


Resolution: 2.8→48.31 Å / SU ML: 0.5143 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 1471 2.47 %
Rwork0.2354 58009 -
obs0.2364 59480 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.13 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13127 0 28 0 13155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004113420
X-RAY DIFFRACTIONf_angle_d0.730418196
X-RAY DIFFRACTIONf_chiral_restr0.05192060
X-RAY DIFFRACTIONf_plane_restr0.00632351
X-RAY DIFFRACTIONf_dihedral_angle_d16.86245020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.890.39811220.35834670X-RAY DIFFRACTION88.76
2.89-2.990.37571300.35515113X-RAY DIFFRACTION97.09
2.99-3.110.41891330.36385253X-RAY DIFFRACTION99.63
3.11-3.260.35281320.31715274X-RAY DIFFRACTION99.93
3.26-3.430.34791340.27615281X-RAY DIFFRACTION99.89
3.43-3.640.29711340.26015286X-RAY DIFFRACTION99.93
3.64-3.920.26561340.26195311X-RAY DIFFRACTION99.98
3.92-4.320.29331360.21345367X-RAY DIFFRACTION100
4.32-4.940.21721350.18295371X-RAY DIFFRACTION99.98
4.94-6.220.24531370.20325416X-RAY DIFFRACTION100
6.22-48.310.25031440.21555667X-RAY DIFFRACTION99.69
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)
11.64205369420.132112949634-0.4078780382871.98756637078-0.9082554792654.467555921170.177855293978-0.5701555150010.302791801437-0.113613863431-0.189277033981-0.172465679374-0.7956383009660.904667998457-0.1253208906030.611794875529-0.06268999569140.02316775970460.495328261416-0.1503517227110.775303456893-11.735317438950.6274644685-31.7264494773
20.9271268580990.117765646177-0.842275731297-0.6595138501490.7385144262363.110260392850.09999596662940.4436384505110.200108277811-0.205514629020.1064706752940.281655384179-0.258461411276-0.753837379489-0.02126929010790.801829012420.110709565648-0.1107628598160.698907369475-0.04092082154410.687316930469-23.840208232442.9640935242-62.7119453781
32.95666884476-0.1208619563351.467954932972.717773676990.6145314043945.15083927436-0.356285963289-0.755200667584-0.04081288644150.404240122560.252146221632-0.0498919114333-1.09456180050.564794692505-0.1866680988420.5575066602250.06234659890620.04258462932721.02924303729-0.237113810460.731650340566-20.737773750547.2711390323-1.48749537148
43.118702596290.224626743813-0.07153434980121.16666878963-0.06825645406181.883907815930.120258183019-1.086921989720.1713705960110.0635821480129-0.1296143797580.0836174197618-0.05976502278890.07486825247720.04390888809410.4941767653990.0431073434010.06607962716540.993707152687-0.1033080822780.636808546559-29.359400002840.4351074595-4.95663096925
53.959701583880.7951923421610.2048436255143.86925483641.537379772165.35688449647-0.0448070428971-0.729702953278-0.4125323993570.235052279268-0.172683622543-0.208426225870.207876959995-0.1487044342230.2819079984750.5545958235120.05474163640080.1226701114590.9303905328570.2744782176550.749338824014-40.676786365521.9872201054-7.37462936387
64.99616419548-0.040787595330.9684687286533.87126812996-0.2829263390518.80404930845-0.106220650173-0.0532920209012-0.3364292972860.0692359893011-0.23390806197-0.225029393948-0.3515440216430.2175171663270.3033198996250.6464284148770.05969498951440.0781429201240.71213181670.09578524934610.711066348914-54.860594498453.582724889920.8189217559
72.62042929105-0.4507578607960.7646175680532.610105218350.7080015596922.77185399098-0.182088685478-0.9201567569150.3416257885580.536125696329-0.340991548357-0.13997136975-0.64254958995-1.158991123310.2790375880480.6039550282480.04718915977420.2521512201311.65324530996-0.2991710348091.02866981632-49.650548576343.28556232571.47684108233
