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

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Basic information

Entry
Database: PDB / ID: 6osh
TitlePotent and Selective Antitumor Antibody Targeting a Membrane-Proximal Epitope of ROR2
Components
  • Antibody Light chain variable region
  • Antibody heavy chain variable region
  • Tyrosine-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 / positive regulation of macrophage differentiation / Wnt-protein binding / 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 / positive regulation of macrophage differentiation / Wnt-protein binding / male genitalia development / astrocyte development / mitogen-activated protein kinase kinase kinase binding / PCP/CE pathway / regulation of postsynapse organization / bone mineralization / coreceptor activity / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / positive regulation of synaptic transmission, glutamatergic / clathrin-coated endocytic vesicle membrane / receptor protein-tyrosine kinase / Wnt signaling pathway / positive regulation of neuron projection development / postsynapse / microtubule / receptor complex / positive regulation of cell migration / phosphorylation / neuronal cell body / glutamatergic synapse / dendrite / 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. / 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
Tyrosine-protein kinase transmembrane receptor ROR2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.117 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 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)35,0193
Polymers35,0193
Non-polymers00
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-12 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.165, 67.201, 89.610
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: 11957.256 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: 10688.834 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: 12372.758 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.: 426 / 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: 2.04 Å3/Da / Density % sol: 39.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Na citrate tribasic 20% PEG3350

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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
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.117→40.33 Å / Num. obs: 81433 / % possible obs: 89 % / Redundancy: 4.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04451 / Rpim(I) all: 0.02156 / Rrim(I) all: 0.04969 / Net I/σ(I): 17.3
Reflection shellResolution: 1.117→1.157 Å / Rmerge(I) obs: 0.561 / Num. unique obs: 4074 / CC1/2: 0.53 / Rpim(I) all: 0.5024 / Rrim(I) all: 0.7565

