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- PDB-3laf: Structure of DCC, a netrin-1 receptor -

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Basic information

Entry
Database: PDB / ID: 3laf
TitleStructure of DCC, a netrin-1 receptor
ComponentsDeleted in Colorectal Cancer
KeywordsAPOPTOSIS / netrin-1 receptor / immunoglobulin superfamily / horseshoe
Function / homology
Function and homology information


Netrin-1 signaling / DCC mediated attractive signaling / Caspase activation via Dependence Receptors in the absence of ligand / netrin receptor activity / dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / growth cone membrane / corpus callosum development / optic nerve development ...Netrin-1 signaling / DCC mediated attractive signaling / Caspase activation via Dependence Receptors in the absence of ligand / netrin receptor activity / dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / growth cone membrane / corpus callosum development / optic nerve development / axon development / postsynaptic modulation of chemical synaptic transmission / response to amphetamine / axon guidance / postsynaptic density membrane / Schaffer collateral - CA1 synapse / cerebral cortex development / cell-cell adhesion / positive regulation of neuron projection development / neuron migration / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / axon / apoptotic process / cell surface / identical protein binding / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsChen, Q. / Liu, J.-H. / Wang, J.-H.
CitationJournal: J.Cell.Sci. / Year: 2013
Title: N-terminal horseshoe conformation of DCC is functionally required for axon guidance and might be shared by other neural receptors.
Authors: Chen, Q. / Sun, X. / Zhou, X.H. / Liu, J.H. / Wu, J. / Zhang, Y. / Wang, J.H.
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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 / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deleted in Colorectal Cancer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,90117
Polymers44,1331
Non-polymers2,76816
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.380, 109.380, 129.442
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Deleted in Colorectal Cancer / Deleted in colorectal carcinoma / isoform CRA_a


Mass: 44132.738 Da / Num. of mol.: 1 / Fragment: UNP residues 39-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dcc, rCG_46581 / Plasmid: pMelBac / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High-Five / References: UniProt: Q63155
#2: 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.: 2
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
#3: 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.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
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: 5.06 Å3/Da / Density % sol: 75.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.0 M Ammonium Sulfate, 0.1 M Bis-tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11.072
SYNCHROTRONAPS 19-ID20.9794
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDDec 17, 2008Cryogenically-cooled double crystal Si(111) monochromator. Triple striped vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry.
ADSC QUANTUM 3152CCDMar 25, 2009Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Cryo-Cooled Si(111) double crystal.SINGLE WAVELENGTHMx-ray1
2Rosenbaum-Rock high-resolution double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0721
20.97941
ReflectionRedundancy: 22.5 % / Av σ(I) over netI: 33.24 / Number: 359469 / Rmerge(I) obs: 0.129 / Χ2: 1.7 / D res high: 3.1 Å / D res low: 50 Å / Num. obs: 15982 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.675010010.0755.10922
5.36.6799.910.0892.17222.2
4.635.310010.0931.72322.6
4.214.6310010.0891.50422.7
3.914.2110010.1231.21222.7
3.683.9110010.1921.11922.7
3.493.6810010.2531.09522.7
3.343.4910010.3731.05222.7
3.213.3410010.5751.00222.7
3.13.2110010.8190.96221.9
ReflectionResolution: 2.4→50 Å / Num. all: 34453 / Num. obs: 34427 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Rmerge(I) obs: 0.082 / Χ2: 1.079 / Net I/σ(I): 8.7
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.89 / Num. unique all: 2288 / Χ2: 1.233 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.7 Å / D res low: 35.4 Å / FOM acentric: 0.182 / FOM centric: 0.056 / Reflection acentric: 22943 / Reflection centric: 721
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1002.735.422943721
ANO_10.702.735.4153790
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_111.46-35.40027737
ISO_18.32-11.460047435
ISO_16.86-8.320061037
ISO_15.97-6.860072136
ISO_15.35-5.970081637
ISO_14.9-5.350089637
ISO_14.54-4.90098233
ISO_14.25-4.5400104939
ISO_14.01-4.2500111934
ISO_13.81-4.0100119140
ISO_13.63-3.8100125133
ISO_13.48-3.6300128837
ISO_13.34-3.4800136837
ISO_13.22-3.3400141635
ISO_13.11-3.2200145136
ISO_13.02-3.1100150435
ISO_12.93-3.0200156834
ISO_12.85-2.9300161537
ISO_12.77-2.8500163838
ISO_12.7-2.7700170934
ANO_111.46-35.40.26802760
ANO_18.32-11.460.30204740
ANO_16.86-8.320.38606100
ANO_15.97-6.860.46707210
ANO_15.35-5.970.55208150
ANO_14.9-5.350.62508960
ANO_14.54-4.90.72309820
ANO_14.25-4.540.793010490
ANO_14.01-4.250.881011190
ANO_13.81-4.010.932011910
ANO_13.63-3.810.963012510
ANO_13.48-3.630.981012880
ANO_13.34-3.480.991013680
ANO_13.22-3.340.997014150
ANO_13.11-3.220.999014500
ANO_13.02-3.11104740
ANO_12.93-3.020000
ANO_12.85-2.930000
ANO_12.77-2.850000
ANO_12.7-2.770000
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
18.734-88.935-6.362PT163.922.24
2-23.261-97.739-22.262PT108.931.43
3-1.884-82.449-0.214PT178.591.77
423.296-98.16.745PT163.11.58
513.253-24.789-0.379PT182.691.55
64.275-91.798-16.563PT144.511.25
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
11.46-35.40.720.23527737
8.32-11.460.6630.14247435
6.86-8.320.5920.13161037
5.97-6.860.5640.13572136
5.35-5.970.5070.10581637
4.9-5.350.4540.07689637
4.54-4.90.3880.04298233
4.25-4.540.3210.043104939
4.01-4.250.2650.04111934
3.81-4.010.2030.033119140
3.63-3.810.160.022125133
3.48-3.630.1210.029128837
3.34-3.480.0890.014136837
3.22-3.340.0620.014141635
3.11-3.220.0480.011145136
3.02-3.110.0310.01150435
2.93-3.020.0230.011156834
2.85-2.930.0210.008161537
2.77-2.850.0190.01163838
2.7-2.770.0170.008170934

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.4→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.83 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1635 4.8 %Random
Rwork0.211 ---
all0.218 34453 --
obs0.216 34427 100 %-
Solvent computationBsol: 47.582 Å2
Displacement parametersBiso max: 158.13 Å2 / Biso mean: 51.911 Å2 / Biso min: 22.03 Å2
Baniso -1Baniso -2Baniso -3
1-8.672 Å20 Å20 Å2
2--8.672 Å20 Å2
3----17.343 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 166 218 3327
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.2281.5
X-RAY DIFFRACTIONc_scbond_it3.5462
X-RAY DIFFRACTIONc_mcangle_it3.7182
X-RAY DIFFRACTIONc_scangle_it5.1592.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2carbohydrate.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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