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- PDB-6iaa: hRobo2 ectodomain -

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Basic information

Entry
Database: PDB / ID: 6iaa
TitlehRobo2 ectodomain
ComponentsRoundabout homolog 2
KeywordsSIGNALING PROTEIN / Slit / Robo / Axon Guidance / Cell Surface Receptor
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 / ROBO receptors bind AKAP5 / Formation of the ureteric bud / axon guidance receptor activity / 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 / ROBO receptors bind AKAP5 / Formation of the ureteric bud / axon guidance receptor activity / Regulation of commissural axon pathfinding by SLIT and ROBO / endocardial cushion formation / Signaling by ROBO receptors / pulmonary valve morphogenesis / outflow tract septum morphogenesis / metanephros development / aortic valve morphogenesis / axon midline choice point recognition / aorta development / ureteric bud development / positive regulation of axonogenesis / retinal ganglion cell axon guidance / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / axolemma / cellular response to hormone stimulus / central nervous system development / axon guidance / brain development / Regulation of expression of SLITs and ROBOs / cell-cell adhesion / 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. / Fibronectin type III ...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
Similarity search - Domain/homology
Roundabout homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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 26, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
C: Roundabout homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,9259
Polymers287,9203
Non-polymers4,0066
Water00
1
A: Roundabout homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3083
Polymers95,9731
Non-polymers1,3352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Roundabout homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3083
Polymers95,9731
Non-polymers1,3352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Roundabout homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3083
Polymers95,9731
Non-polymers1,3352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)290.767, 81.569, 158.656
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A22 - 840
2010B22 - 840
1020A22 - 840
2020C22 - 840
1030B22 - 840
2030C22 - 840

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Roundabout homolog 2


Mass: 95973.234 Da / Num. of mol.: 3
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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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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: 3.28 Å3/Da / Density % sol: 62.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: protein concentrated to 13.5 mg/ml and precipitant mixture containing 10% PEG 8000, 0.1M HEPES pH 7 - 7.125, 9.5% Ethylene glycol and 2% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.6→78.65 Å / Num. obs: 43176 / % possible obs: 99.5 % / Redundancy: 3.93 % / Biso Wilson estimate: 110.8 Å2 / Net I/σ(I): 6.6
Reflection shellResolution: 3.6→3.74 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4487 / CC1/2: 0.7 / Rrim(I) all: 0.161 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→78.65 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.87 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28676 1909 5.2 %RANDOM
Rwork0.22238 ---
obs0.22571 35116 85.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-1.79 Å2
2--1.45 Å20 Å2
3----0.72 Å2
Refinement stepCycle: 1 / Resolution: 3.6→78.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19029 0 267 0 19296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01219752
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.67926973
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28152439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00121.6371026
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.091153144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.47715168
X-RAY DIFFRACTIONr_chiral_restr0.0930.22730
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215120
X-RAY DIFFRACTIONr_gen_planes_other
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_it6.32611.3339774
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.34717.00612207
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.71711.8149978
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined17.81927339
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A235060.08
12B235060.08
21A235010.09
22C235010.09
31B234950.08
32C234950.08
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 53 -
Rwork0.31 1167 -
obs--38.29 %

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