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- PDB-8q6r: Structure of complement FP in complex with the TPP-3077 VHH -

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Basic information

Entry
Database: PDB / ID: 8q6r
TitleStructure of complement FP in complex with the TPP-3077 VHH
Components
  • (Properdin) x 2
  • The properdin specific VHH TPP-3077
KeywordsIMMUNE SYSTEM / complement / antibody / properdin / alternative pathway
Function / homology
Function and homology information


cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Alternative complement activation / Activation of C3 and C5 / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / positive regulation of immune response ...cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Alternative complement activation / Activation of C3 and C5 / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / positive regulation of immune response / specific granule lumen / tertiary granule lumen / defense response to bacterium / immune response / endoplasmic reticulum lumen / Neutrophil degranulation / extracellular space / extracellular region
Similarity search - Function
: / : / Thrombospondin type 1 repeat / CFP-like, C-terminal thrombospondin type 1 domain / : / 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
Similarity search - Domain/homology
GLYCOCHOLIC ACID / alpha-D-mannopyranose / Properdin
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAndersen, G.R. / Pedersen, D.V.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Mabs / Year: 2024
Title: Characterization of the bispecific VHH antibody tarperprumig (ALXN1820) specific for properdin and designed for low-volume administration.
Authors: Tamburini, P. / Pedersen, D.V. / Devore, D. / Cone, J. / Patel, R. / Hunter, T. / Sun, F. / Andersen, G.R. / Hunter, J.
History
DepositionAug 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 13, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: The properdin specific VHH TPP-3077
B: The properdin specific VHH TPP-3077
C: Properdin
D: Properdin
E: Properdin
F: Properdin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,27334
Polymers100,7886
Non-polymers6,48528
Water6,557364
1
A: The properdin specific VHH TPP-3077
C: Properdin
D: Properdin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,20418
Polymers50,3943
Non-polymers3,81015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: The properdin specific VHH TPP-3077
E: Properdin
F: Properdin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,06916
Polymers50,3943
Non-polymers2,67513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.210, 63.701, 119.249
Angle α, β, γ (deg.)90.000, 103.752, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 and (name N or name...
d_2ens_1(chain "B" and ((resid 1 and (name N or name...
d_1ens_2(chain "C" and ((resid 28 and (name N or name...
d_2ens_2(chain "E" and ((resid 28 and (name N or name...
d_1ens_3(chain "D" and ((resid 255 and (name N or name...
d_2ens_3(chain "F" and ((resid 255 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLUGLUSERSERAA1 - 1191 - 119
d_21ens_1GLUGLUSERSERBB1 - 1191 - 119
d_11ens_2ASPASPPROPROCC28 - 1341 - 107
d_12ens_2MANMANMANMANCN201
d_13ens_2MANMANMANMANCO202
d_14ens_2FUCFUCFUCFUCGG1
d_15ens_2BGCBGCBGCBGCGG2
d_21ens_2ASPASPPROPROEE28 - 1341 - 107
d_22ens_2MANMANMANMANEX201
d_23ens_2MANMANMANMANEY202
d_24ens_2FUCFUCFUCFUCJJ1
d_25ens_2BGCBGCBGCBGCJJ2
d_11ens_3GLYGLYGLUGLUDD255 - 4651 - 211
d_12ens_3MANMANMANMANDP501
d_13ens_3FUCFUCFUCFUCHH1
d_14ens_3BGCBGCBGCBGCHH2
d_15ens_3MANMANMANMANDQ502
d_16ens_3MANMANMANMANDR503
d_17ens_3MANMANMANMANDS504
d_18ens_3NAGNAGNAGNAGII1
d_19ens_3MANMANMANMANDT505
d_110ens_3MANMANMANMANDU506
d_111ens_3MANMANMANMANDV507
d_21ens_3GLYGLYGLUGLUFF255 - 4651 - 211
d_22ens_3MANMANMANMANFZ501
d_23ens_3FUCFUCFUCFUCKK1
d_24ens_3BGCBGCBGCBGCKK2
d_25ens_3MANMANMANMANFAA502
d_26ens_3MANMANMANMANFBA503
d_27ens_3MANMANMANMANFCA504
d_28ens_3NAGNAGNAGNAGFDA505
d_29ens_3MANMANMANMANFFA507
d_210ens_3MANMANMANMANFGA508
d_211ens_3MANMANMANMANFHA509

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.997878886671, 0.0644448375723, 0.00919730650041), (-0.0633725187751, 0.99399928255, -0.0891591282753), (-0.0148879616026, 0.088387155181, 0.995974929101)-3.07859885098, 34.9772527312, 4.68952597711
2given(0.999714624262, 0.013208877372, -0.0199046626646), (-0.0136646616619, 0.999643474983, -0.0229390484994), (0.0195945670758, 0.0232044927323, 0.999538695828)-1.19151415681, 32.5561978758, 5.01775881399
3given(0.999833438385, -0.0181536515525, 0.00188160110169), (0.0182042210589, 0.999331054058, -0.0317183027617), (-0.00130453939609, 0.0317472727924, 0.99949507695)-1.91703596044, 31.3840819432, 5.40472537855

