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- PDB-6ffy: Structure of the mouse SorCS2-NGF complex -

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Basic information

Entry
Database: PDB / ID: 6ffy
TitleStructure of the mouse SorCS2-NGF complex
Components
  • Beta-nerve growth factor
  • VPS10 domain-containing receptor SorCS2
KeywordsAPOPTOSIS / SorCS2 / proNGF / p75NTR / VPS10 / Sortilin / neuroplasticity
Function / homology
Function and homology information


TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / Axonal growth stimulation / Frs2-mediated activation / positive regulation of neurotrophin TRK receptor signaling pathway / PI3K/AKT activation / ARMS-mediated activation / NRIF signals cell death from the nucleus ...TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / Axonal growth stimulation / Frs2-mediated activation / positive regulation of neurotrophin TRK receptor signaling pathway / PI3K/AKT activation / ARMS-mediated activation / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / Retrograde neurotrophin signalling / NF-kB is activated and signals survival / metalloendopeptidase inhibitor activity / positive regulation of neuron maturation / nerve growth factor signaling pathway / regulation of neurotransmitter secretion / positive regulation of collateral sprouting / peripheral nervous system development / transmembrane receptor protein tyrosine kinase activator activity / regulation of release of sequestered calcium ion into cytosol / axon extension / positive regulation of Ras protein signal transduction / long-term synaptic depression / regulation of neuron differentiation / positive regulation of DNA binding / neurotrophin TRK receptor signaling pathway / positive regulation of axon extension / extrinsic apoptotic signaling pathway in absence of ligand / sensory perception of pain / neuron projection morphogenesis / positive regulation of protein ubiquitination / endosome lumen / intracellular protein transport / growth factor activity / postsynaptic density membrane / positive regulation of neuron projection development / recycling endosome membrane / circadian rhythm / neuron projection development / early endosome membrane / neuron apoptotic process / dendritic spine / perikaryon / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / postsynaptic density / endoplasmic reticulum lumen / lipid binding / positive regulation of gene expression / extracellular space / extracellular region / plasma membrane / cytosol
Similarity search - Function
Nerve growth factor, beta subunit, mammalian / Nerve growth factor, beta subunit / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor family profile. / Nerve growth factor (NGF or beta-NGF) / VPS10 ...Nerve growth factor, beta subunit, mammalian / Nerve growth factor, beta subunit / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor family profile. / Nerve growth factor (NGF or beta-NGF) / VPS10 / Sortilin, C-terminal / Sortilin, N-terminal / : / Sortilin, neurotensin receptor 3, C-terminal / Sortilin, neurotensin receptor 3, / VPS10 / PKD domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Beta-nerve growth factor / VPS10 domain-containing receptor SorCS2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsLeloup, N.O.L. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
ManiFold Marie Curie FP7317371 Netherlands
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights into SorCS2-Nerve Growth Factor complex formation.
Authors: Leloup, N. / Chataigner, L.M.P. / Janssen, B.J.C.
History
DepositionJan 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_validate_close_contact / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VPS10 domain-containing receptor SorCS2
B: Beta-nerve growth factor
C: Beta-nerve growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,0887
Polymers137,8383
Non-polymers1,2504
Water00
1
A: VPS10 domain-containing receptor SorCS2
B: Beta-nerve growth factor
C: Beta-nerve growth factor
hetero molecules

A: VPS10 domain-containing receptor SorCS2
B: Beta-nerve growth factor
C: Beta-nerve growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,17514
Polymers275,6756
Non-polymers2,5008
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area18930 Å2
ΔGint-53 kcal/mol
Surface area111810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.755, 117.706, 90.000
Angle α, β, γ (deg.)90.00, 111.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein VPS10 domain-containing receptor SorCS2


Mass: 109115.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sorcs2 / Production host: Homo sapiens (human) / References: UniProt: Q9EPR5
#2: Protein Beta-nerve growth factor / Beta-NGF


Mass: 14361.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngf, Ngfb / Production host: Homo sapiens (human) / References: UniProt: P01139
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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.: 3
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
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: 3.84 Å3/Da / Density % sol: 67.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 0.225 M MES/bis-tris pH 6.6 and 6.6 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 3.6→61 Å / Num. obs: 25900 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.34 / Net I/σ(I): 4.8
Reflection shellResolution: 3.6→3.85 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4621 / CC1/2: 0.178 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EAX,4MSL,1WGO,4AQO

4eax

4msl

1wgo

4aqo


Resolution: 3.9→60.841 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.305 1045 5.12 %
Rwork0.2583 --
obs0.2607 20399 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.9→60.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9030 0 81 0 9111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039329
X-RAY DIFFRACTIONf_angle_d0.61212699
X-RAY DIFFRACTIONf_dihedral_angle_d9.015558
X-RAY DIFFRACTIONf_chiral_restr0.0471462
X-RAY DIFFRACTIONf_plane_restr0.0051608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.10560.35461480.33462722X-RAY DIFFRACTION100
4.1056-4.36270.37511620.29452745X-RAY DIFFRACTION100
4.3627-4.69950.27681560.25962737X-RAY DIFFRACTION100
4.6995-5.17220.30441400.24862769X-RAY DIFFRACTION100
5.1722-5.92010.30081380.26662785X-RAY DIFFRACTION100
5.9201-7.45650.31521410.27492775X-RAY DIFFRACTION100
7.4565-60.84880.27781600.21872821X-RAY DIFFRACTION100

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