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- PDB-6ba5: Potent and Selective Antitumor Activity of a T-Cell Engaging Bisp... -

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Basic information

Entry
Database: PDB / ID: 6ba5
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 Heavy chain, antibody R11
  • Variable domain of Light Chain, antibody R11
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 / stress fiber / coreceptor activity / axon terminus / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway ...WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt receptor activity / Wnt-protein binding / astrocyte development / inner ear development / stress fiber / coreceptor activity / axon terminus / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / sensory perception of sound / positive regulation of NF-kappaB transcription factor activity / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / cell population proliferation / receptor complex / axon / 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. / 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 / Immunoglobulins / Protein kinase-like domain superfamily / Beta Barrel / Immunoglobulin-like / 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 / MOLECULAR REPLACEMENT / Resolution: 1.62 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: 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. / Park, H. / Rader, C.
History
DepositionOct 12, 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
Revision 1.3Apr 3, 2024Group: 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Variable domain of Light Chain, antibody R11
B: Variable domain Heavy chain, antibody R11
C: Variable domain of Light Chain, antibody R11
D: Variable domain Heavy chain, antibody R11
E: Variable domain of Light Chain, antibody R11
F: Variable domain Heavy chain, antibody R11
G: Variable domain of Light Chain, antibody R11
H: Variable domain Heavy chain, antibody R11
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
Water24,5721364
1
A: Variable domain of Light Chain, antibody R11
B: Variable domain Heavy chain, antibody R11
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 Light Chain, antibody R11
D: Variable domain Heavy chain, antibody R11
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 Light Chain, antibody R11
F: Variable domain Heavy chain, antibody R11
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 Light Chain, antibody R11
H: Variable domain Heavy chain, antibody R11
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)58.020, 73.900, 84.120
Angle α, β, γ (deg.)89.86, 71.30, 84.49
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
Variable domain of Light Chain, antibody R11


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: Antibody
Variable domain Heavy chain, antibody R11


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


Mass: 18.015 Da / Num. of mol.: 1364 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growMethod: 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 / Details: single crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.62→54.85 Å / Num. obs: 160894 / % possible obs: 96.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.44 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.054 / Rrim(I) all: 0.103 / Net I/σ(I): 8.5
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7849 / CC1/2: 0.717 / Rpim(I) all: 0.321 / Rrim(I) all: 0.595 / % possible all: 94.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Antibody R11

Resolution: 1.62→39.53 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.928 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.093 / SU Rfree Cruickshank DPI: 0.09
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3234 2.01 %RANDOM
Rwork0.194 ---
obs0.194 160881 96.1 %-
Displacement parametersBiso mean: 22.08 Å2
Baniso -1Baniso -2Baniso -3
1--3.9425 Å2-0.3664 Å21.7603 Å2
2--1.717 Å20.0895 Å2
3---2.2254 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.62→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9266 0 0 1364 10630
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019496HARMONIC2
X-RAY DIFFRACTIONt_angle_deg112936HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3066SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes196HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1407HARMONIC5
X-RAY DIFFRACTIONt_it9496HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.73
X-RAY DIFFRACTIONt_other_torsion14.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1273SEMIHARMONIC5
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_contact11721SEMIHARMONIC4
LS refinement shellResolution: 1.62→1.66 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 240 2.04 %
Rwork0.204 11498 -
all0.205 11738 -
obs--94.73 %
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)
15.31020.3729-1.7822.9222-0.92232.93030.1215-0.56020.0970.314-0.02470.4493-0.2029-0.2182-0.0967-0.07620.00230.035-0.0234-0.0408-0.1014-2.634343.040851.9833
20.916-0.21690.76580.6484-0.26221.78980.01640.04540.064-0.0163-0.0536-0.0667-0.02320.13340.0372-0.0208-0.0101-0.0055-0.00790.0104-0.041710.55163.21025.2799
39.32350.41391.2292.24130.88452.65390.0008-0.0997-0.21090.1950.1366-0.42170.33650.5832-0.1374-0.14540.0781-0.0599-0.00590.0204-0.079136.4204-9.015538.1965
40.410.11470.19250.93110.24450.77310.03840.03120.0115-0.0019-0.0271-0.0430.0824-0.026-0.0113-0.0026-0.0007-0.0095-0.0027-0.0021-0.0554-4.0125-5.4689-6.7671
55.21380.3296-0.06332.9277-0.25351.6648-0.1007-0.3552-0.3085-0.1142-0.1509-0.51020.25170.64290.2516-0.11210.1385-0.00090.08760.1099-0.117926.527529.4885-2.5905
61.0206-0.00381.00290.73970.14592.0508-0.05220.13160.0061-0.03150.038-0.0434-0.0910.25310.0142-0.013-0.0264-0.0175-0.00950.0015-0.066327.300339.401243.6973
70.5894-0.07840.24340.79030.24980.7413-0.03260.03840.02210.02930.0101-0.0392-0.01950.02010.02250.0001-0.014-0.0096-0.00510-0.056213.188929.411432.08
80.5307-0.10090.32410.57330.23211.8493-0.0179-0.0307-0.03550.033-0.01840.0363-0.0119-0.14120.0363-0.0107-0.0154-0.0127-0.00750.0012-0.04627.74-4.510750.2155
90.3745-0.1313-0.03581.1534-0.170.6716-0.01780.03380.00560.0693-0.0191-0.0052-0.0315-0.0160.0369-0.0279-0.0082-0.02160.00790.0044-0.040912.29275.221932.5084
100.4873-0.05270.32880.6778-0.27552.13470.0144-0.0452-0.0128-0.0722-0.00670.07980.0702-0.204-0.00780.0099-0.0009-0.0354-0.03380.005-0.0561-2.444632.93338.9587
110.4181-0.0743-0.1560.7731-0.14651.0513-0.04820.01110.01550.06820.040.0280.0474-0.01560.00830.0060.0055-0.0387-0.01770.0078-0.05551.962443.8616-8.0683
124.05970.4028-2.89570.9855-1.11955.52010.0537-0.23840.12180.05280.07610.1814-0.1009-0.4734-0.1298-0.1147-0.00350.02270.0245-0.0245-0.1045-19.52028.081913.4731
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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