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- PDB-3zyi: NetrinG2 in complex with NGL2 -

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Basic information

Entry
Database: PDB / ID: 3zyi
TitleNetrinG2 in complex with NGL2
Components
  • LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4
  • NETRIN-G2
KeywordsCELL ADHESION / LRRC4 COMPLEX / SYNAPSE
Function / homology
Function and homology information


regulation of neuron projection arborization / excitatory synapse assembly / postsynaptic density protein 95 clustering / postsynaptic specialization assembly / Post-translational modification: synthesis of GPI-anchored proteins / synaptic membrane adhesion / regulation of neuron migration / regulation of neuron projection development / excitatory synapse / regulation of presynapse assembly ...regulation of neuron projection arborization / excitatory synapse assembly / postsynaptic density protein 95 clustering / postsynaptic specialization assembly / Post-translational modification: synthesis of GPI-anchored proteins / synaptic membrane adhesion / regulation of neuron migration / regulation of neuron projection development / excitatory synapse / regulation of presynapse assembly / side of membrane / presynaptic active zone membrane / axonogenesis / modulation of chemical synaptic transmission / postsynaptic density membrane / Schaffer collateral - CA1 synapse / dendritic spine / axon / glutamatergic synapse / extracellular region / plasma membrane
Similarity search - Function
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, 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 / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / 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 / Laminin / Laminin / Galactose-binding domain-like / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Epidermal growth factor-like domain. / Leucine-rich repeat profile. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Leucine-rich repeat domain superfamily / Ribbon / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Jelly Rolls / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Netrin-G2 / Leucine-rich repeat-containing protein 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Jul 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 4
B: NETRIN-G2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3207
Polymers91,6482
Non-polymers6725
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-9.9 kcal/mol
Surface area31920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.420, 153.390, 158.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4 / BRAIN TUMOR-ASSOCIATED PROTEIN BAG / NASOPHARYNGEAL CARCINOMA-ASSOCIATED GENE 14 PROTEIN / NETRIN- ...BRAIN TUMOR-ASSOCIATED PROTEIN BAG / NASOPHARYNGEAL CARCINOMA-ASSOCIATED GENE 14 PROTEIN / NETRIN-G2 LIGAND / NGL-2


Mass: 50962.410 Da / Num. of mol.: 1 / Fragment: LRR AND IG DOMAINS, RESIDUES 1-444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK 293 GNTI(-) / Production host: HOMO SAPIENS (human) / References: UniProt: Q9HBW1
#2: Protein NETRIN-G2 / LAMINET-2 / NETRING2


Mass: 40685.191 Da / Num. of mol.: 1 / Fragment: LAM AND EGF1 DOMAINS, RESIDUES 423-767
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): 293 HEK GNTI (-) / Production host: HOMO SAPIENS (human) / References: UniProt: Q96CW9
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY
Sequence detailsN-TERMINUS IS CLEAVED DURING PROTEIN PRODUCTION. C- TERMINUS CONTAINS A 6 X HISTIDINE TAG.

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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: 2.5 Å3/Da / Density % sol: 50.89 % / Description: NONE
Crystal growDetails: 50% V/V 2-METHYL-2, 4-PENTANEDIOL, 0.2 M AMMONIUM DI-HYDROGEN PHOSPHATE, 0.1 M TRIS PH 8.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Type: DIAMOND / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→29 Å / Num. obs: 28390 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Biso Wilson estimate: 67.21 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 16.6
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZYG

3zyg


Resolution: 2.6→28.95 Å / Cor.coef. Fo:Fc: 0.8699 / Cor.coef. Fo:Fc free: 0.8368 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2868 1439 5.08 %RANDOM
Rwork0.2434 ---
obs0.2456 28340 --
Displacement parametersBiso mean: 58.89 Å2
Baniso -1Baniso -2Baniso -3
1--25.3293 Å20 Å20 Å2
2--26.7385 Å20 Å2
3----1.4092 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.6→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5411 0 39 0 5450
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085596HARMONIC2
X-RAY DIFFRACTIONt_angle_deg17625HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1845SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes131HARMONIC2
X-RAY DIFFRACTIONt_gen_planes840HARMONIC5
X-RAY DIFFRACTIONt_it5596HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.14
X-RAY DIFFRACTIONt_other_torsion18.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion724SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5745SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.7 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3433 153 5.23 %
Rwork0.2816 2771 -
all0.2846 2924 -

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