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- PDB-5x83: Structure of DCC FN456 domains -

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Basic information

Entry
Database: PDB / ID: 5x83
TitleStructure of DCC FN456 domains
Components(Netrin receptor DCC) x 2
KeywordsSIGNALING PROTEIN / DCC / Netrin-1 / axon guidance
Function / homology
Function and homology information


dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / negative regulation of collateral sprouting / Role of second messengers in netrin-1 signaling / Netrin-1 signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / negative regulation of dendrite development / Netrin mediated repulsion signals / Caspase activation via Dependence Receptors in the absence of ligand ...dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / negative regulation of collateral sprouting / Role of second messengers in netrin-1 signaling / Netrin-1 signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / negative regulation of dendrite development / Netrin mediated repulsion signals / Caspase activation via Dependence Receptors in the absence of ligand / DCC mediated attractive signaling / DSCAM interactions / postsynaptic modulation of chemical synaptic transmission / axonal growth cone / axonogenesis / axon guidance / postsynaptic density membrane / neuron migration / Schaffer collateral - CA1 synapse / cell-cell adhesion / transmembrane signaling receptor activity / negative regulation of neuron projection development / apoptotic process / cell surface / plasma membrane / cytosol
Similarity search - Function
Neogenin, C-terminal / Neogenin C-terminus / 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 ...Neogenin, C-terminal / Neogenin C-terminus / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.997 Å
AuthorsFinci, F.I. / Xiao, J. / Wang, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation of China (NSFC)81425009 China
NIH grantHL48675 China
CitationJournal: Protein Cell / Year: 2017
Title: Structure of unliganded membrane-proximal domains FN4-FN5-FN6 of DCC
Authors: Finci, L.I. / Zhang, J. / Sun, X. / Smock, R.G. / Meijers, R. / Zhang, Y. / Xiao, J. / Wang, J.H.
History
DepositionFeb 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Netrin receptor DCC
B: Netrin receptor DCC
C: Netrin receptor DCC
D: Netrin receptor DCC


Theoretical massNumber of molelcules
Total (without water)70,7584
Polymers70,7584
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-15 kcal/mol
Surface area31950 Å2
Unit cell
Length a, b, c (Å)53.459, 126.971, 57.162
Angle α, β, γ (deg.)90.00, 99.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Netrin receptor DCC / / Colorectal cancer suppressor / Immunoglobulin superfamily DCC subclass member 1 / Tumor suppressor protein DCC


Mass: 12021.081 Da / Num. of mol.: 2 / Fragment: UNP residues 721-815
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCC, IGDCC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P43146
#2: Protein Netrin receptor DCC / / Colorectal cancer suppressor / Immunoglobulin superfamily DCC subclass member 1 / Tumor suppressor protein DCC


Mass: 23357.670 Da / Num. of mol.: 2 / Fragment: UNP residues 844-1043
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCC, IGDCC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P43146
Compound detailsEntities 1 and 2 are genetically manipulated as one entire chain. Hence, the structure contains 2 ...Entities 1 and 2 are genetically manipulated as one entire chain. Hence, the structure contains 2 molecules. However, residues 816-843 are disordered in both molecules. Currently each molecule is split into 2 chains in this structure. N-terminal domains are assigned chain IDs A/C, and C-terminal domains are assigned chain IDs B/D. Author are not certain whether chains A/B or A/D (C/D or C/B) belongs to one molecule.

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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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Sodium Phosphate Monobasic Monohydrate, 0.1M Potassium Phosphate Monobasic, 0.1M MES Monohydrate pH 6.5, 2.0M Sodium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.997→50 Å / Num. obs: 14589 / % possible obs: 96.36 % / Redundancy: 6 % / Net I/σ(I): 8.58
Reflection shellResolution: 2.997→3.05 Å / Redundancy: 5.9 % / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.997→42.142 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.75
RfactorNum. reflection% reflection
Rfree0.2778 716 4.91 %
Rwork0.2208 --
obs0.2237 14589 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.997→42.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4627 0 0 0 4627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034740
X-RAY DIFFRACTIONf_angle_d0.5996461
X-RAY DIFFRACTIONf_dihedral_angle_d9.9421739
X-RAY DIFFRACTIONf_chiral_restr0.025738
X-RAY DIFFRACTIONf_plane_restr0.004814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9967-3.2280.35711470.26692800X-RAY DIFFRACTION98
3.228-3.55270.27911240.26752774X-RAY DIFFRACTION95
3.5527-4.06640.35641320.26892539X-RAY DIFFRACTION89
4.0664-5.12180.24891660.18012853X-RAY DIFFRACTION100
5.1218-42.14650.23131470.18822907X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.1646 Å / Origin y: -31.6489 Å / Origin z: 63.4535 Å
111213212223313233
T0.2416 Å20.0167 Å20.0296 Å2-0.3586 Å20.0072 Å2--0.2435 Å2
L0.2663 °20.1255 °2-0.1137 °2-1.8286 °2-0.0914 °2--0.2329 °2
S0.0336 Å °-0.002 Å °0.0261 Å °0.1453 Å °-0.0629 Å °0.157 Å °0.0248 Å °-0.0131 Å °0.0354 Å °
Refinement TLS groupSelection details: all

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