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- PDB-8coh: Structure of the complement C5 specific nanobody TPP-3444 -

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Basic information

Entry
Database: PDB / ID: 8coh
TitleStructure of the complement C5 specific nanobody TPP-3444
ComponentsNanobody TPP-3444
KeywordsIMMUNE SYSTEM / innate immunity / complement / terminal pathway / nanobody / antigen-antibody complex
Function / homologyCITRIC ACID / :
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPedersen, D.V. / Andersen, G.R.
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
Revision 1.1Oct 23, 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

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Assembly

Deposited unit
A: Nanobody TPP-3444
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8753
Polymers14,6281
Non-polymers2472
Water4,089227
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-7 kcal/mol
Surface area7170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.489, 81.489, 36.601
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-506-

HOH

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Components

#1: Antibody Nanobody TPP-3444


Mass: 14627.962 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): HEK293 Expi / Production host: Homo sapiens (human)
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.1
Details: 54 mM citric acid, 36 mM BIS-TRIS propane pH 4.1, 14.4% w/v polyethylene glycol 3350, and 10 mM NiCl2.

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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: Nov 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→36.44 Å / Num. obs: 30885 / % possible obs: 99.94 % / Redundancy: 25.9 % / Biso Wilson estimate: 12.47 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1071 / Net I/σ(I): 22.55
Reflection shellResolution: 1.3→1.347 Å / Redundancy: 25 % / Rmerge(I) obs: 1.447 / Num. unique obs: 3019 / CC1/2: 0.884 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→36.44 Å / SU ML: 0.1088 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.8299
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1746 2000 6.48 %
Rwork0.1462 28879 -
obs0.1481 30879 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.17 Å2
Refinement stepCycle: LAST / Resolution: 1.3→36.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 14 227 1270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00991127
X-RAY DIFFRACTIONf_angle_d1.20041537
X-RAY DIFFRACTIONf_chiral_restr0.0901152
X-RAY DIFFRACTIONf_plane_restr0.0111208
X-RAY DIFFRACTIONf_dihedral_angle_d16.4642170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.23731390.20572004X-RAY DIFFRACTION99.54
1.33-1.370.23581400.19962030X-RAY DIFFRACTION100
1.37-1.410.21641420.17122043X-RAY DIFFRACTION99.95
1.41-1.450.19741390.16472023X-RAY DIFFRACTION100
1.45-1.510.20061400.15312016X-RAY DIFFRACTION99.91
1.51-1.570.18261430.1492048X-RAY DIFFRACTION100
1.57-1.640.18651400.14382033X-RAY DIFFRACTION100
1.64-1.720.1821420.14082047X-RAY DIFFRACTION100
1.72-1.830.17591430.13772058X-RAY DIFFRACTION99.95
1.83-1.970.14641410.12822049X-RAY DIFFRACTION100
1.97-2.170.16191450.1282082X-RAY DIFFRACTION100
2.17-2.490.15791440.13882094X-RAY DIFFRACTION100
2.49-3.130.17331470.15172113X-RAY DIFFRACTION99.96
3.13-36.440.17011550.14592239X-RAY DIFFRACTION99.83

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