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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: 1.117→40.332 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1692 1221 1.5 %
Rwork0.1621 --
obs0.1622 81417 76.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.117→40.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 0 426 2758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082449
X-RAY DIFFRACTIONf_angle_d0.9833337
X-RAY DIFFRACTIONf_dihedral_angle_d3.0671384
X-RAY DIFFRACTIONf_chiral_restr0.081363
X-RAY DIFFRACTIONf_plane_restr0.007430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.117-1.16170.3197230.28971562X-RAY DIFFRACTION14
1.1617-1.21460.232700.24844603X-RAY DIFFRACTION40
1.2146-1.27870.23151190.22397735X-RAY DIFFRACTION67
1.2787-1.35880.22211670.202710977X-RAY DIFFRACTION95
1.3588-1.46370.19061760.182811558X-RAY DIFFRACTION100
1.4637-1.6110.18251760.163311608X-RAY DIFFRACTION100
1.611-1.84410.1741770.153511603X-RAY DIFFRACTION100
1.8441-2.32330.15331420.14969329X-RAY DIFFRACTION79
2.3233-40.35810.1471710.146511221X-RAY DIFFRACTION93
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)
13.7498-2.2116-2.45432.57073.2284.1053-0.3796-0.3676-0.03610.97850.3024-0.30250.27390.45740.09590.1540.0222-0.03060.17670.00240.134629.1536-2.89313.1623
23.82850.33420.34230.7197-0.57450.5584-0.1593-0.75190.45180.97030.3958-0.31090.08360.3870.04140.2905-0.1299-0.03780.2142-0.02540.262126.754512.31772.5524
31.1562-0.5887-0.69372.7062.29142.14490.08050.07540.5375-0.1472-0.0820.0648-0.74680.0767-0.04050.2956-0.02780.00330.11230.00090.248920.830918.3489-3.1329
41.9585-1.1013-0.67422.55620.3960.90230.01020.00270.04490.0774-0.0368-0.1334-0.02790.06440.01490.0639-0.0077-0.00130.07130.00410.065324.1056-1.6292-2.7057
51.150.5122-0.01221.2032-0.22391.8773-0.01350.0655-0.02860.0485-0.0130.1157-0.0949-0.04880.00670.0585-0.00890.00260.06030.00760.061214.61470.8489-7.2515
62.2424-0.31830.37792.1224-0.02842.3824-0.03680.11770.1637-0.03280.0252-0.1602-0.15670.16320.0040.0739-0.02880.00740.08840.01770.07823.29285.7062-9.949
71.2605-0.3384-0.31342.45450.68391.490.06290.0390.10530.0088-0.0685-0.0026-0.1504-0.04040.02120.07740.00740.00840.0764-0.00060.064816.89383.5916-0.7324
81.6294-0.5316-0.03666.1853-0.12921.550.0615-0.05160.12170.1228-0.0941-0.0822-0.09610.02990.02660.0632-0.01410.00290.0761-0.00750.065420.45823.78534.241
93.4361-0.51482.02091.65890.07341.8765-0.34090.19760.0146-0.09850.01430.14450.0001-0.0475-0.51350.3777-0.1984-0.01290.4594-0.17750.37230.8453-26.5456-28.5363
102.5548-0.31620.15381.8619-0.542.1648-0.10730.1999-0.3133-0.0229-0.02190.13370.3586-0.29290.0850.1321-0.0367-0.00630.136-0.02930.13997.0695-20.7067-25.8129
111.112-0.4358-1.05631.09670.68793.39990.0547-0.0699-0.14610.0468-0.0077-0.04090.27840.0738-0.04870.0806-0-0.02520.08250.00590.082211.4153-17.3016-13.7673
123.6008-0.32240.1460.88760.22192.90130.0088-0.00690.0593-0.0204-0.0107-0.06350.0549-0.1313-0.01150.0947-0.02590.00310.1131-0.00280.11545.2737-17.7901-20.6707
134.31851.2756-0.45372.98811.23543.3198-0.11870.1579-0.0501-0.12990.18070.01990.06750.0763-0.02550.0716-0.0135-0.0040.0863-0.0040.05910.4016-13.8688-23.2709
141.99440.62491.24751.6324-0.65251.538-0.07210.20250.1903-0.11450.0833-0.1003-0.39240.46890.06180.1156-0.04950.01860.152-0.02240.096416.5633-6.6764-22.0575
157.9616.674-0.47358.0077-0.46619.0562-0.1290.27870.0961-0.36330.31010.0196-0.0713-0.22150.07720.0923-0.01060.0080.12110.00820.09679.0006-13.2436-26.576
161.1676-0.3009-0.0870.2283-0.18360.2897-0.11870.284-0.1528-0.08460.2905-0.0289-0.33140.04520.04840.5663-0.24890.23710.4966-0.12550.41182.6176-23.9117-32.3178
176.57832.5973-1.14665.2202-2.09438.6703-0.09210.13520.57380.2401-0.09180.1971-0.6876-0.11560.24070.13270.0179-0.0030.13680.03970.20651.24170.684-5.5546
180.46350.0307-0.02041.388-1.81314.60470.0737-0.06820.07620.04110.02760.0321-0.1128-0.1094-0.09740.0908-0.00760.02640.1102-0.00350.08780.9576-7.417514.497
192.4540.3554-0.00870.75760.20822.31940.00160.1260.0414-0.0080.01030.0765-0.0403-0.07110.0110.05-0.00730.00970.04970.0120.05985.3939-9.1271.3597
202.64911.31320.11971.7899-0.17540.40030.165-0.31780.21560.3278-0.2090.119-0.01420.0335-0.03030.084-0.03290.00680.1132-0.01920.075715.5667-7.40868.7798
210.7873-0.1967-1.03071.142-0.02471.7603-0.0015-0.3255-0.0477-0.00370.019-0.03660.0520.1189-0.01630.0580.0047-0.00450.1011-0.00710.07129.0381-16.72418.5755
224.68661.28114.59070.74851.24374.49920.0549-0.07190.0160.0252-0.04410.0058-0.0061-0.1319-0.00070.06010.0010.00630.0872-0.01620.07184.4438-13.500213.0073
230.35280.1572-0.08450.10290.36514.92810.0738-0.02070.05280.04110.01750.0436-0.10230.1061-0.03680.0826-0.01420.00970.0743-0.00150.07957.8256-5.82333.44
240.27140.1193-0.35780.1759-0.85094.64460.1556-0.09120.05950.13530.00860.0398-0.401-0.0206-0.0410.1256-0.02070.02340.0947-0.00790.08285.6824-2.449912.296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 0:5)
2X-RAY DIFFRACTION2(chain H and resid 6:9)
3X-RAY DIFFRACTION3(chain H and resid 10:19)
4X-RAY DIFFRACTION4(chain H and resid 20:40)
5X-RAY DIFFRACTION5(chain H and resid 41:62)
6X-RAY DIFFRACTION6(chain H and resid 63:82)
7X-RAY DIFFRACTION7(chain H and resid 83:100)
8X-RAY DIFFRACTION8(chain H and resid 101:113)
9X-RAY DIFFRACTION9(chain K and resid 314:318)
10X-RAY DIFFRACTION10(chain K and resid 319:335)
11X-RAY DIFFRACTION11(chain K and resid 336:362)
12X-RAY DIFFRACTION12(chain K and resid 363:372)
13X-RAY DIFFRACTION13(chain K and resid 373:381)
14X-RAY DIFFRACTION14(chain K and resid 382:385)
15X-RAY DIFFRACTION15(chain K and resid 386:389)
16X-RAY DIFFRACTION16(chain K and resid 390:394)
17X-RAY DIFFRACTION17(chain L and resid -2:3)
18X-RAY DIFFRACTION18(chain L and resid 4:23)
19X-RAY DIFFRACTION19(chain L and resid 24:38)
20X-RAY DIFFRACTION20(chain L and resid 39:51)
21X-RAY DIFFRACTION21(chain L and resid 52:69)
22X-RAY DIFFRACTION22(chain L and resid 70:79)
23X-RAY DIFFRACTION23(chain L and resid 80:98)
24X-RAY DIFFRACTION24(chain L and resid 99:110)

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