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Components

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Protein , 2 types, 4 molecules CEDF

#2: Protein Properdin


Mass: 11831.308 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P27918
#3: Protein Properdin


Mass: 24758.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P27918

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Antibody , 1 types, 2 molecules AB

#1: Antibody The properdin specific VHH TPP-3077


Mass: 13804.423 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human) / Strain (production host): HEP293Expi

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Sugars , 4 types, 26 molecules

#4: Polysaccharide
beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3LFucpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1221m-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Fucp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: 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.: 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

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Non-polymers , 2 types, 366 molecules

#6: Chemical ChemComp-GCH / GLYCOCHOLIC ACID / N-CHOLYLGLYCINE


Mass: 465.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H43NO6 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 95% Morpheus Screen III, condition G1

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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: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→47.86 Å / Num. obs: 89619 / % possible obs: 98.07 % / Redundancy: 6.8 % / Biso Wilson estimate: 32.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1127 / Net I/σ(I): 9.05
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.137 / Num. unique obs: 8051 / CC1/2: 0.751 / % possible all: 88.69

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.86 Å / SU ML: 0.2861 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.2519
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.238 1899 2.12 %
Rwork0.2024 87603 -
obs0.2031 89502 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.96 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6716 0 412 364 7492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01727315
X-RAY DIFFRACTIONf_angle_d1.70089948
X-RAY DIFFRACTIONf_chiral_restr0.12551112
X-RAY DIFFRACTIONf_plane_restr0.01641245
X-RAY DIFFRACTIONf_dihedral_angle_d33.89091215
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.641120366466
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS0.75879398284
ens_3d_2DDX-RAY DIFFRACTIONTorsion NCS6.6179354816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.36841210.35145552X-RAY DIFFRACTION87.38
1.95-20.36261310.31576043X-RAY DIFFRACTION95.4
2-2.060.32691350.2826284X-RAY DIFFRACTION99.07
2.06-2.130.28681370.25416278X-RAY DIFFRACTION99.06
2.13-2.20.28211370.24376312X-RAY DIFFRACTION99.18
2.2-2.290.26651360.23356284X-RAY DIFFRACTION99.4
2.29-2.390.29891370.24256289X-RAY DIFFRACTION99.06
2.39-2.520.25931370.21286301X-RAY DIFFRACTION99.32
2.52-2.680.26131360.21566362X-RAY DIFFRACTION99.24
2.68-2.880.21721380.21026335X-RAY DIFFRACTION99.46
2.88-3.170.26251380.2146355X-RAY DIFFRACTION99.28
3.17-3.630.21831370.1966344X-RAY DIFFRACTION99.14
3.63-4.580.20131380.15866379X-RAY DIFFRACTION99.36
4.58-47.860.20391410.17246485X-RAY DIFFRACTION98.81
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)
13.36437856656-2.017164260271.267604292994.52446496952-1.101915313262.09522692495-0.09237794127650.000641814602423-0.0006410882772310.07672934555310.04248067175950.0874397167822-0.0874941491504-0.0333411322250.04275125321630.226857521827-0.0229037135319-0.001110477358570.185795408125-0.01426698084680.2790469600820.309088912613.144914490340.3338958614
22.74109904869-0.7629385789811.189279690994.52196187556-1.184176620371.849109876030.04307392390650.0628713642688-0.1567378857450.056743125458-0.005782617496730.09895947062880.04148516064740.00912295120478-0.05358055325690.209776772267-0.00776626874177-0.01230207438770.179183744613-0.02469280461250.25078074423118.546889667942.965082836645.8595719974
36.095059682961.45722051295-2.23772178244.851363351081.214074128068.48982613777-0.1438681768631.81614178213-0.0618018977982-0.4661200429190.109500773727-0.3648606881590.1344730990930.5920786554020.06832375637780.428664497434-0.0618450573795-0.04371393000741.102865313510.09184223139430.4313512674929.41572621825.83725238827.59079524347
43.7676402581-5.37907844202-1.805932357436.698560708162.472652916353.676634637610.1277946928740.184701949281-0.180592282479-0.26912715067-0.04808588932110.1100251004820.165572304489-0.0356179721829-0.03057991502330.336652325867-0.0582636407259-0.06049704070970.7891019497840.03632791155790.35012001034452.366145662520.996552657811.0700071661
57.5256120568-0.656228560656-1.035241208246.866514008332.477855360616.237703079460.8276606239731.360498257340.657095775339-0.871068301454-0.4024295566010.424649389811-1.528226027010.182372922098-0.3476633280450.6097137391220.02480674192510.1326010686920.9650528570330.1139282222450.4507730717681.9969918137133.6304014947-11.0632825293
