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- PDB-6pok: Crystal structure of the Robo3 FN2-3 domains -

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Basic information

Entry
Database: PDB / ID: 6pok
TitleCrystal structure of the Robo3 FN2-3 domains
ComponentsRoundabout homolog 3
KeywordsSIGNALING PROTEIN / Axon guidance / Nervous system / Cell surface receptor / Fibronectin type III domains
Function / homology
Function and homology information


ROBO receptors bind AKAP5 / dendrite self-avoidance / Regulation of commissural axon pathfinding by SLIT and ROBO / cell-cell adhesion mediator activity / axon midline choice point recognition / positive regulation of axon guidance / homophilic cell adhesion via plasma membrane adhesion molecules / axon guidance / Regulation of expression of SLITs and ROBOs / chemotaxis ...ROBO receptors bind AKAP5 / dendrite self-avoidance / Regulation of commissural axon pathfinding by SLIT and ROBO / cell-cell adhesion mediator activity / axon midline choice point recognition / positive regulation of axon guidance / homophilic cell adhesion via plasma membrane adhesion molecules / axon guidance / Regulation of expression of SLITs and ROBOs / chemotaxis / axon / membrane / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Roundabout homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å
AuthorsWang, J. / Pak, J.S. / Ozkan, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS097161 United States
CitationJournal: Nat Commun / Year: 2020
Title: NELL2-Robo3 complex structure reveals mechanisms of receptor activation for axon guidance.
Authors: Pak, J.S. / DeLoughery, Z.J. / Wang, J. / Acharya, N. / Park, Y. / Jaworski, A. / Ozkan, E.
History
DepositionJul 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Roundabout homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5862
Polymers22,4941
Non-polymers921
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.986, 36.607, 64.896
Angle α, β, γ (deg.)90.00, 114.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Roundabout homolog 3 / Roundabout-like protein 3


Mass: 22494.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminus was proteolysed during crystallization. Exact N-terminus residue is unknown.
Source: (gene. exp.) Homo sapiens (human) / Gene: ROBO3 / Cell line (production host): High Five Cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96MS0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5, 12% PEG 6,000

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 6, 2017 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double Si(111) crystal, cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.796→55 Å / Num. obs: 21801 / % possible obs: 91.2 % / Redundancy: 1.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.092 / Net I/σ(I): 6.59
Reflection shellResolution: 1.796→1.91 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.86 / Num. unique obs: 5642 / CC1/2: 0.586 / Rrim(I) all: 1.207 / % possible all: 80.8

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3177: ???)refinement
XDS20170601data reduction
XDS20170601data scaling
MoRDa1.3.02, database v. 20phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HLJ

4hlj


Resolution: 1.796→50.06 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / Phase error: 31.74
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 1083 4.97 %Random selection
Rwork0.2173 ---
obs0.2185 21770 97.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.796→50.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 6 138 1585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021515
X-RAY DIFFRACTIONf_angle_d0.5312078
X-RAY DIFFRACTIONf_dihedral_angle_d9.728907
X-RAY DIFFRACTIONf_chiral_restr0.044239
X-RAY DIFFRACTIONf_plane_restr0.003274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7964-1.87810.41091260.42142341X-RAY DIFFRACTION90
1.8781-1.97720.33351310.33122587X-RAY DIFFRACTION98
1.9772-2.1010.29521350.27332586X-RAY DIFFRACTION99
2.101-2.26330.2741400.23432603X-RAY DIFFRACTION99
2.2633-2.4910.27551370.22152625X-RAY DIFFRACTION100
2.491-2.85150.27831350.22182627X-RAY DIFFRACTION99
2.8515-3.59240.20351400.19712616X-RAY DIFFRACTION98
3.5924-50.07920.20591390.18322702X-RAY DIFFRACTION98
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)
13.7644-0.84630.64913.38420.77672.7374-0.8073-2.0730.2561.05440.5455-0.349-0.3808-0.34690.30020.60250.258-0.07651.0069-0.03960.525515.093915.533118.5496
25.42441.63531.9392.49341.19581.9001-0.16590.3668-0.0844-0.3280.09690.125-0.09370.17680.06690.256-0.00170.04290.18610.01830.2763-21.56620.2204-3.6218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 668 through 762 )
2X-RAY DIFFRACTION2chain 'A' and (resid 763 through 866 )

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