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- PDB-6a78: Crystal structure of the fifth immunoglobulin domain (Ig5) of hum... -

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Basic information

Entry
Database: PDB / ID: 6a78
TitleCrystal structure of the fifth immunoglobulin domain (Ig5) of human Robo1 in complex with the scFv fragment of murine monoclonal antibody B5209B
Components
  • Heavy chain and linker region of the anti-human Robo1 antibody B5209B scFv
  • Light chain region of the anti-human Robo1 antibody B5209B scFv
  • Roundabout homolog 1
KeywordsIMMUNE SYSTEM / hepatocellular carcinoma antigen / angiogenesis / antibody drug / single chain Fv fragment
Function / homology
Function and homology information


chemorepulsion involved in postnatal olfactory bulb interneuron migration / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of mammary gland epithelial cell proliferation / LRR domain binding / negative regulation of chemokine-mediated signaling pathway / heart induction / axon guidance receptor activity / Netrin-1 signaling / Regulation of commissural axon pathfinding by SLIT and ROBO ...chemorepulsion involved in postnatal olfactory bulb interneuron migration / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of mammary gland epithelial cell proliferation / LRR domain binding / negative regulation of chemokine-mediated signaling pathway / heart induction / axon guidance receptor activity / Netrin-1 signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / Role of ABL in ROBO-SLIT signaling / Inactivation of CDC42 and RAC1 / SLIT2:ROBO1 increases RHOA activity / Roundabout signaling pathway / endocardial cushion formation / Signaling by ROBO receptors / pulmonary valve morphogenesis / outflow tract septum morphogenesis / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of axonogenesis / Activation of RAC1 / cell migration involved in sprouting angiogenesis / aortic valve morphogenesis / axon midline choice point recognition / positive regulation of vascular endothelial growth factor receptor signaling pathway / aorta development / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / positive regulation of Rho protein signal transduction / homophilic cell adhesion via plasma membrane adhesion molecules / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of MAP kinase activity / negative regulation of cell migration / Regulation of expression of SLITs and ROBOs / nervous system development / cell adhesion / cilium / axon / negative regulation of gene expression / positive regulation of gene expression / cell surface / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Roundabout homologue 1 / : / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type ...Roundabout homologue 1 / : / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Roundabout homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMizohata, E. / Nakayama, T. / Kado, Y. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
FIRST Program (MDADD) Japan
CitationJournal: Structure / Year: 2019
Title: Affinity Improvement of a Cancer-Targeted Antibody through Alanine-Induced Adjustment of Antigen-Antibody Interface.
Authors: Yamashita, T. / Mizohata, E. / Nagatoishi, S. / Watanabe, T. / Nakakido, M. / Iwanari, H. / Mochizuki, Y. / Nakayama, T. / Kado, Y. / Yokota, Y. / Matsumura, H. / Kawamura, T. / Kodama, T. / ...Authors: Yamashita, T. / Mizohata, E. / Nagatoishi, S. / Watanabe, T. / Nakakido, M. / Iwanari, H. / Mochizuki, Y. / Nakayama, T. / Kado, Y. / Yokota, Y. / Matsumura, H. / Kawamura, T. / Kodama, T. / Hamakubo, T. / Inoue, T. / Fujitani, H. / Tsumoto, K.
History
DepositionJul 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Oct 16, 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
A: Roundabout homolog 1
L: Light chain region of the anti-human Robo1 antibody B5209B scFv
H: Heavy chain and linker region of the anti-human Robo1 antibody B5209B scFv
B: Roundabout homolog 1
M: Light chain region of the anti-human Robo1 antibody B5209B scFv
I: Heavy chain and linker region of the anti-human Robo1 antibody B5209B scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4938
Polymers72,3016
Non-polymers1922
Water5,819323
1
A: Roundabout homolog 1
L: Light chain region of the anti-human Robo1 antibody B5209B scFv
H: Heavy chain and linker region of the anti-human Robo1 antibody B5209B scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2464
Polymers36,1503
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-36 kcal/mol
Surface area14220 Å2
MethodPISA
2
B: Roundabout homolog 1
M: Light chain region of the anti-human Robo1 antibody B5209B scFv
I: Heavy chain and linker region of the anti-human Robo1 antibody B5209B scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2464
Polymers36,1503
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-34 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.690, 149.943, 66.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11L-311-

HOH

21M-318-

HOH

31M-326-

HOH

41M-356-

HOH

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Components

#1: Protein Roundabout homolog 1 / Deleted in U twenty twenty / H-Robo-1


Mass: 9776.106 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROBO1, DUTT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6N7
#2: Antibody Light chain region of the anti-human Robo1 antibody B5209B scFv


Mass: 11999.374 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody Heavy chain and linker region of the anti-human Robo1 antibody B5209B scFv


Mass: 14374.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 85mM Tris-HCl (pH 8.5), 27.5% (w/v) PEG 4000, 170mM lithium sulfate monohydrate, 670mM sodium thiocyanate, 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 39986 / % possible obs: 95.1 % / Redundancy: 3.8 % / Net I/σ(I): 11.9
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.612 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.23 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28476 1979 5 %RANDOM
Rwork0.2388 ---
obs0.24104 37871 95.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.513 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---0.87 Å20 Å2
3---1.45 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4869 0 10 323 5202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.025047
X-RAY DIFFRACTIONr_bond_other_d0.0020.024598
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.9596864
X-RAY DIFFRACTIONr_angle_other_deg1.0573.00110685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.935.015652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06323.713202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88715825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1111532
X-RAY DIFFRACTIONr_chiral_restr0.1070.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025613
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021027
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0952.542580
X-RAY DIFFRACTIONr_mcbond_other2.0892.5392579
X-RAY DIFFRACTIONr_mcangle_it3.3063.7933221
X-RAY DIFFRACTIONr_mcangle_other3.3063.7953222
X-RAY DIFFRACTIONr_scbond_it2.692.7812467
X-RAY DIFFRACTIONr_scbond_other2.6912.7722459
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2354.053626
X-RAY DIFFRACTIONr_long_range_B_refined6.91147.8520469
X-RAY DIFFRACTIONr_long_range_B_other6.86847.83120356
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 157 -
Rwork0.374 2722 -
obs--94.64 %

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