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- PDB-4v2a: human Unc5A ectodomain -

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Basic information

Entry
Database: PDB / ID: 4v2a
Titlehuman Unc5A ectodomain
ComponentsNETRIN RECEPTOR UNC5A
KeywordsAPOPTOSIS / UNCOORDINATED-5 / UNC5A / NETRIN RECEPTOR / FLRT
Function / homology
Function and homology information


netrin receptor activity / neuron projection membrane / anterior/posterior axon guidance / netrin-activated signaling pathway / Netrin-1 signaling / Netrin mediated repulsion signals / Caspase activation via Dependence Receptors in the absence of ligand / neuronal cell body membrane / neuron projection development / membrane raft ...netrin receptor activity / neuron projection membrane / anterior/posterior axon guidance / netrin-activated signaling pathway / Netrin-1 signaling / Netrin mediated repulsion signals / Caspase activation via Dependence Receptors in the absence of ligand / neuronal cell body membrane / neuron projection development / membrane raft / apoptotic process / plasma membrane
Similarity search - Function
UNC5A, death domain / UPA domain / Netrin receptor UNC5 / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. ...UNC5A, death domain / UPA domain / Netrin receptor UNC5 / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Death-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Netrin receptor UNC5A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSeiradake, E. / del Toro, D. / Nagel, D. / Cop, F. / Haertl, R. / Ruff, T. / Seyit-Bremer, G. / Harlos, K. / Border, E.C. / Acker-Palmer, A. ...Seiradake, E. / del Toro, D. / Nagel, D. / Cop, F. / Haertl, R. / Ruff, T. / Seyit-Bremer, G. / Harlos, K. / Border, E.C. / Acker-Palmer, A. / Jones, E.Y. / Klein, R.
CitationJournal: Neuron / Year: 2014
Title: Flrt Structure: Balancing Repulsion and Cell Adhesion in Cortical and Vascular Development
Authors: Seiradake, E. / Del Toro, D. / Nagel, D. / Cop, F. / Haertl, R. / Ruff, T. / Seyit-Bremer, G. / Harlos, K. / Border, E.C. / Acker-Palmer, A. / Jones, E.Y. / Klein, R.
History
DepositionOct 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NETRIN RECEPTOR UNC5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7822
Polymers33,5611
Non-polymers2211
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.830, 87.770, 133.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NETRIN RECEPTOR UNC5A / PROTEIN UNC-5 HOMOLOG 1 / PROTEIN UNC-5 HOMOLOG A / UNC5A


Mass: 33561.012 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, UNP RESIDUES 1-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Production host: HOMO SAPIENS (human) / References: UniProt: Q6ZN44
#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.: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINUS IS PROTEOLYTICALLY CLEAVED DURING EXPRESSION. CONTAINS POLY-HIS TAG.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.57 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0401
DetectorType: PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0401 Å / Relative weight: 1
ReflectionResolution: 2.4→44 Å / Num. obs: 11029 / % possible obs: 86.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 68.17 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.88
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 0.61 / % possible all: 46.5

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
xia2data reduction
XDSdata reduction
xia2data scaling
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.4→43.88 Å / Cor.coef. Fo:Fc: 0.8292 / Cor.coef. Fo:Fc free: 0.7943 / SU R Cruickshank DPI: 0.62 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.657 / SU Rfree Blow DPI: 0.358 / SU Rfree Cruickshank DPI: 0.357
RfactorNum. reflection% reflectionSelection details
Rfree0.3436 544 4.78 %RANDOM
Rwork0.3268 ---
obs0.3276 11381 89.91 %-
Displacement parametersBiso mean: 80.49 Å2
Baniso -1Baniso -2Baniso -3
1--6.1924 Å20 Å20 Å2
2---14.5478 Å20 Å2
3---20.7402 Å2
Refine analyzeLuzzati coordinate error obs: 1.062 Å
Refinement stepCycle: LAST / Resolution: 2.4→43.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 14 19 1995
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072031HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.852773HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d689SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes301HARMONIC5
X-RAY DIFFRACTIONt_it2031HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.96
X-RAY DIFFRACTIONt_other_torsion19.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion262SEMIHARMONIC5
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_contact1969SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.63 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2495 108 5.78 %
Rwork0.2812 1760 -
all0.2794 1868 -
obs--89.91 %
Refinement TLS params.Method: refined / Origin x: 3.2411 Å / Origin y: -24.3785 Å / Origin z: -18.0082 Å
111213212223313233
T-0.1538 Å2-0.055 Å2-0.0349 Å2-0.0032 Å20.0833 Å2---0.0249 Å2
L0.1553 °20.4747 °2-0.724 °2-1.8161 °2-1.5266 °2--4.0875 °2
S-0.016 Å °0.0159 Å °-0.0578 Å °-0.0797 Å °-0.0387 Å °0.1332 Å °0.0665 Å °-0.0757 Å °0.0547 Å °
Refinement TLS groupSelection details: CHAIN A

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