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- PDB-5o5i: Robo1 Ig5 -

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Basic information

Entry
Database: PDB / ID: 5o5i
TitleRobo1 Ig5
ComponentsRoundabout homolog 1
KeywordsSIGNALING PROTEIN / Neuronal receptor
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 / axon guidance receptor activity / heart induction / positive regulation of vascular endothelial growth factor signaling pathway / Netrin-1 signaling ...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 / axon guidance receptor activity / heart induction / positive regulation of vascular endothelial growth factor signaling pathway / 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 / aortic valve morphogenesis / cell migration involved in sprouting angiogenesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / Activation of RAC1 / axon midline choice point recognition / aorta development / positive regulation of Rho protein signal transduction / positive regulation of axonogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / endoplasmic reticulum-Golgi intermediate compartment membrane / negative regulation of cell migration / positive regulation of MAP kinase activity / Regulation of expression of SLITs and ROBOs / activation of cysteine-type endopeptidase activity involved in apoptotic process / nervous system development / cell adhesion / neuron projection / axon / negative regulation of gene expression / positive regulation of gene expression / cell surface / identical protein binding / plasma membrane / 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 / Fibronectin type-III domain profile. ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Roundabout homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsAleksandrova, N. / Gutsche, I. / Kandiah, E. / Avilov, S.V. / Petoukhov, M.V. / Seiradake, E. / McCarthy, A.A.
CitationJournal: Structure / Year: 2018
Title: Robo1 Forms a Compact Dimer-of-Dimers Assembly.
Authors: Aleksandrova, N. / Gutsche, I. / Kandiah, E. / Avilov, S.V. / Petoukhov, M.V. / Seiradake, E. / McCarthy, A.A.
History
DepositionJun 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all ..._reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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


Theoretical massNumber of molelcules
Total (without water)9,8131
Polymers9,8131
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.820, 80.820, 26.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 9813.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROBO1, DUTT1 / Plasmid: pTT3 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9Y6N7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 25% PEG 3350, 100 mM Sodium acetate,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2011 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 2082 / % possible obs: 98.3 % / Redundancy: 3 % / Biso Wilson estimate: 74.92 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.148 / Net I/σ(I): 7.3
Reflection shellResolution: 3→3.2 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1026 / CC1/2: 0.64 / Rpim(I) all: 0.798 / % possible all: 94.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDS2 November 2014data reduction
XSCALE2 November 2014data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v9q

2v9q


Resolution: 3.01→40.41 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.859 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.427
RfactorNum. reflection% reflectionSelection details
Rfree0.245 100 4.81 %RANDOM
Rwork0.193 ---
obs0.195 2081 99.2 %-
Displacement parametersBiso mean: 68.15 Å2
Baniso -1Baniso -2Baniso -3
1--2.1215 Å20 Å20 Å2
2---2.1215 Å20 Å2
3---4.2431 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 3.01→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms673 0 0 8 681
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.008716HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.13982HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d241SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes17HARMONIC2
X-RAY DIFFRACTIONt_gen_planes106HARMONIC5
X-RAY DIFFRACTIONt_it716HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.32
X-RAY DIFFRACTIONt_other_torsion18.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion100SEMIHARMONIC5
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_contact785SEMIHARMONIC4
LS refinement shellResolution: 3.01→3.37 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3198 -5.46 %
Rwork0.2326 554 -
all0.2378 586 -
obs--99.66 %
Refinement TLS params.Method: refined / Origin x: 27.1298 Å / Origin y: -28.4573 Å / Origin z: 6.1192 Å
111213212223313233
T-0.2587 Å2-0.1788 Å20.1951 Å2--0.0934 Å2-0.0983 Å2--0.0796 Å2
L7.6549 °20.5879 °20.6084 °2-14.8721 °2-3.5043 °2--6.075 °2
S0.431 Å °-0.3811 Å °-0.481 Å °0.194 Å °0.036 Å °0.4532 Å °-0.7193 Å °0.098 Å °-0.4671 Å °
Refinement TLS groupSelection details: { A|* }

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