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- PDB-6osn: Potent and Selective Antitumor Antibody Targeting a Membrane-Prox... -

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Basic information

Entry
Database: PDB / ID: 6osn
TitlePotent and Selective Antitumor Antibody Targeting a Membrane-Proximal Epitope of ROR2
ComponentsTyrosine-protein kinase transmembrane receptor ROR2
KeywordsIMMUNE SYSTEM / Single chain Fv / ScFv / Antibody / ROR2 / Kringle domain / receptor tyrosine kinase-like orphan receptor / Phage display
Function / homology
Function and homology information


regulation of synaptic signaling by nitric oxide / macrophage migration / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt-protein binding / positive regulation of macrophage differentiation / male genitalia development / astrocyte development / mitogen-activated protein kinase kinase kinase binding / PCP/CE pathway / regulation of postsynapse organization ...regulation of synaptic signaling by nitric oxide / macrophage migration / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt-protein binding / positive regulation of macrophage differentiation / male genitalia development / astrocyte development / mitogen-activated protein kinase kinase kinase binding / PCP/CE pathway / regulation of postsynapse organization / bone mineralization / coreceptor activity / transmembrane receptor protein tyrosine kinase activity / positive regulation of synaptic transmission, glutamatergic / clathrin-coated endocytic vesicle membrane / positive regulation of neuron projection development / receptor protein-tyrosine kinase / Wnt signaling pathway / cell surface receptor protein tyrosine kinase signaling pathway / postsynapse / microtubule / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration / phosphorylation / dendrite / neuronal cell body / glutamatergic synapse / cell surface / signal transduction / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, receptor ROR / Plasminogen Kringle 4 / Plasminogen Kringle 4 / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Immunoglobulin I-set / Kringle domain / Immunoglobulin I-set domain ...Tyrosine-protein kinase, receptor ROR / Plasminogen Kringle 4 / Plasminogen Kringle 4 / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Immunoglobulin I-set / Kringle domain / Immunoglobulin I-set domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Tyrosine-protein kinase transmembrane receptor ROR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.083 Å
AuthorsPark, H. / Rader, C.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Affinity maturation, humanization, and co-crystallization of a rabbit anti-human ROR2 monoclonal antibody for therapeutic applications.
Authors: Goydel, R.S. / Weber, J. / Peng, H. / Qi, J. / Soden, J. / Freeth, J. / Park, H. / Rader, C.
History
DepositionMay 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase transmembrane receptor ROR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0172
Polymers10,9581
Non-polymers591
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.606, 41.917, 52.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein kinase transmembrane receptor ROR2 / Neurotrophic tyrosine kinase / receptor-related 2


Mass: 10958.179 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROR2, NTRKR2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q01974, receptor protein-tyrosine kinase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1.68 Å3/Da / Density % sol: 26.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Li acetate 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.021→32.671 Å / Num. obs: 29243 / % possible obs: 76.7 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02117 / Rpim(I) all: 0.01345 / Rrim(I) all: 0.02522 / Net I/σ(I): 35.5
Reflection shellResolution: 1.083→1.122 Å / Rmerge(I) obs: 0.05935 / Num. unique obs: 29243 / CC1/2: 0.993 / Rpim(I) all: 0.0507 / Rrim(I) all: 0.07851

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BA5

6ba5


Resolution: 1.083→22.141 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1609 1367 4.98 %
Rwork0.1529 --
obs0.1533 27453 85.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.083→22.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms652 0 4 165 821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008693
X-RAY DIFFRACTIONf_angle_d0.948939
X-RAY DIFFRACTIONf_dihedral_angle_d2.988394
X-RAY DIFFRACTIONf_chiral_restr0.06987
X-RAY DIFFRACTIONf_plane_restr0.006129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0833-1.12210.179810.17321740X-RAY DIFFRACTION58
1.1221-1.1670.17481280.16662319X-RAY DIFFRACTION78
1.167-1.22010.15081450.15632873X-RAY DIFFRACTION95
1.2201-1.28440.1778690.16271378X-RAY DIFFRACTION46
1.2844-1.36490.1581700.15592968X-RAY DIFFRACTION99
1.3649-1.47020.16071490.15113019X-RAY DIFFRACTION100
1.4702-1.61810.16511610.14363021X-RAY DIFFRACTION100
1.6181-1.85220.14511630.14333027X-RAY DIFFRACTION99
1.8522-2.33320.1651550.14222829X-RAY DIFFRACTION92
2.3332-22.14530.16181460.16132912X-RAY DIFFRACTION90
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)
11.2608-0.27291.75071.46692.21797.2211-0.0199-0.14840.4543-0.210.1209-0.2686-0.50080.3509-0.02260.09680.0017-0.00620.067-0.01390.104412.863718.76111.306
20.77060.15970.68581.6993-0.11181.96660.00440.0132-0.0291-0.04660.04760.0527-0.0143-0.0853-0.04470.03610.0034-0.00030.03720.00730.033211.27038.97764.0278
32.7814-0.45390.28421.1636-0.40672.0822-0.0347-0.0695-0.02180.1212-0.0525-0.0450.01290.05850.06680.0760.0024-0.01420.0216-0.00540.028518.74178.8818.747
41.7302-0.2971-0.00430.68520.12291.50480.0245-0.0269-0.0290.001-0.0528-0.03380.01640.09660.01720.04280.007-0.00250.030.00490.022919.56627.32368.6766
50.66670.1810.08690.04910.02360.0114-0.1022-0.2622-0.06060.34760.05650.137-0.11620.0234-0.01510.13840.02680.01540.07220.01260.042516.62746.477223.5153
62.2561-0.44882.9321.527-1.42214.7880.0641-0.1059-0.02040.10850.08960.09690.0556-0.3256-0.03070.0506-0.0020.0120.0730.01430.05897.87155.465410.5649
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 310:313)
2X-RAY DIFFRACTION2(chain A and resid 314:330)
3X-RAY DIFFRACTION3(chain A and resid 331:350)
4X-RAY DIFFRACTION4(chain A and resid 351:377)
5X-RAY DIFFRACTION5(chain A and resid 378:385)
6X-RAY DIFFRACTION6(chain A and resid 386:394)

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