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- PDB-6j7w: Crystal Structure of Human BCMA in complex with UniAb(TM) VH -

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Basic information

Entry
Database: PDB / ID: 6j7w
TitleCrystal Structure of Human BCMA in complex with UniAb(TM) VH
Components
  • Tumor necrosis factor receptor superfamily member 17
  • UniAb
KeywordsIMMUNE SYSTEM / Heavy chain antibodies / VH domains / domain antibodies
Function / homology
Function and homology information


lymphocyte homeostasis / TNFs bind their physiological receptors / endomembrane system / tumor necrosis factor-mediated signaling pathway / signaling receptor activity / adaptive immune response / signal transduction / membrane / plasma membrane
Similarity search - Function
BCMA, TALL-1 binding / Tumour necrosis factor receptor 17 / BCMA, TALL-1 binding / Tumor necrosis factor receptor 13C/17
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsClarke, S.C. / Ma, B. / Trinklein, N.D. / Schellenberger, U. / Osborn, M. / Ouisse, L. / Boudreau, A. / Davison, L. / Harris, K.E. / Ugamraj, H. ...Clarke, S.C. / Ma, B. / Trinklein, N.D. / Schellenberger, U. / Osborn, M. / Ouisse, L. / Boudreau, A. / Davison, L. / Harris, K.E. / Ugamraj, H. / Balasubramani, A. / Dang, K. / Jorgensen, B. / Ogana, H. / Pham, D. / Pratap, P. / Sankaran, P. / Anegon, I. / van Schooten, W. / Bruggemann, M. / Buelow, R. / Force Aldred, S.
CitationJournal: Front Immunol / Year: 2018
Title: Multispecific Antibody Development Platform Based on Human Heavy Chain Antibodies
Authors: Clarke, S.C. / Ma, B. / Trinklein, N.D. / Schellenberger, U. / Osborn, M.J. / Ouisse, L.H. / Boudreau, A. / Davison, L.M. / Harris, K.E. / Ugamraj, H.S. / Balasubramani, A. / Dang, K.H. / ...Authors: Clarke, S.C. / Ma, B. / Trinklein, N.D. / Schellenberger, U. / Osborn, M.J. / Ouisse, L.H. / Boudreau, A. / Davison, L.M. / Harris, K.E. / Ugamraj, H.S. / Balasubramani, A. / Dang, K.H. / Jorgensen, B. / Ogana, H.A.N. / Pham, D.T. / Pratap, P.P. / Sankaran, P. / Anegon, I. / van Schooten, W.C. / Bruggemann, M. / Buelow, R. / Force Aldred, S.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UniAb
C: Tumor necrosis factor receptor superfamily member 17
B: UniAb
D: Tumor necrosis factor receptor superfamily member 17


Theoretical massNumber of molelcules
Total (without water)33,8894
Polymers33,8894
Non-polymers00
Water61334
1
A: UniAb
C: Tumor necrosis factor receptor superfamily member 17


Theoretical massNumber of molelcules
Total (without water)16,9452
Polymers16,9452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-9 kcal/mol
Surface area7870 Å2
MethodPISA
2
B: UniAb
D: Tumor necrosis factor receptor superfamily member 17


Theoretical massNumber of molelcules
Total (without water)16,9452
Polymers16,9452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-10 kcal/mol
Surface area7500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.392, 73.806, 133.491
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody UniAb


Mass: 12588.841 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Heavy chain Antibody / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Protein/peptide Tumor necrosis factor receptor superfamily member 17 / B-cell maturation protein


Mass: 4355.890 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Human B-Cell Maturation Antigen / Source: (gene. exp.) Homo sapiens (human) / Gene: BCMA / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q02223
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.2M sodium malonate pH 4.0 and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.59→48.99 Å / Num. obs: 10364 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Net I/σ(I): 11.6
Reflection shellResolution: 2.59→2.7 Å / Redundancy: 7 % / Rmerge(I) obs: 0.268 / Num. unique obs: 1219 / CC1/2: 0.977 / Rpim(I) all: 0.108 / Rrim(I) all: 0.289 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zhk, 4zfo

3zhk

4zfo


Resolution: 2.6→48.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.2 / SU ML: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.41 / ESU R Free: 0.352
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2713 514 5 %RANDOM
Rwork0.2085 ---
obs0.2118 9739 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 132.76 Å2 / Biso mean: 55.386 Å2 / Biso min: 32.25 Å2
Baniso -1Baniso -2Baniso -3
1--2.68 Å2-0 Å20 Å2
2--0.9 Å2-0 Å2
3---1.78 Å2
Refinement stepCycle: final / Resolution: 2.6→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 0 34 2345
Biso mean---51.05 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0142365
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171963
X-RAY DIFFRACTIONr_angle_refined_deg1.351.6543210
X-RAY DIFFRACTIONr_angle_other_deg0.8681.6444621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5555307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99721.933119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.84415354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8151516
X-RAY DIFFRACTIONr_chiral_restr0.0630.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 32 -
Rwork0.279 701 -
all-733 -
obs--99.73 %

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