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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 / anterior commissure morphogenesis / netrin receptor activity / dorsal/ventral axon guidance / negative regulation of hippocampal neuron apoptotic process / spinal cord ventral commissure morphogenesis ...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 / anterior commissure morphogenesis / netrin receptor activity / dorsal/ventral axon guidance / negative regulation of hippocampal neuron apoptotic process / spinal cord ventral commissure morphogenesis / anterior/posterior axon guidance / hippocampal neuron apoptotic process / 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 / forebrain development / response to amphetamine / axon guidance / neuron migration / postsynaptic density membrane / negative regulation of canonical Wnt signaling pathway / Schaffer collateral - CA1 synapse / cerebral cortex development / Wnt signaling pathway / positive regulation of neuron projection development / cell-cell adhesion / negative regulation of neuron projection development / neuron apoptotic process / postsynapse / transcription coactivator activity / molecular adaptor 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: Ying Liu / Tuhin Bhowmick / Yiqiong Liu / Xuefan Gao / Haydyn D T Mertens / Dmitri I Svergun / Junyu Xiao / Yan Zhang / Jia-Huai Wang / Rob Meijers /
Abstract: Axon guidance involves the spatiotemporal interplay between guidance cues and membrane-bound cell-surface receptors, present on the growth cone of the axon. Netrin-1 is a prototypical guidance cue ...Axon guidance involves the spatiotemporal interplay between guidance cues and membrane-bound cell-surface receptors, present on the growth cone of the axon. Netrin-1 is a prototypical guidance cue that binds to deleted in colorectal cancer (DCC), and it has been proposed that the guidance cue Draxin modulates this interaction. Here, we present structural snapshots of Draxin/DCC and Draxin/Netrin-1 complexes, revealing a triangular relationship that affects Netrin-mediated haptotaxis and fasciculation. Draxin interacts with DCC through the N-terminal four immunoglobulin domains, and Netrin-1 through the EGF-3 domain, in the same region where DCC binds. Netrin-1 and DCC bind to adjacent sites on Draxin, which appears to capture Netrin-1 and tether it to the DCC receptor. We propose the conformational flexibility of the single-pass membrane receptor DCC is used to promote fasciculation and regulate axon guidance through concerted Netrin-1/Draxin binding. VIDEO ABSTRACT.
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
Revision 2.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: 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


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


Mass: 18.015 Da / Num. of mol.: 33 / 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: 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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