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- PDB-4v2b: rat Unc5D Ig domain 1 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4v2b
Titlerat Unc5D Ig domain 1
ComponentsPROTEIN UNC5D
KeywordsAPOPTOSIS / UNCOORDINATED-5 / IG DOMAIN / NETRIN RECEPTOR / FLRT
Function / homology
Function and homology information


netrin receptor activity / regulation of neuron migration / cell-cell adhesion via plasma-membrane adhesion molecules / pyramidal neuron differentiation / axon guidance / apoptotic process / cell surface / plasma membrane
Similarity search - Function
UNC5D, 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 domain / Thrombospondin type-1 (TSP1) repeat superfamily ...UNC5D, 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 domain / 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 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Netrin receptor UNC5D
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN UNC5D
B: PROTEIN UNC5D


Theoretical massNumber of molelcules
Total (without water)36,2572
Polymers36,2572
Non-polymers00
Water724
1
A: PROTEIN UNC5D


Theoretical massNumber of molelcules
Total (without water)18,1281
Polymers18,1281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN UNC5D


Theoretical massNumber of molelcules
Total (without water)18,1281
Polymers18,1281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.110, 70.110, 214.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein PROTEIN UNC5D / RAT UNC5D


Mass: 18128.379 Da / Num. of mol.: 2 / Fragment: IG DOMAIN 1, RESIDUES 1-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Production host: HOMO SAPIENS (human) / References: UniProt: F1LW30
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINUS IS PROTEOLYTICALLY CLEAVED DURING EXPRESSION. CONTAINS C-TERMINAL 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: 2.09 Å3/Da / Density % sol: 41.26 % / Description: NONE

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONDiamond I2411.0069
SYNCHROTRONDiamond I2421.0714
Detector
TypeIDDetector
MARRESEARCH1CCD
2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.00691
21.07141
ReflectionResolution: 2→61 Å / Num. obs: 410812 / % possible obs: 99.8 % / Redundancy: 18 % / Biso Wilson estimate: 58.74 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.63
Reflection shellResolution: 2→2.2 Å / Redundancy: 19.3 % / Mean I/σ(I) obs: 0.67 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
xia2data reduction
XDSdata reduction
xia2data scaling
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 2→60.72 Å / Cor.coef. Fo:Fc: 0.8847 / Cor.coef. Fo:Fc free: 0.8783 / SU R Cruickshank DPI: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.224 / SU Rfree Blow DPI: 0.189 / SU Rfree Cruickshank DPI: 0.189
RfactorNum. reflection% reflectionSelection details
Rfree0.3256 1046 4.96 %RANDOM
Rwork0.314 ---
obs0.3146 21085 95.9 %-
Displacement parametersBiso mean: 88.44 Å2
Baniso -1Baniso -2Baniso -3
1--13.8584 Å20 Å20 Å2
2---13.8584 Å20 Å2
3---27.7167 Å2
Refine analyzeLuzzati coordinate error obs: 0.815 Å
Refinement stepCycle: LAST / Resolution: 2→60.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 0 4 1734
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0061780HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.862412HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d615SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes254HARMONIC5
X-RAY DIFFRACTIONt_it1780HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.65
X-RAY DIFFRACTIONt_other_torsion18.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion224SEMIHARMONIC5
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_contact1756SEMIHARMONIC4
LS refinement shellResolution: 2→2.1 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3669 110 5.54 %
Rwork0.3385 1877 -
all0.34 1987 -
obs--95.9 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-6.095941.54723.0211
23.074413.74311.02
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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