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- PDB-5l5k: Plexin A4 full extracellular region, domains 1 to 10, data to 7.5... -

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Basic information

Entry
Database: PDB / ID: 5l5k
TitlePlexin A4 full extracellular region, domains 1 to 10, data to 7.5 angstrom, spacegroup P4(1)
ComponentsPlexin-A4
KeywordsSIGNALING PROTEIN / receptor / signaling / axon guidance
Function / homology
Function and homology information


glossopharyngeal nerve morphogenesis / chemorepulsion of branchiomotor axon / regulation of negative chemotaxis / vagus nerve morphogenesis / anterior commissure morphogenesis / cranial nerve morphogenesis / trigeminal nerve morphogenesis / regulation of axon extension involved in axon guidance / postganglionic parasympathetic fiber development / facial nerve morphogenesis ...glossopharyngeal nerve morphogenesis / chemorepulsion of branchiomotor axon / regulation of negative chemotaxis / vagus nerve morphogenesis / anterior commissure morphogenesis / cranial nerve morphogenesis / trigeminal nerve morphogenesis / regulation of axon extension involved in axon guidance / postganglionic parasympathetic fiber development / facial nerve morphogenesis / sympathetic neuron axon guidance / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / cerebellar climbing fiber to Purkinje cell synapse / trigeminal nerve structural organization / facial nerve structural organization / branchiomotor neuron axon guidance / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin-plexin signaling pathway involved in axon guidance / maintenance of synapse structure / semaphorin receptor complex / sympathetic nervous system development / semaphorin receptor activity / embryonic heart tube development / negative regulation of cell adhesion / motor neuron axon guidance / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / regulation of cell migration / neuron projection morphogenesis / axon guidance / nervous system development / regulation of cell shape / plasma membrane
Similarity search - Function
Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat ...Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.501 Å
AuthorsJanssen, B.J.C. / Kong, Y. / Malinauskas, T. / Vangoor, V.R. / Coles, C.H. / Kaufmann, R. / Ni, T. / Gilbert, R.J.C. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y.
CitationJournal: Neuron / Year: 2016
Title: Structural Basis for Plexin Activation and Regulation.
Authors: Kong, Y. / Janssen, B.J. / Malinauskas, T. / Vangoor, V.R. / Coles, C.H. / Kaufmann, R. / Ni, T. / Gilbert, R.J. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y.
History
DepositionMay 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / pdbx_validate_symm_contact ...pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plexin-A4


Theoretical massNumber of molelcules
Total (without water)134,8141
Polymers134,8141
Non-polymers00
Water0
1
A: Plexin-A4

A: Plexin-A4


Theoretical massNumber of molelcules
Total (without water)269,6282
Polymers269,6282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z+3/41
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)220.593, 220.593, 65.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Plexin-A4


Mass: 134813.844 Da / Num. of mol.: 1 / Fragment: UNP residues 36-1229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxna4, Kiaa1550 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q80UG2

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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: 5.95 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 29% (v/v) glycerol, 4.3% (w/v) PEG 8k, 53 mM TRIS hydrochloride, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 7.5→62 Å / Num. obs: 4253 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.207 / Net I/σ(I): 12.2
Reflection shellHighest resolution: 7.5 Å / Rmerge(I) obs: 1.21

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L56

5l56


Resolution: 7.501→55.148 Å / SU ML: 1.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 45.37
Details: THE AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY. THE STRUCTURE IS BASED ON A ...Details: THE AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY. THE STRUCTURE IS BASED ON A HOMOLOGY MODEL GENERATED WITH PDB ENTRY 5L56 AS TEMPLATE (53% SEQUENCE IDENTITY). THE AUTHORS HAVE NOT FURTHER REFINED THE RESULTING COORDINATES NOR CORRECTED RESULTING CLASHES BETWEEN ATOMS AND DEVIATING PEPTIDE LINKAGES BETWEEN DOMAINS.
RfactorNum. reflection% reflection
Rfree0.3714 197 4.63 %
Rwork0.3526 --
obs0.3537 4253 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 7.501→55.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9134 0 0 0 9134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0199345
X-RAY DIFFRACTIONf_angle_d2.43912628
X-RAY DIFFRACTIONf_dihedral_angle_d13.4493481
X-RAY DIFFRACTIONf_chiral_restr0.1311420
X-RAY DIFFRACTIONf_plane_restr0.021641
LS refinement shellResolution: 7.5012→55.1497 Å
RfactorNum. reflection% reflection
Rfree0.3714 197 -
Rwork0.3526 4056 -
obs--99 %

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