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- PDB-3zyg: NETRING2 LAM AND EGF1 DOMAINS -

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Basic information

Entry
Database: PDB / ID: 3zyg
TitleNETRING2 LAM AND EGF1 DOMAINS
ComponentsNETRIN-G2
KeywordsCELL ADHESION / SYNAPSE
Function / homology
Function and homology information


regulation of neuron projection arborization / postsynaptic specialization assembly / Post-translational modification: synthesis of GPI-anchored proteins / synaptic membrane adhesion / regulation of neuron migration / regulation of neuron projection development / regulation of presynapse assembly / side of membrane / presynaptic active zone membrane / axonogenesis ...regulation of neuron projection arborization / postsynaptic specialization assembly / Post-translational modification: synthesis of GPI-anchored proteins / synaptic membrane adhesion / regulation of neuron migration / regulation of neuron projection development / regulation of presynapse assembly / side of membrane / presynaptic active zone membrane / axonogenesis / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / 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-type 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 / Laminin / Laminin / Galactose-binding domain-like / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 22, 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_conn_type / 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.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 / _struct_conn_type.id
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: NETRIN-G2
B: NETRIN-G2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3358
Polymers81,3702
Non-polymers9656
Water3,747208
1
A: NETRIN-G2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1684
Polymers40,6851
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NETRIN-G2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1684
Polymers40,6851
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.500, 64.880, 120.080
Angle α, β, γ (deg.)90.00, 103.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NETRIN-G2 / LAMINET-2 / NETRING


Mass: 40685.191 Da / Num. of mol.: 2 / 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): HEK 293 GNTI(-) / Production host: HOMO SAPIENS (human) / References: UniProt: Q96CW9
#2: 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.: 4
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL SECRETION SIGNAL IS CLEAVED DURING PROTEIN PRODUCTION. C-TERMINUS CONTAINS 6X 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: 2.6 Å3/Da / Density % sol: 52.69 % / Description: NONE
Crystal growDetails: 20% MME550, 0.1M NACL, 0.1M BICINE PH9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0, 0.979400
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97941
ReflectionResolution: 2.2→29.2 Å / Num. obs: 42208 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.32 / Net I/σ(I): 6.4
Reflection shellResolution: 2.2→2.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.35 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0077refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TVG

1tvg


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 13.952 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.29684 2125 5 %RANDOM
Rwork0.24816 ---
obs0.25056 40042 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.277 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20.1 Å2
2---0.55 Å20 Å2
3---2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5117 0 58 208 5383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215330
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.967237
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5815634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55522.756254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17815859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2741548
X-RAY DIFFRACTIONr_chiral_restr0.1350.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214122
X-RAY DIFFRACTIONr_gen_planes_other
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: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 153 -
Rwork0.305 2801 -
obs--95.78 %
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)
10.49760.21460.15390.25930.23880.29470.0094-0.0417-0.00010.0017-0.01180.02910.00670.00260.00240.0186-0.0017-0.00450.00940.0040.0247-13.7241-19.17210.569
20.4077-0.24430.13230.3247-0.22310.25360.01750.0399-0.0206-0.0021-0.0257-0.0017-0.00190.00620.00830.01270.0035-0.0040.0066-0.00770.02810.52515.194748.1741
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 345
2X-RAY DIFFRACTION2B19 - 345

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