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- PDB-5z5k: Structure of the DCC-Draxin complex -

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Basic information

Entry
Database: PDB / ID: 5z5k
TitleStructure of the DCC-Draxin complex
Components
  • Draxin
  • Netrin receptor DCC
KeywordsAPOPTOSIS/INBITITOR / axon guidance / APOPTOSIS-INBITITOR complex
Function / homology
Function and homology information


commissural neuron differentiation in spinal cord / Netrin-1 signaling / DCC mediated attractive signaling / Caspase activation via Dependence Receptors in the absence of ligand / dorsal spinal cord development / netrin receptor activity / dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / growth cone membrane ...commissural neuron differentiation in spinal cord / Netrin-1 signaling / DCC mediated attractive signaling / Caspase activation via Dependence Receptors in the absence of ligand / dorsal spinal cord development / netrin receptor activity / dorsal/ventral axon guidance / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / growth cone membrane / negative regulation of axon extension / corpus callosum development / optic nerve development / postsynaptic modulation of chemical synaptic transmission / axon development / axonal growth cone / response to amphetamine / forebrain development / axon guidance / postsynaptic density membrane / neuron migration / negative regulation of canonical Wnt signaling pathway / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / cell-cell adhesion / cerebral cortex development / Wnt signaling pathway / postsynapse / negative regulation of neuron apoptotic process / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / axon / apoptotic process / cell surface / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Draxin / Draxin / 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 ...Draxin / Draxin / 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
Draxin / Netrin receptor DCC
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.493 Å
AuthorsLiu, Y. / Xiao, J. / Wang, J.
Funding support China, United States, 2items
OrganizationGrant numberCountry
National Science Foundation (China)31570735 China
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL103526 United States
CitationJournal: Neuron / Year: 2018
Title: Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC.
Authors: Liu, Y. / Bhowmick, T. / Liu, Y. / Gao, X. / Mertens, H.D.T. / Svergun, D.I. / Xiao, J. / Zhang, Y. / Wang, J.H. / Meijers, R.
History
DepositionJan 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 2.1Mar 10, 2021Group: Author supporting evidence / Structure summary / Category: audit_author / chem_comp / pdbx_audit_support / Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Netrin receptor DCC
B: Draxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6456
Polymers49,1512
Non-polymers1,4944
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint15 kcal/mol
Surface area24250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.069, 108.069, 130.266
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Netrin receptor DCC / / Tumor suppressor protein DCC


Mass: 41429.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dcc / Production host: Homo sapiens (human) / References: UniProt: Q63155
#2: Protein Draxin / Dorsal inhibitory axon guidance protein / Dorsal repulsive axon guidance protein


Mass: 7720.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Draxin, DRAXIN / Production host: Homo sapiens (human) / References: UniProt: D3ZDG4
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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 / N-Acetylglucosamine


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 4.47 Å3/Da / Density % sol: 72.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.493→50 Å / Num. obs: 29938 / % possible obs: 99.8 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.036 / Rrim(I) all: 0.107 / Χ2: 2.406 / Net I/av σ(I): 38.321 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)CC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.5-2.5410.60.7980.4851.438100
2.54-2.5910.60.8550.4071.47899.7
2.59-2.6410.80.8840.3311.48999.7
2.64-2.6910.90.9050.2911.56299.70.9180.963
2.69-2.7510.90.9270.2421.54499.70.7660.804
2.75-2.82110.9610.191.64299.90.6020.632
2.82-2.8911.10.9750.1441.71599.70.4580.48
2.89-2.9611.20.9770.1231.79499.80.3930.412
2.96-3.0511.20.9850.0931.88899.90.2970.311
3.05-3.1511.20.990.0772.0499.90.2460.258
3.15-3.2611.20.9920.0612.24699.80.1940.204
3.26-3.3911.20.9950.0492.47299.90.1550.162
3.39-3.5511.10.9960.0392.78799.90.1230.129
3.55-3.7311.10.9960.0343.13899.90.1070.113
3.73-3.9710.80.9960.0313.4999.90.0980.103
3.97-4.2710.60.9970.0273.8941000.0840.089
4.27-4.710.50.9970.0244.0071000.0760.08
4.7-5.3810.50.9980.0223.6041000.070.073
5.38-6.7810.90.9980.0193.07699.80.0620.065
6.78-5010.70.9970.0182.89698.60.0550.058

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.493→35.374 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7
RfactorNum. reflection% reflection
Rfree0.2475 1485 4.97 %
Rwork0.2125 --
obs0.2143 29867 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 176.52 Å2 / Biso mean: 71.9063 Å2 / Biso min: 35.94 Å2
Refinement stepCycle: final / Resolution: 2.493→35.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 98 33 3566
Biso mean--108.42 62.21 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033620
X-RAY DIFFRACTIONf_angle_d0.5814909
X-RAY DIFFRACTIONf_chiral_restr0.043557
X-RAY DIFFRACTIONf_plane_restr0.004637
X-RAY DIFFRACTIONf_dihedral_angle_d14.182202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4933-2.57370.37391340.31672463259795
2.5737-2.66570.32061300.297325742704100
2.6657-2.77230.31781330.294126012734100
2.7723-2.89850.34631330.27525562689100
2.8985-3.05120.29481370.268425842721100
3.0512-3.24220.2741390.24325882727100
3.2422-3.49240.26271370.237226042741100
3.4924-3.84350.28171310.218825952726100
3.8435-4.39870.23041340.185425882722100
4.3987-5.53850.18491350.172726092744100
5.5385-35.37740.21661420.18052620276299
Refinement TLS params.Method: refined / Origin x: 28.0904 Å / Origin y: 128.8253 Å / Origin z: -5.9251 Å
111213212223313233
T0.4612 Å2-0.0387 Å2-0.0031 Å2-0.5281 Å20.0011 Å2--0.4488 Å2
L0.1783 °2-0.1747 °20.4675 °2-0.587 °2-0.9308 °2--1.4112 °2
S0.055 Å °0.0519 Å °-0.0644 Å °-0.0783 Å °-0.0604 Å °-0.0375 Å °0.0726 Å °0.2378 Å °-0.011 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA39 - 447
2X-RAY DIFFRACTION1allB264 - 329
3X-RAY DIFFRACTION1allS1 - 33

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