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- PDB-6ban: Potent and Selective Antitumor Activity of a T-Cell Engaging Bisp... -

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Basic information

Entry
Database: PDB / ID: 6ban
TitlePotent and Selective Antitumor Activity of a T-Cell Engaging Bispecific Antibody Targeting a Membrane-Proximal Epitope of ROR1
Components
  • Inactive tyrosine-protein kinase transmembrane receptor ROR1
  • Variable domain R11 Heavy chain
  • Variable domain of R11 Light Chain
KeywordsIMMUNE SYSTEM / Single chain Fv / ScFv / Antibody / ROR1 / Kringle domain / receptor tyrosine kinase-like orphan receptor / Phage display
Function / homology
Function and homology information


WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt receptor activity / Wnt-protein binding / astrocyte development / inner ear development / coreceptor activity / axon terminus / stress fiber / transmembrane receptor protein tyrosine kinase activity / sensory perception of sound ...WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt receptor activity / Wnt-protein binding / astrocyte development / inner ear development / coreceptor activity / axon terminus / stress fiber / transmembrane receptor protein tyrosine kinase activity / sensory perception of sound / positive regulation of neuron projection development / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / phosphorylation / cell surface / ATP binding / plasma membrane / cytoplasm
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 / Immunoglobulins / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Inactive tyrosine-protein kinase transmembrane receptor ROR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsPark, H. / Rader, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA181258 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)TR001114 United States
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Potent and selective antitumor activity of a T cell-engaging bispecific antibody targeting a membrane-proximal epitope of ROR1.
Authors: Qi, J. / Li, X. / Peng, H. / Cook, E.M. / Dadashian, E.L. / Wiestner, A. / Park, H. / Rader, C.
#1: Journal: PLoS One / Year: 2011
Title: Therapeutic potential and challenges of targeting receptor tyrosine kinase ROR1 with monoclonal antibodies in B-cell malignancies
Authors: Yang, J. / Baskar, S. / Kwong, K.Y. / Kennedy, M.G. / Wiestner, A. / Rader, C.
History
DepositionOct 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Variable domain of R11 Light Chain
B: Variable domain R11 Heavy chain
C: Variable domain of R11 Light Chain
D: Variable domain R11 Heavy chain
E: Variable domain of R11 Light Chain
F: Variable domain R11 Heavy chain
G: Variable domain of R11 Light Chain
H: Variable domain R11 Heavy chain
M: Inactive tyrosine-protein kinase transmembrane receptor ROR1
N: Inactive tyrosine-protein kinase transmembrane receptor ROR1
O: Inactive tyrosine-protein kinase transmembrane receptor ROR1
P: Inactive tyrosine-protein kinase transmembrane receptor ROR1


Theoretical massNumber of molelcules
Total (without water)135,66612
Polymers135,66612
Non-polymers00
Water25,6711425
1
A: Variable domain of R11 Light Chain
B: Variable domain R11 Heavy chain
M: Inactive tyrosine-protein kinase transmembrane receptor ROR1


Theoretical massNumber of molelcules
Total (without water)33,9163
Polymers33,9163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Variable domain of R11 Light Chain
D: Variable domain R11 Heavy chain
N: Inactive tyrosine-protein kinase transmembrane receptor ROR1


Theoretical massNumber of molelcules
Total (without water)33,9163
Polymers33,9163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Variable domain of R11 Light Chain
F: Variable domain R11 Heavy chain
O: Inactive tyrosine-protein kinase transmembrane receptor ROR1


Theoretical massNumber of molelcules
Total (without water)33,9163
Polymers33,9163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Variable domain of R11 Light Chain
H: Variable domain R11 Heavy chain
P: Inactive tyrosine-protein kinase transmembrane receptor ROR1


Theoretical massNumber of molelcules
Total (without water)33,9163
Polymers33,9163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.790, 84.360, 102.740
Angle α, β, γ (deg.)90.00, 113.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
Variable domain of R11 Light Chain


Mass: 11894.146 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein
Variable domain R11 Heavy chain


Mass: 12665.929 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein
Inactive tyrosine-protein kinase transmembrane receptor ROR1 / Neurotrophic tyrosine kinase / receptor-related 1