82.194154556030.761942499068-2.119301838912.599774791470.6550360441254.35263029611-0.286840526334-0.2056307252320.351026501360.2045276538860.1437597995740.382191708103-1.74194635353-0.8403818392380.1727612977431.628263054490.566418543551-0.3135240018141.386195234080.03038120555240.780907962023-54.427690363268.2444296001-89.6995140793
91.59571019506-0.2125020959370.5255988260371.38572290384-1.68464437723.192216968480.2093812543880.3343476282210.5255853604140.2896417499980.3202284425640.263918641175-1.34454407217-0.713342855777-0.4896595254411.379327346520.391173894360.01170972929011.498359716980.04277711236761.07948194929-54.896187980462.7962144173-36.870671539
102.404020696650.62561433427-0.05136189549322.398744022580.9334365471712.778150935410.06140738450340.4709930286760.88937630566-0.4925324332380.2899804709660.221950345563-0.722263184943-0.653251180829-0.3242758666771.154045773050.172789782541-0.1051420528520.7654813557850.2842841820880.879645192407-21.614372028859.652543674-76.3929926277
112.35077956353-0.136183619952-0.536929444341.95396682814-0.9853777480133.679004576310.3562791373530.1818094982290.41709962468-0.3976916400920.1082082367270.494274264701-0.470162912013-0.836153796264-0.4543529481980.6743305694160.21932785074-0.02914142554550.510905415425-0.01468604399450.737960609978-32.535496188154.0256071351-41.4937034799
121.84954358506-0.277655779385-0.3942132712553.788885277612.18769714063.01986075458-0.249654487197-0.299972955518-0.405089643228-0.189625021712-0.1443551993740.2746395680590.102445942521-0.1342867263250.3514923234950.5825918416020.0188346322070.1461705070690.3600162148270.02223087631530.821625644695-29.520826617719.7106138411-33.944241611
132.61996331888-0.0184702572168-0.5837522450583.01791245148-1.287103389483.60684774189-0.1281404460870.53135721026-0.254523546635-0.0551160634647-0.4727981994080.266667920290.2439153200260.08846916520330.6083167304490.7169468261830.01190858471970.02631095547680.486457350074-0.1021467308650.687937510382-14.705524660722.7953079556-66.1247992403
143.76703418206-0.792844453435-0.1073964676782.36070094165-0.8951452232473.963312803690.05794092910840.571125172246-0.0372782099191-0.401972745960.143812226450.08567468727450.01997408651830.893891433123-0.2475731062210.8896287373930.092382974734-0.06936423534980.78928240668-0.06019710078420.563320749038-7.0005034480242.3702551179-74.9834664649
152.151805199710.9247682847880.5237980961422.86776263938-0.2110156999472.13891441601-0.648179906748-0.4336139070210.948374421680.2137444260720.50353225892-0.528698532799-0.2109732016910.5036921357340.1342952105950.7536159762130.0602889903517-0.1479159401851.85547968901-0.4245191902361.200594521142.8352246151948.21121192886.14845275988
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDAuth asym-IDAuth seq-IDLabel asym-IDLabel seq-IDSelection details
11A557 - 599
21B557 - 599
31A768 - 828
41B768 - 828
52A600 - 665A573 - 638
62B600 - 665B573 - 638
73A753 - 767A1 - 15
83B753 - 767B1 - 15
94A829 - 933A77 - 181
104B829 - 933B77 - 181
115A1353 - 1496A601 - 736
125B1353 - 1496B601 - 736
136A1518 - 1663A758 - 903
146B1518 - 1663B758 - 903
157A1497 - 1517A737 - 757
167B1497 - 1517B737 - 757
178A986 - 1290A234 - 538
188B986 - 1290B234 - 538
199A934 - 985
209B934 - 985
219A1291 - 1352
229B1291 - 1352
2310A23 - 127A1 - 100
2410B23 - 127B1 - 100
2511A128 - 228A101 - 201
2611B128 - 228B101 - 201
2712A229 - 351A202 - 324
2812B229 - 351B202 - 324
2913A352 - 452A325 - 425
3013B352 - 452B325 - 425
3114A453 - 556A426 - 529
3214B453 - 556B426 - 529
3315C5 - 128C1 - 124chain C

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