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- PDB-6pog: Crystal structure of the NELL2 EGF1-6-Robo3 FN1 complex -

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Basic information

Entry
Database: PDB / ID: 6pog
TitleCrystal structure of the NELL2 EGF1-6-Robo3 FN1 complex
Components
  • Protein kinase C-binding protein NELL2
  • Roundabout homolog 3
KeywordsSIGNALING PROTEIN / Axon guidance / Nervous system / Heterodimeric complex / Glycoprotein
Function / homology
Function and homology information


dendrite self-avoidance / ROBO receptors bind AKAP5 / cell-cell adhesion mediator activity / Regulation of commissural axon pathfinding by SLIT and ROBO / commissural neuron axon guidance / fertilization / axon midline choice point recognition / positive regulation of axon guidance / homophilic cell adhesion via plasma membrane adhesion molecules / axon guidance ...dendrite self-avoidance / ROBO receptors bind AKAP5 / cell-cell adhesion mediator activity / Regulation of commissural axon pathfinding by SLIT and ROBO / commissural neuron axon guidance / fertilization / axon midline choice point recognition / positive regulation of axon guidance / homophilic cell adhesion via plasma membrane adhesion molecules / axon guidance / protein kinase C binding / Regulation of expression of SLITs and ROBOs / neuron cellular homeostasis / chemotaxis / heparin binding / axon / calcium ion binding / extracellular space / extracellular region / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / EGF domain / : / Thrombospondin N-terminal -like domains. / EGF domain / Laminin G domain / von Willebrand factor (vWF) type C domain / von Willebrand factor type C domain / Laminin G domain / Laminin G domain ...: / EGF domain / : / Thrombospondin N-terminal -like domains. / EGF domain / Laminin G domain / von Willebrand factor (vWF) type C domain / von Willebrand factor type C domain / Laminin G domain / Laminin G domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / : / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / Immunoglobulin domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / EGF-like 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 / Concanavalin A-like lectin/glucanase domain superfamily / 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 3 / Protein kinase C-binding protein NELL2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.755 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 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Roundabout homolog 3
B: Protein kinase C-binding protein NELL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5437
Polymers39,6312
Non-polymers9125
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint1 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.873, 90.439, 171.576
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 3 / Roundabout-like protein 3


Mass: 12145.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal end of construct created by non-specific proteolysis. C-terminal end not certain
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: Protein Protein kinase C-binding protein NELL2 / NEL-like protein 2 / Nel-related protein 2


Mass: 27485.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NELL2, NRP2 / Cell line (production host): High Five Cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q99435
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
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: 4.43 Å3/Da / Density % sol: 72.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 17% PEG 3,350, 0.4 M NaSCN

