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

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Basic information

Entry
Database: PDB / ID: 6osv
TitlePotent and Selective Antitumor Antibody Targeting a Membrane-Proximal Epitope of ROR2
Components
  • Antibody heavy chain variable region
  • Antibody light chain variable region
  • Tyrosine-protein kinase transmembrane receptor ROR2
Keywordsimmune sytem/transferase / Single chain Fv / ScFv / Antibody / ROR2 / Kringle domain / receptor tyrosine kinase-like orphan receptor / Phage display / IMMUNE SYSTEM / immune sytem-transferase complex
Function / homology
Function and homology information


regulation of synaptic signaling by nitric oxide / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / macrophage migration / Wnt-protein binding / positive regulation of macrophage differentiation / astrocyte development / male genitalia development / mitogen-activated protein kinase kinase kinase binding / PCP/CE pathway / regulation of postsynapse organization ...regulation of synaptic signaling by nitric oxide / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / macrophage migration / Wnt-protein binding / positive regulation of macrophage differentiation / astrocyte development / male genitalia 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 / cell surface receptor protein tyrosine kinase signaling pathway / clathrin-coated endocytic vesicle membrane / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / Wnt signaling pathway / microtubule / receptor complex / postsynapse / positive regulation of cell migration / axon / neuronal cell body / dendrite / 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. / Kringle domain / Kringle / Kringle, conserved site ...Tyrosine-protein kinase, receptor ROR / Plasminogen Kringle 4 / Plasminogen Kringle 4 / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Kringle-like fold / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Tyrosine-protein kinase transmembrane receptor ROR2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 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 2, 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 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
L: Antibody light chain variable region
K: Tyrosine-protein kinase transmembrane receptor ROR2
H: Antibody heavy chain variable region


Theoretical massNumber of molelcules
Total (without water)36,1113
Polymers36,1113
Non-polymers00
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-10 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.109, 60.105, 102.756
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: Antibody Antibody light chain variable region


Mass: 11818.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli)
#2: Protein Tyrosine-protein kinase transmembrane receptor ROR2 / Neurotrophic tyrosine kinase / receptor-related 2


Mass: 10932.098 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
#3: Antibody Antibody heavy chain variable region


Mass: 13360.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.01 M Magnesium chloride hexahydrate, 0.005 M Nickel(II) chloride 0.1 M HEPES sodium pH 7.0, 15% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 7, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34→51.881 Å / Num. obs: 55957 / % possible obs: 91.5 % / Redundancy: 5.9 % / CC1/2: 1 / Rmerge(I) obs: 0.03314 / Rpim(I) all: 0.01436 / Rrim(I) all: 0.0362 / Net I/σ(I): 22
Reflection shellResolution: 1.34→1.406 Å / Rmerge(I) obs: 0.6778 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 2799 / CC1/2: 0.635 / Rpim(I) all: 0.4093 / Rrim(I) all: 0.7953

