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- PDB-4hlj: Axon Guidance Receptor -

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Basic information

Entry
Database: PDB / ID: 4hlj
TitleAxon Guidance Receptor
ComponentsRoundabout homolog 1
KeywordsCELL ADHESION
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 / 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 / heart induction / axon guidance receptor activity / positive regulation of vascular endothelial growth factor signaling pathway / Netrin-1 signaling / Role of ABL in ROBO-SLIT signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / SLIT2:ROBO1 increases RHOA activity / Roundabout signaling pathway / Inactivation of CDC42 and RAC1 / endocardial cushion formation / Signaling by ROBO receptors / pulmonary valve morphogenesis / outflow tract septum morphogenesis / aortic valve morphogenesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / cell migration involved in sprouting angiogenesis / axon midline choice point recognition / Activation of RAC1 / aorta development / positive regulation of axonogenesis / positive regulation of Rho protein signal transduction / 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 / synapse organization / 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 / neuronal cell body / 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 / SAD-molecular replacement / Resolution: 1.8 Å
AuthorsBarak, R. / Opatowsky, Y.
CitationJournal: To be Published
Title: Crystal Structure of Axon Guidance Receptor
Authors: Barak, R. / Opatowsky, Y.
History
DepositionOct 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Roundabout homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6042
Polymers26,3651
Non-polymers2381
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.700, 77.710, 91.900
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: Protein Roundabout homolog 1 / Deleted in U twenty twenty / H-Robo-1


Mass: 26365.334 Da / Num. of mol.: 1 / Fragment: Juxtamembrane domains, UNP RESIDUES 660-897 / Mutation: Q883R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUTT1, ROBO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6N7
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1.94 Å3/Da / Density % sol: 36.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 35% PEG 400, 0.1M Sodium acetate trihydrate, 5% glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97626 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2010
RadiationMonochromator: Band pass 1.9x10-4 for a Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.67→45.95 Å / Num. all: 24627 / Num. obs: 21364 / % possible obs: 86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.045
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.67-1.7186.6
1.7-1.73194.1
1.73-1.76197.5
1.76-1.8199.8
1.8-1.841100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD-molecular replacement / Resolution: 1.8→45.95 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 1555 8.26 %RANDOM
Rwork0.1844 ---
all0.1866 21364 --
obs0.1866 18822 95.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.253 Å2 / ksol: 0.394 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.505 Å20 Å20 Å2
2--0.0455 Å20 Å2
3---0.4595 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 16 213 1949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031849
X-RAY DIFFRACTIONf_angle_d0.772529
X-RAY DIFFRACTIONf_dihedral_angle_d13.422683
X-RAY DIFFRACTIONf_chiral_restr0.054277
X-RAY DIFFRACTIONf_plane_restr0.003337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.85810.24181110.2061114473
1.8581-1.92450.26611230.2003141786
1.9245-2.00160.24041330.1966153095
2.0016-2.09270.22181420.192157097
2.0927-2.2030.24961450.1911160798
2.203-2.3410.21651450.1856160198
2.341-2.52180.23151470.187161899
2.5218-2.77550.23731500.20431652100
2.7755-3.17710.21511470.18981664100
3.1771-4.00240.18341510.1651681100
4.0024-45.9650.17751610.1751783100
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)
10.1220.0766-0.26330.20490.17150.59190.00170.03280.06880.086-0.05520.03570.1437-0.1336-0.01210.0719-0.01790.00340.0969-0.00020.084511.9236-25.6222-37.4349
20.1446-0.0403-0.0370.09670.08930.1811-0.05780.01540.0663-0.36390.05210.1401-0.1256-0.01010.07240.2625-0.0594-0.0171-0.0161-0.04030.119411.7718-4.8401-0.4153
30.55310.15520.12511.1690.27030.4808-0.2078-0.1221-0.030.10280.0540.5067-0.246-0.1998-0.09540.06830.0319-0.01580.0905-0.06650.058512.2478-10.41016.5242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 660:782)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 783:805)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 806:885)

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