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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 7, 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: 2.755→50 Å / Num. obs: 17564 / % possible obs: 99.4 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.116 / Net I/σ(I): 10.53
Reflection shellResolution: 2.755→2.92 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.599 / Mean I/σ(I) obs: 0.81 / Num. unique obs: 2703 / CC1/2: 0.43 / Rrim(I) all: 1.736 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(dev_3374: ???)refinement
XDS20170601data reduction
XDS20170601data scaling
AutoSolphasing
PHASER2.8.0phasing
RefinementMethod to determine structure: SAD / Resolution: 2.755→48.338 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / Phase error: 31.43
RfactorNum. reflection% reflectionSelection details
Rfree0.2637 1315 7.52 %Random selection
Rwork0.2368 ---
obs0.2388 17498 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.755→48.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 55 0 2447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032493
X-RAY DIFFRACTIONf_angle_d0.5943403
X-RAY DIFFRACTIONf_dihedral_angle_d11.1921516
X-RAY DIFFRACTIONf_chiral_restr0.041390
X-RAY DIFFRACTIONf_plane_restr0.004456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.755-2.86530.361370.35271682X-RAY DIFFRACTION95
2.8653-2.99570.38321460.34211794X-RAY DIFFRACTION100
2.9957-3.15360.34991420.30311756X-RAY DIFFRACTION100
3.1536-3.35110.34071420.25671769X-RAY DIFFRACTION100
3.3511-3.60980.29461460.24351806X-RAY DIFFRACTION100
3.6098-3.97290.24281450.23671779X-RAY DIFFRACTION100
3.9729-4.54750.25021490.19931819X-RAY DIFFRACTION100
4.5475-5.72780.20131480.20241831X-RAY DIFFRACTION100
5.7278-48.34510.26821600.24711947X-RAY DIFFRACTION100
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)
12.0451-0.4645-1.15035.2074.95564.90350.3356-0.2506-1.37850.31240.1526-1.73581.21770.1014-0.06090.5673-0.07090.05840.85070.02320.8621-8.041120.6173-22.9391
26.79655.1825-7.22826.0274-6.30878.01280.10751.34420.5494-1.24880.56412.19910.3378-4.5470.3610.8181-0.0596-0.41471.7017-0.5871.4185-18.320320.595-40.9437
39.56961.0445-5.05234.6271-1.98973.06080.38990.7715-0.2911-0.51880.31450.81690.65-1.08-0.86720.5729-0.1056-0.14120.5711-0.01510.921-14.281722.5483-31.3316
48.3954-4.0189-7.08595.73086.24017.2392-0.1374-0.2424-1.0075-0.7949-0.5690.9033-1.51211.30071.33760.52830.0928-0.21370.7933-0.26530.6797-7.571426.3856-30.3404
59.0119-4.7143-0.22793.94184.0558.2802-0.20520.55090.38920.25970.3492-0.5127-0.40150.1267-0.15640.4993-0.0853-0.00410.91370.00110.5751-5.173526.2772-36.5631
67.44280.45691.26388.70053.42548.62510.50021.4886-0.548-1.2480.01540.7456-0.0663-0.5562-0.63820.58010.0023-0.06820.79-0.07110.6702-8.949424.295-39.6637
77.03793.71356.85537.72165.79517.47350.5402-1.1629-1.17243.95380.9584-1.53052.0869-1.1066-1.29180.4157-0.0572-0.27211.14250.05831.1179-4.033222.7336-23.5707
81.988-2.40417.35726.779-1.14395.0299-0.08331.5933-0.6685-2.5852-0.43791.49242.5578-1.5683-0.30871.0335-0.0193-0.2721.6809-0.29110.839-12.222618.2067-49.0041
93.6953-5.8436-0.54569.46661.84795.3049-1.0484-1.84253.0621-0.69240.496-0.3015-1.2853-0.81440.50381.567-0.0065-0.44561.6651-0.05842.2551-10.780552.3407-22.8011
108.27832.30681.70447.25144.88286.51430.08480.3052-1.03750.45040.7584-0.91740.65371.1896-0.90960.50630.0313-0.07680.80620.01180.72865.962321.137-31.6599
117.12113.9495.89779.48886.94419.58490.4640.7953-1.0943-0.42680.6246-0.96590.57590.541-1.15590.59190.04670.05340.9311-0.1080.8669-22.5117-20.5232-70.6462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 553 through 562 )
2X-RAY DIFFRACTION2chain 'A' and (resid 563 through 567 )
3X-RAY DIFFRACTION3chain 'A' and (resid 568 through 585 )
4X-RAY DIFFRACTION4chain 'A' and (resid 586 through 594 )
5X-RAY DIFFRACTION5chain 'A' and (resid 595 through 612 )
6X-RAY DIFFRACTION6chain 'A' and (resid 613 through 633 )
7X-RAY DIFFRACTION7chain 'A' and (resid 634 through 643 )
8X-RAY DIFFRACTION8chain 'A' and (resid 644 through 653 )
9X-RAY DIFFRACTION9chain 'B' and (resid 399 through 440 )
10X-RAY DIFFRACTION10chain 'B' and (resid 441 through 510 )
11X-RAY DIFFRACTION11chain 'B' and (resid 511 through 642 )

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