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- PDB-4wnx: Netrin 4 lacking the C-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 4wnx
TitleNetrin 4 lacking the C-terminal Domain
ComponentsNetrin-4
KeywordsLaminin Binding Protein / Basement Membrane / Laminin Binding / N-linked glycosylation / Epidermal Growth Factor Like Domain
Function / homology
Function and homology information


regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling / Netrin-1 signaling / laminin complex / basement membrane assembly / laminin-1 binding / tissue development / neuron remodeling / basement membrane / substrate adhesion-dependent cell spreading / animal organ morphogenesis ...regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling / Netrin-1 signaling / laminin complex / basement membrane assembly / laminin-1 binding / tissue development / neuron remodeling / basement membrane / substrate adhesion-dependent cell spreading / animal organ morphogenesis / cell migration / plasma membrane
Similarity search - Function
Netrin-4, NTR domain / : / Laminin, N-terminal / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain ...Netrin-4, NTR domain / : / Laminin, N-terminal / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / EGF-like domain signature 1.
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.723 Å
AuthorsMcDougall, M. / Patel, T. / Reuten, R. / Meier, M. / Koch, M. / Stetefeld, J.
CitationJournal: Nat Commun / Year: 2016
Title: Structural decoding of netrin-4 reveals a regulatory function towards mature basement membranes.
Authors: Reuten, R. / Patel, T.R. / McDougall, M. / Rama, N. / Nikodemus, D. / Gibert, B. / Delcros, J.G. / Prein, C. / Meier, M. / Metzger, S. / Zhou, Z. / Kaltenberg, J. / McKee, K.K. / Bald, T. / ...Authors: Reuten, R. / Patel, T.R. / McDougall, M. / Rama, N. / Nikodemus, D. / Gibert, B. / Delcros, J.G. / Prein, C. / Meier, M. / Metzger, S. / Zhou, Z. / Kaltenberg, J. / McKee, K.K. / Bald, T. / Tuting, T. / Zigrino, P. / Djonov, V. / Bloch, W. / Clausen-Schaumann, H. / Poschl, E. / Yurchenco, P.D. / Ehrbar, M. / Mehlen, P. / Stetefeld, J. / Koch, M.
History
DepositionOct 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.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_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Netrin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6447
Polymers48,1501
Non-polymers1,4956
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint5 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.755, 75.049, 74.672
Angle α, β, γ (deg.)90.000, 96.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Netrin-4 / / Beta-netrin


Mass: 48149.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ntn4 / Plasmid: pCEP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9JI33

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Sugars , 2 types, 4 molecules

#2: 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.: 2 / Source method: obtained synthetically
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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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

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Non-polymers , 3 types, 29 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.88 Å3/Da / Density % sol: 57.27 % / Description: Thin Plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350, calcium acetate, sodium cacodylate, NDSB-256

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.72→33.49 Å / Num. obs: 14673 / % possible obs: 91.75 % / Redundancy: 3.4 % / Biso Wilson estimate: 40.7 Å2 / Net I/σ(I): 5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
CrystalCleardata collection
HKL-2000data scaling
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
Cootmodel building
PHASERphasing
REFMACrefinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AQS

4aqs


Resolution: 2.723→33.49 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 740 5.04 %Random selection
Rwork0.2198 13930 --
obs0.2219 14670 91.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.8 Å2 / Biso mean: 49.9657 Å2 / Biso min: 19.98 Å2
Refinement stepCycle: final / Resolution: 2.723→33.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 189 27 3475
Biso mean--120.19 32.64 -
Num. residues----429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033471
X-RAY DIFFRACTIONf_angle_d0.84691
X-RAY DIFFRACTIONf_chiral_restr0.047496
X-RAY DIFFRACTIONf_plane_restr0.004622
X-RAY DIFFRACTIONf_dihedral_angle_d21.42096
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.723-2.93310.3962830.33591754183758
2.9331-3.22810.30931670.302830273194100
3.2281-3.69470.31630.234830163179100
3.6947-4.65290.21291690.184130373206100
4.6529-33.49330.2371580.180530963254100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.18810.20190.08352.1075-1.05780.77520.1540.0087-0.20450.0359-0.05410.06030.1198-0.0563-0.10240.419-0.0051-0.1780.1778-0.00480.303733.31033.953767.1661
20.20.26310.00872.9-1.36010.94020.06070.01290.0074-0.1005-0.04580.08260.044-0.0352-0.0260.48490.0199-0.14880.08810.03450.363837.669926.070754.2208
33.6795-0.19810.63814.71710.30632.51460.18680.1816-0.00350.0577-0.0998-0.0474-0.3460.1178-0.02860.38030.0371-0.04040.19440.1440.405422.827777.940721.9274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 30:181 OR RESID 508:508 ) )A30 - 181
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 30:181 OR RESID 508:508 ) )A508
3X-RAY DIFFRACTION2( CHAIN A AND RESID 182:395 )A182 - 395
4X-RAY DIFFRACTION3( CHAIN A AND RESID 396:462 )A396 - 462

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