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- PDB-5l7n: Plexin A1 extracellular fragment, domains 7-10 (IPT3-IPT6) -

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Basic information

Entry
Database: PDB / ID: 5l7n
TitlePlexin A1 extracellular fragment, domains 7-10 (IPT3-IPT6)
ComponentsPlexin-A1
KeywordsSIGNALING PROTEIN / IPT domain / receptor / axon guidance
Function / homology
Function and homology information


olfactory nerve formation / Other semaphorin interactions / RHOD GTPase cycle / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / neuron projection guidance / dichotomous subdivision of terminal units involved in salivary gland branching / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / RND1 GTPase cycle / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...olfactory nerve formation / Other semaphorin interactions / RHOD GTPase cycle / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / neuron projection guidance / dichotomous subdivision of terminal units involved in salivary gland branching / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / RND1 GTPase cycle / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / regulation of smooth muscle cell migration / neuron projection extension / positive regulation of axonogenesis / regulation of GTPase activity / regulation of cell migration / regulation of cell shape / plasma membrane => GO:0005886 / membrane / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Plexin-A1, Sema domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat ...Plexin-A1, Sema domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG 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 / Rho GTPase activation protein / ig-like, plexins, transcription factors / 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
DI(HYDROXYETHYL)ETHER / Plexin-A1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsKong, Y. / Janssen, B.J.C. / 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.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKA10976 United Kingdom
Medical Research Council (United Kingdom)G9900061 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
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
DepositionJun 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.occupancy / _chem_comp.name ..._atom_site.occupancy / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plexin-A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7616
Polymers42,9291
Non-polymers8325
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint16 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.880, 82.510, 125.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1521-

HOH

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Components

#1: Protein Plexin-A1 / Plexin-1


Mass: 42928.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxna1, Kiaa4053 / Cell line (production host): HEK293 S / Production host: Homo sapiens (human) / References: UniProt: P70206
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) polyethylene glycol 3,350, 100mM BIS-TRIS pH 5.5 and 200mM potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen stream
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→62.8 Å / Num. obs: 20394 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 1 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 5 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2283: ???)refinement
iMOSFLMdata reduction
Aimless0.1.27data scaling
PHASERphasing
RefinementResolution: 2.2→62.8 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2702 1032 5.07 %
Rwork0.2296 --
obs0.2317 20361 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→62.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 53 130 2821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022753
X-RAY DIFFRACTIONf_angle_d0.5193752
X-RAY DIFFRACTIONf_dihedral_angle_d14.8741678
X-RAY DIFFRACTIONf_chiral_restr0.046437
X-RAY DIFFRACTIONf_plane_restr0.004487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.31610.40211370.34342718X-RAY DIFFRACTION99
2.3161-2.46120.33571520.27112721X-RAY DIFFRACTION100
2.4612-2.65120.31421440.25932732X-RAY DIFFRACTION100
2.6512-2.9180.36421630.26092722X-RAY DIFFRACTION100
2.918-3.34020.31771410.24212764X-RAY DIFFRACTION100
3.3402-4.20820.23981480.20572779X-RAY DIFFRACTION100
4.2082-62.82560.20431470.19962893X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.7743-1.5786-0.49365.68341.09354.2252-0.13420.138-0.4432-0.12150.0650.08740.76710.35210.0810.46840.0464-0.04910.27730.03020.297730.3325-23.8216-12.0202
21.5426-1.650.85146.0773-3.52763.7465-0.04220.0143-0.05460.02620.13960.26670.09210.0776-0.11210.2826-0.0258-0.02970.30310.01070.281324.7799-2.429-18.7286
34.546-0.6474-4.09760.87691.07825.02650.10790.07540.123-0.05240.03640.0136-0.1438-0.1649-0.14950.37740.0023-0.09090.27360.03010.234734.145420.1874-44.8883
44.04794.6393-0.73136.50670.20763.94810.2905-0.38010.6570.0170.2958-1.2092-0.79240.712-0.22010.5485-0.10560.04190.3959-0.22230.792453.554333.8572-46.7681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 861 through 934 )
2X-RAY DIFFRACTION2chain 'A' and (resid 935 through 1046 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1047 through 1145 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1146 through 1227 )

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