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→51.378 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.95
RfactorNum. reflection% reflection
Rfree0.189 1119 2 %
Rwork0.162 --
obs0.1625 55957 86.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.34→51.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 0 338 2700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092446
X-RAY DIFFRACTIONf_angle_d1.0433323
X-RAY DIFFRACTIONf_dihedral_angle_d9.671189
X-RAY DIFFRACTIONf_chiral_restr0.085350
X-RAY DIFFRACTIONf_plane_restr0.007430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.4010.3058490.25942419X-RAY DIFFRACTION31
1.401-1.47490.24561080.23155315X-RAY DIFFRACTION68
1.4749-1.56730.22451490.19457247X-RAY DIFFRACTION92
1.5673-1.68830.21191580.16867801X-RAY DIFFRACTION99
1.6883-1.85820.18911610.1687864X-RAY DIFFRACTION99
1.8582-2.12710.17981620.16247941X-RAY DIFFRACTION100
2.1271-2.680.18351630.17067974X-RAY DIFFRACTION100
2.68-51.41580.18451690.1498277X-RAY DIFFRACTION100
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)
11.13680.7169-1.36155.6826-0.01331.7777-0.23090.28860.4031-0.24720.00850.3624-0.0575-0.33760.09230.25390.0851-0.08530.2558-0.01160.4002-27.22834.0371.1299
20.39320.12450.34312.07451.10321.37310.0034-0.01310.0131-0.0628-0.03670.0928-0.0293-0.0387-0.01150.42550.0574-0.020.2213-0.17450.8332-17.406922.94488.7834
30.5160.65320.04181.1643-0.22340.24210.0046-0.1630.35060.0448-0.00970.2133-0.1223-0.17490.07650.22390.03630.00330.1998-0.06460.3151-25.5020.99658.6516
40.5391-0.0720.10141.1707-0.41711.41990.0421-0.02250.5626-0.1133-0.1574-0.0938-0.25720.0424-0.00420.26120.0281-0.00460.13350.01730.2927-12.69723.97695.0785
51.1929-0.1559-0.10250.9331-0.13080.845-0.0922-0.35190.38690.1418-0.0510.1268-0.2954-0.1167-0.00430.24880.0304-0.02640.2029-0.08420.267-16.48531.160715.5465
62.91512.53090.92683.68021.05531.5578-0.1044-0.07950.20350.03440.150.0712-0.2436-0.23220.01060.30970.071-0.04570.2318-0.08380.422-22.3787.675612.9768
70.54390.4055-0.29852.47950.07280.67290.0868-0.02380.35230.06-0.1089-0.2325-0.1671-0.0272-0.02960.26270.0174-0.0260.1468-0.0010.3797-15.02997.64174.9999
80.84860.66430.18331.39440.22551.09070.06570.02240.4243-0.1706-0.20490.0098-0.22890.0101-0.01180.23880.0087-0.00940.14480.0170.3346-16.53934.63222.9777
98.67882.517-1.67439.0571-2.14084.4411-0.26280.2071-0.7195-0.1004-0.01450.07170.7969-0.4001-0.1740.4377-0.072-0.07550.43660.18190.34920.1349-32.028726.8296
100.42240.1071-0.31180.18340.0830.43370.2301-0.131-0.08780.313-0.12-0.1636-0.31730.31260.5760.2535-0.00040.09250.50980.34520.2102-2.0402-26.700822.5233
110.4959-0.1709-0.86750.0590.29921.61640.0596-0.23120.04070.1225-0.07680.0282-0.039-0.0456-0.15980.65690.150.25390.49380.09060.2097-12.77-20.034529.875
120.8156-0.1451-0.00361.3306-0.22630.8023-0.012-0.276-0.26010.0132-0.06790.22030.063-0.07430.02130.16560.0080.00410.1830.01410.1722-9.1675-18.170213.1844
134.05720.48110.47232.19320.25863.0915-0.1178-0.22310.10310.2224-0.04110.1236-0.40550.4795-0.00380.2241-0.0391-0.00920.32250.10560.1733-3.3936-21.881519.4151
143.8687-1.8543-0.96682.7718-0.97531.3924-0.0494-0.42590.00290.6195-0.008-0.1859-0.15750.01160.06090.29890.0102-0.02310.33590.06040.1484-6.8888-18.002223.3445
151.62350.1775-1.25660.11510.2722.716-0.0373-0.31070.14040.38130.07030.163-0.2458-0.1708-0.050.39210.11830.06520.3758-0.02290.157-14.7153-10.559124.6411
162.4187-3.68480.70217.2848-1.14380.2019-0.037-0.2725-0.12910.31950.0263-0.2159-0.1571-0.0751-0.00440.38310.02-0.0750.36130.10090.1832-2.6656-23.717928.9305
171.75120.2257-0.82951.0854-1.58013.65490.1659-0.25580.44970.13330.024-0.1103-0.58440.09180.12580.2647-0.0190.01860.1727-0.00290.29041.3091-0.32220.6841
180.02310.08010.14720.27620.50820.93530.05080.29430.1568-0.0550.07840.1324-0.1364-0.16930.56350.24530.06380.04930.53030.18980.2505-1.4197-2.1666-21.3242
191.1998-0.24880.44411.29641.2291.5740.0970.33360.32460.0618-0.0743-0.11450.00880.1849-0.05060.19030.02110.00520.2320.05750.18821.2418-6.8243-9.4273
200.9820.019-0.36041.0673-0.02451.01830.10970.16120.24830.0004-0.0658-0.0074-0.12220.02570.03410.16330.01390.00980.17070.04440.1821-5.9688-5.5199-1.4306
211.8791-2.6733-0.11749.8915-0.41641.13790.08480.29480.3143-0.2552-0.12210.2753-0.16-0.04370.00180.19170.043-0.01190.23370.07910.2227-14.7913-3.3199-6.7828
220.65670.0187-0.2470.6028-0.07040.81120.02060.3396-0.0178-0.03560.0182-0.02030.0026-0.08960.00320.13860.0051-0.00510.23870.03020.1323-5.9421-12.4009-8.2697
231.1361-0.2701-0.6230.604-0.09110.40970.0520.18310.39630.0349-0.1015-0.1046-0.1692-0.07240.04050.17370.014-0.00950.17850.0480.2249-5.9008-3.6244-1.2272
241.12430.6039-0.05640.6109-1.16065.6775-0.0540.42170.3534-0.2884-0.0931-0.0865-0.46240.069-0.22080.30550.1320.08060.50130.29920.4381-2.96113.8539-17.5412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 0:9)
2X-RAY DIFFRACTION2(chain H and resid 10:13)
3X-RAY DIFFRACTION3(chain H and resid 14:32)
4X-RAY DIFFRACTION4(chain H and resid 33:50)
5X-RAY DIFFRACTION5(chain H and resid 51:73)
6X-RAY DIFFRACTION6(chain H and resid 74:84)
7X-RAY DIFFRACTION7(chain H and resid 85:97)
8X-RAY DIFFRACTION8(chain H and resid 98:118)
9X-RAY DIFFRACTION9(chain K and resid 314:317)
10X-RAY DIFFRACTION10(chain K and resid 318:331)
11X-RAY DIFFRACTION11(chain K and resid 332:336)
12X-RAY DIFFRACTION12(chain K and resid 337:361)
13X-RAY DIFFRACTION13(chain K and resid 362:372)
14X-RAY DIFFRACTION14(chain K and resid 373:380)
15X-RAY DIFFRACTION15(chain K and resid 381:385)
16X-RAY DIFFRACTION16(chain K and resid 386:394)
17X-RAY DIFFRACTION17(chain L and resid 0:10)
18X-RAY DIFFRACTION18(chain L and resid 11:17)
19X-RAY DIFFRACTION19(chain L and resid 18:24)
20X-RAY DIFFRACTION20(chain L and resid 25:41)
21X-RAY DIFFRACTION21(chain L and resid 42:48)
22X-RAY DIFFRACTION22(chain L and resid 49:78)
23X-RAY DIFFRACTION23(chain L and resid 79:105)
24X-RAY DIFFRACTION24(chain L and resid 106:110)

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