67.977871628120.1400143968287.912432063641.343482292890.9363465612718.243042322090.1476017194990.541262472252-0.466827325183-0.06714200224950.0852429121749-0.2809301384230.14711598063-0.263411024268-0.2125243811950.414595721104-0.146436704041-0.05897006378511.010357695590.122577565110.44705496638313.584535148226.13441146089.02777661677
77.99118137704-1.180554703683.47663357055-0.172305014187-0.3548722978742.48851366528-0.115406607105-0.5479210553070.5200624364720.00687443726218-0.0792451781355-0.200141470316-0.1285555189150.2285090609370.2008965613610.315012781142-0.100237827219-0.04590743679560.4968807088680.06923539402820.44556473395943.581172524920.957660900341.9013237832
81.06906927355-0.5736048347590.312182712231.51100719371-1.618351493495.763311164260.1479764988410.289582844319-0.138179515973-0.1427848773840.06352537005760.0729340259420.4643236963520.528440946674-0.2009360057970.292756973513-0.0106904586222-0.02955576736360.6550971124240.01938794994680.39776015234763.854428938317.638916442530.9760503238
90.0252889770461-0.0706165054351-0.03022322363470.1991057506670.08208988457650.03316763791640.6702613303360.736065878783-1.07573853905-0.06584451880540.6778278627-0.2936283400270.4319024400980.616344324327-1.350297843831.42520383970.0944810271864-0.009111626482381.8366397342-0.1278411101081.7649742265848.43743994424.0495181773137.7428761412
106.086353218170.574475323895-3.00527587914.125923281941.668021075522.91711815069-0.2394395857392.398979468110.123837438108-0.6467113831240.0865072278498-0.520067771575-0.04595400648591.460562484510.08597365376720.4997249888010.00575636015981-0.01607436367041.25548659080.008917000826030.45824125109928.037061751757.975961187813.9102940203
117.42935375947-3.55587332749-0.4647904218015.439303716441.738703029693.6634085515-0.03556962884590.201312301869-0.0128832130499-0.307562886554-0.0172175940851-0.01179274307250.09548076638090.135641580448-0.006516283504050.380826817911-0.0261076324461-0.04626747245610.97530425079-0.003837764642570.41334575690851.479504204752.457037536917.5182577811
123.55797186168-0.238356159743-1.453030564618.54678278033-0.829260031894.009623304990.6887493283551.330909306230.454608833136-0.779382028495-0.2474707344980.341555482845-0.6232401871050.882051333309-0.3949792360370.5351747648130.08621859575440.05520305362961.117474546550.07522147416450.4249690476590.42069789863764.421872031-5.48235207425
136.3065217402-1.033722652085.038304406221.42292183813-0.9946040728263.97748402629-0.09128545904480.616201200852-0.102060502947-0.09990330180460.0515318473602-0.08886699335960.000510073189049-0.7633822547960.1046189242930.368514949471-0.0055599544674-0.04472358581020.747668480855-0.006872192595290.35083775305312.140437848858.32413679115.6132469008
146.21887824277-0.7068866288292.15673661814-0.1010922209540.351205576662.0941976624-0.118481557921-0.945792005384-0.1867400932760.08262079831240.0972599939293-0.0949269664047-0.003114420238770.132014575645-0.009370843592550.291114875784-0.00762158473024-0.04950896778040.4986420772750.1263724430030.43211862645741.949404406651.269169839348.3415813798
152.89486019486-0.7848506104580.968007855581.37296408751-0.6268455555264.39081246520.05801918596620.315659833842-0.359954899929-0.09962877716770.1208406007030.1117902016010.3116602954990.277361736465-0.1380503294830.258999359619-0.0134068959581-0.03670207488890.464258260810.02048755093810.44969378129462.543332297548.954726605537.5622768576
161.99994564434-1.373503990311.999810806215.2318522115-0.1694436083491.99975532368-2.19085513132-5.249764152882.161451468980.4222730973611.42688248367-1.315324883211.45881407421.91981232490.8025128311681.042219131340.147197175589-0.8701291069241.276408152730.4780269378222.1451104775447.349818078735.744434290946.1266635986
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA1 - 1191 - 119
22chain BBB1 - 1201 - 120
33chain C and (resid 28:75)CC28 - 751 - 48
44chain C and (resid 76:135 or resid 1025:1026 or resid 1027:1028)CC - G76 - 102849
55chain D and (resid 255:264 or resid 281:301 or resid 1096:1097)DH - T255 - 10971
66chain D and (resid 265:280 or resid 302:312 or resid 1036:1037)DH - K265 - 103711
77chain D and (resid 313:378 or resid 1035+1038+1039)DH313 - 37859 - 124
88chain D and (resid 379:480 or resid 1040+1048+1046)DH379 - 465125 - 211
99chain D and (resid 1042:1044)DO - P1043 - 1044
1010chain E and (resid 28:75)EU28 - 751 - 48
1111chain E and (resid 76:135 or resid 1025:1026 or resid 1027:1028)EU - Y76 - 102849
1212chain F and (resid 255:264 or resid 281:301 or resid 1096:1097)FZ - HA255 - 10971
1313chain F and (resid 265:280 or resid 302:312 or resid 1036:1037)FZ - F265 - 103711
1414chain F and (resid 313:378 or resid 1035+1038+1039)FZ313 - 37859 - 124
1515chain F and (resid 379:480 or resid 1040+1048+1046)FZ379 - 465125 - 211
1616chain F and (resid 1043)FDA1043

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