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- PDB-3zyo: Crystal structure of the N-terminal leucine rich repeats and immu... -

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Basic information

Entry
Database: PDB / ID: 3zyo
TitleCrystal structure of the N-terminal leucine rich repeats and immunoglobulin domain of netrin-G ligand-3
ComponentsLEUCINE-RICH REPEAT-CONTAINING PROTEIN 4B
KeywordsCELL ADHESION / SYNAPSE
Function / homology
Function and homology information


Receptor-type tyrosine-protein phosphatases / synaptic membrane adhesion / regulation of postsynaptic density assembly / cerebellar mossy fiber / positive regulation of synapse assembly / regulation of presynapse assembly / postsynaptic density membrane / presynaptic membrane / signaling receptor binding / glutamatergic synapse / plasma membrane
Similarity search - Function
Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype ...Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine-rich repeat profile. / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Leucine-rich repeat domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Leucine-rich repeat-containing protein 4B
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSeiradake, E. / Coles, C.H. / Perestenko, P.V. / Harlos, K. / McIlhinney, R.A.J. / Aricescu, A.R. / Jones, E.Y.
CitationJournal: Embo J. / Year: 2011
Title: Structural Basis for Cell Surface Patterning Through Netring-Ngl Interactions.
Authors: Seiradake, E. / Coles, C.H. / Perestenko, P.V. / Harlos, K. / Mcilhinney, R.A.J. / Aricescu, A.R. / Jones, E.Y.
History
DepositionAug 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 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: LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7243
Polymers46,4381
Non-polymers2872
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.330, 131.330, 174.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4B / NETRIN-G3 LIGAND / NGL-3


Mass: 46437.859 Da / Num. of mol.: 1
Fragment: N-TERMINAL LEUCINE RICH REPEATS AND IMMUNOGLOBULIN DOMAIN, RESIDUES 57-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293S / Production host: HOMO SAPIENS (human) / References: UniProt: P0C192
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#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.: 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

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M NAH2PO4, 0.1 M KH2PO4, 2M NACL, 0.1 M MES, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0714
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0714 Å / Relative weight: 1
ReflectionResolution: 3.1→38.6 Å / Num. obs: 10743 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.2
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZYN

3zyn


Resolution: 3.1→38.6 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 49.006 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CLEAR ELECTRON DENSITY FOR AMINO ACID RESIDUES Q68-A69 AND N335-C338 WAS NOT OBSERVED AND THESE ARE OMITTED FROM THE MODEL. DISORDERED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CLEAR ELECTRON DENSITY FOR AMINO ACID RESIDUES Q68-A69 AND N335-C338 WAS NOT OBSERVED AND THESE ARE OMITTED FROM THE MODEL. DISORDERED SIDECHAINS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26931 517 4.8 %RANDOM
Rwork0.22856 ---
obs0.23044 10223 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.797 Å2
Baniso -1Baniso -2Baniso -3
1-3.43 Å21.72 Å20 Å2
2--3.43 Å20 Å2
3----5.15 Å2
Refinement stepCycle: LAST / Resolution: 3.1→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 15 0 3115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023183
X-RAY DIFFRACTIONr_bond_other_d0.0010.022147
X-RAY DIFFRACTIONr_angle_refined_deg0.8571.9664334
X-RAY DIFFRACTIONr_angle_other_deg0.7543.0045211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7795388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36823.517145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31615542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8351527
X-RAY DIFFRACTIONr_chiral_restr0.0510.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02636
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 30 -
Rwork0.301 705 -
obs--100 %
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)
17.5366-4.07913.1445.6981-2.469510.9649-0.04570.2296-0.9632-0.35210.0836-0.61321.55570.4534-0.03781.1121-0.1441-0.24230.2748-0.2370.9402-2.939530.80029.2578
22.8146-0.5674-0.651312.76982.42552.22070.03130.2575-0.3849-0.20490.3314-0.04050.4912-0.4794-0.36270.4059-0.2251-0.28080.31890.09350.2581-18.367250.927412.6595
33.38431.6486-1.10475.35940.35382.90410.25050.27270.4973-0.0870.15070.2791-0.1808-0.6565-0.40120.22870.0001-0.05430.35310.18240.1685-24.152975.444416.7973
44.63910.8764-2.4152.88310.22484.19520.08870.5344-0.59760.3869-0.22651.02460.6184-0.89470.13770.4008-0.153-0.11010.97040.25930.9158-42.952168.076721.1882
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A58 - 160
2X-RAY DIFFRACTION2A161 - 278
3X-RAY DIFFRACTION3A279 - 401
4X-RAY DIFFRACTION4A402 - 454

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