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- PDB-4bqc: Crystal structure of the FN5 and FN6 domains of NEO1 bound to SOS -

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Basic information

Entry
Database: PDB / ID: 4bqc
TitleCrystal structure of the FN5 and FN6 domains of NEO1 bound to SOS
ComponentsNEOGENIN
KeywordsCELL ADHESION
Function / homology
Function and homology information


trans-synaptic signaling, modulating synaptic transmission / negative regulation of axon regeneration / co-receptor binding / BMP receptor binding / regulation of axon regeneration / plasma membrane protein complex / myoblast fusion / positive regulation of BMP signaling pathway / intracellular vesicle / negative regulation of protein secretion ...trans-synaptic signaling, modulating synaptic transmission / negative regulation of axon regeneration / co-receptor binding / BMP receptor binding / regulation of axon regeneration / plasma membrane protein complex / myoblast fusion / positive regulation of BMP signaling pathway / intracellular vesicle / negative regulation of protein secretion / protein secretion / axonal growth cone / axon guidance / postsynaptic density membrane / neuron migration / cell-cell adhesion / multicellular organismal-level iron ion homeostasis / signaling receptor activity / growth cone / intracellular iron ion homeostasis / cadherin binding / neuronal cell body / glutamatergic synapse / regulation of DNA-templated transcription / Golgi apparatus / cell surface / nucleoplasm / membrane / plasma membrane
Similarity search - Function
Neogenin, C-terminal / Neogenin C-terminus / 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. ...Neogenin, C-terminal / Neogenin C-terminus / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
sucrose octasulfate / Neogenin
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBell, C.H. / Healey, E. / vanErp, S. / Bishop, B. / Tang, C. / Gilbert, R.J.C. / Aricescu, A.R. / Pasterkamp, R.J. / Siebold, C.
CitationJournal: Science / Year: 2013
Title: Structure of the Repulsive Guidance Molecule (Rgm)-Neogenin Signaling Hub
Authors: Bell, C.H. / Healey, E. / Van Erp, S. / Bishop, B. / Tang, C. / Gilbert, R.J.C. / Aricescu, A.R. / Pasterkamp, R.J. / Siebold, C.
History
DepositionMay 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_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: NEOGENIN
B: NEOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6767
Polymers58,4442
Non-polymers2,2335
Water00
1
A: NEOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4494
Polymers29,2221
Non-polymers1,2273
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NEOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2283
Polymers29,2221
Non-polymers1,0062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.160, 157.840, 89.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9995, -0.004987, 0.03074), (0.005047, -1, 0.00189), (0.03073, 0.002044, 0.9995)
Vector: 95.05, 38.7, -1.498)

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Components

#1: Protein NEOGENIN


Mass: 29221.842 Da / Num. of mol.: 2 / Fragment: FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133
Source method: isolated from a genetically manipulated source
Details: N-LINKED GLYCOSYLATION AT N940 / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P97798
#2: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / sucrose octasulfate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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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: 2.92 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.15 M POTASSIUM NITRATE, 15% PEG3350, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 11572 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 69.67 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.3
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.9 / % possible all: 98.6

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.9084 / Cor.coef. Fo:Fc free: 0.889 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.419
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 554 4.8 %RANDOM
Rwork0.2172 ---
obs0.2191 11548 99.47 %-
Displacement parametersBiso mean: 102.93 Å2
Baniso -1Baniso -2Baniso -3
1--18.0013 Å20 Å20 Å2
2--31.7515 Å20 Å2
3----13.7503 Å2
Refine analyzeLuzzati coordinate error obs: 0.775 Å
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 126 0 3079
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013160HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.194353HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1044SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes432HARMONIC5
X-RAY DIFFRACTIONt_it3160HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion19.11
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion448SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3479SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.5 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2744 141 5.25 %
Rwork0.2417 2545 -
all0.2434 2686 -
obs--99.47 %
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)
14.29633.2756-0.26953.4924-0.50293.89930.1418-0.2883-0.84140.0162-0.1223-0.22850.6609-0.4349-0.0194-0.0044-0.13990.0132-0.09910.0622-0.03345.5237-7.99589.0397
26.93435.4311.1858.23070.54254.72260.0776-0.21540.1686-0.4323-0.3559-0.5586-0.88840.55870.27830.0506-0.23410.0478-0.15470.0375-0.100467.208930.311213.9546
301.5152-2.84529.7085-0.27462.35320.15350.26791.4868-0.81190.1461-0.2312-0.87220.1314-0.29960.1223-0.0117-0.1168-0.35010.14760.379147.486543.16489.0359
47.05393.7486-1.897410.1916-2.54476.7233-0.3533-0.2487-0.6595-0.3935-0.15451.33461.0532-0.9430.5078-0.1922-0.12160.1415-0.0969-0.1703-0.068528.34158.621114.5913
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|881 - A|982 }
2X-RAY DIFFRACTION2{ A|983 - A|1083 }
3X-RAY DIFFRACTION3{ B|887 - B|982 }
4X-RAY DIFFRACTION4{ B|983 - B|1083 }

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