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- PDB-6i9s: hRobo2 Extracellular Domains 2-3 -

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Basic information

Entry
Database: PDB / ID: 6i9s
TitlehRobo2 Extracellular Domains 2-3
ComponentsRoundabout homolog 2
KeywordsSIGNALING PROTEIN / Slit / Robo / Axon Guidance
Function / homology
Function and homology information


olfactory bulb interneuron development / apoptotic process involved in luteolysis / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of synapse assembly / heart induction / axon guidance receptor activity / ROBO receptors bind AKAP5 / Formation of the ureteric bud / Regulation of commissural axon pathfinding by SLIT and ROBO ...olfactory bulb interneuron development / apoptotic process involved in luteolysis / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of synapse assembly / heart induction / axon guidance receptor activity / ROBO receptors bind AKAP5 / Formation of the ureteric bud / Regulation of commissural axon pathfinding by SLIT and ROBO / endocardial cushion formation / Signaling by ROBO receptors / pulmonary valve morphogenesis / metanephros development / outflow tract septum morphogenesis / positive regulation of axonogenesis / retinal ganglion cell axon guidance / axon midline choice point recognition / aortic valve morphogenesis / ureteric bud development / aorta development / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / homophilic cell-cell adhesion / axolemma / cellular response to hormone stimulus / axon guidance / central nervous system development / cell-cell adhesion / brain development / Regulation of expression of SLITs and ROBOs / chemotaxis / cell surface / extracellular exosome / identical protein binding / 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 / Immunoglobulin V-Type / Fibronectin type-III domain profile. ...: / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsBarak, R. / Isupov, N.M. / Opatowsky, Y.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation182/10 and 1425/15 Israel
CitationJournal: Cell / Year: 2019
Title: Structural Principles in Robo Activation and Auto-inhibition.
Authors: Barak, R. / Yom-Tov, G. / Guez-Haddad, J. / Gasri-Plotnitsky, L. / Maimon, R. / Cohen-Berkman, M. / McCarthy, A.A. / Perlson, E. / Henis-Korenblit, S. / Isupov, M.N. / Opatowsky, Y.
History
DepositionNov 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev / database_PDB_rev_record
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Roundabout homolog 2
B: Roundabout homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8984
Polymers47,8522
Non-polymers462
Water1,22568
1
A: Roundabout homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9492
Polymers23,9261
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Roundabout homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9492
Polymers23,9261
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.220, 70.520, 97.280
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 2


Mass: 23926.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROBO2, KIAA1568 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9HCK4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium format pH 7 and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.48→46.66 Å / Num. obs: 15692 / % possible obs: 99.2 % / Redundancy: 4.6 % / Net I/σ(I): 13.5
Reflection shellResolution: 2.48→2.58 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1690 / CC1/2: 0.751 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→46.66 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.638 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R: 0.596 / ESU R Free: 0.334 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29292 793 5.1 %RANDOM
Rwork0.22581 ---
obs0.22925 14867 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 71.433 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å20 Å2
2---5.07 Å20 Å2
3---6.57 Å2
Refinement stepCycle: 1 / Resolution: 2.48→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 2 68 3024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0143016
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172701
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.6814066
X-RAY DIFFRACTIONr_angle_other_deg0.7951.6396386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.275369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52920.989182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.52315553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7861535
X-RAY DIFFRACTIONr_chiral_restr0.0680.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
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_it5.436.8951482
X-RAY DIFFRACTIONr_mcbond_other5.436.8891481
X-RAY DIFFRACTIONr_mcangle_it8.08310.331849
X-RAY DIFFRACTIONr_mcangle_other8.08110.3371850
X-RAY DIFFRACTIONr_scbond_it6.5557.7121534
X-RAY DIFFRACTIONr_scbond_other6.5547.7181533
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.24211.2452218
X-RAY DIFFRACTIONr_long_range_B_refined13.05277.7662980
X-RAY DIFFRACTIONr_long_range_B_other13.0577.8212979
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.476→2.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 58 -
Rwork0.361 1054 -
obs--96.95 %

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