Mass: 9356.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROR1, NTRKR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01973
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1425 / 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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Li Sulfate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.95→62.77 Å / Num. obs: 98668 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.92 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.069 / Rrim(I) all: 0.096 / Net I/σ(I): 11.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 4904 / CC1/2: 0.816 / Rpim(I) all: 0.208 / Rrim(I) all: 0.396 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLMdata reduction
SCALAdata scaling
BALBES2ZNWphasing
RefinementResolution: 1.95→41.04 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.15 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.126
RfactorNum. reflection% reflectionSelection details
Rfree0.196 4839 4.91 %RANDOM
Rwork0.16 ---
obs0.162 98644 99.8 %-
Displacement parametersBiso mean: 25.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.1937 Å20 Å2-0.2797 Å2
2---3.7448 Å20 Å2
3---0.5512 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.95→41.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9278 0 0 1425 10703
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019507HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0312953HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3071SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes196HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1409HARMONIC5
X-RAY DIFFRACTIONt_it9507HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.67
X-RAY DIFFRACTIONt_other_torsion14.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1276SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11883SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 356 4.88 %
Rwork0.183 6936 -
all0.184 7292 -
obs--99.96 %
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)
12.3866-0.2246-1.54411.4373-0.13712.5437-0.13430.283-0.106-0.17870.0599-0.02640.1699-0.17630.0744-0.0327-0.03850.0231-0.0701-0.0292-0.0942-2.8348-5.6209-24.09
21.46530.26140.17171.95330.13781.194-0.05620.1599-0.0909-0.18090.06540.00530.05440.1479-0.0092-0.0153-0.0010.0085-0.0487-0.0108-0.078922.5019-5.619945.0712
32.5117-0.4817-1.74470-0.01858.2285-0.2281-0.2748-0.2660.133-0.0806-0.02440.70690.08330.3087-0.0255-0.02330.04010.00160.0102-0.13138.8999-9.305827.0182
42.0850.02970.54340.46740.02681.14280.02570.11560.1843-0.00490.05790.194-0.0991-0.1032-0.0836-0.01880.0180.0045-0.06820.0509-0.01448.65418.603250.952
53.27990.3844-1.8053.0718-0.78155.0752-0.22120.2214-0.2772-0.522-0.1111-0.29720.56320.08960.3323-0.03210.03580.07550.01150.0055-0.1424-20.5702-14.474225.5417
61.2568-0.24620.08151.9371-0.35410.97970.0162-0.07450.04250.2357-0.00660.027-0.034-0.1082-0.00950.00050.00340.0077-0.06960.0083-0.0488-5.4779-8.27287.3691
70.97860.25240.04480.3794-0.11030.62240.0346-0.0484-0.00330.08360.0376-0.1074-0.11480.0335-0.07220.03320.008-0.0045-0.0855-0.027-0.01856.46696.85280.109
81.586-0.2507-0.1461.7927-0.05611.95290.0491-0.0849-0.1198-0.1052-0.11630.00510.20550.16270.0672-0.03950.03160.0216-0.03050.0157-0.077539.1159-11.5857-4.1818
92.4214-0.64250.65410.6366-0.11531.37030.0307-0.05410.14150.0176-0.0390.0388-0.12680.10030.0083-0.0186-0.02510.0041-0.0468-0.0136-0.059130.00275.14683.6635
101.8902-0.0460.25981.6740.49781.36230.02370.1509-0.13970.2384-0.0035-0.03220.1840.0867-0.0202-0.0050.0170.0057-0.0591-0.0247-0.0729-19.7639-14.915857.3771
112.12370.68650.32150.720.10110.6852-0.00140.24490.22190.02850.0362-0.0125-0.0460.0233-0.0348-0.03190.0127-0.0078-0.0080.0485-0.0468-14.09262.593348.1233
122.2963-0.3206-0.97371.3532-1.41662.416-0.0457-0.2946-0.02930.06340.00490.0437-0.08570.07640.0408-0.02560.00170.0103-0.0323-0.0066-0.086320.18760.413876.1952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ N|* }
2X-RAY DIFFRACTION2{ A|* }
3X-RAY DIFFRACTION3{ O|* }
4X-RAY DIFFRACTION4{ B|* }
5X-RAY DIFFRACTION5{ P|* }
6X-RAY DIFFRACTION6{ C|* }
7X-RAY DIFFRACTION7{ D|* }
8X-RAY DIFFRACTION8{ E|* }
9X-RAY DIFFRACTION9{ F|* }
10X-RAY DIFFRACTION10{ G|* }
11X-RAY DIFFRACTION11{ H|* }
12X-RAY DIFFRACTION12{ M|* }

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