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- PDB-4e74: Crystal structure of the RHO GTPASE BINDING DOMAIN of Plexin A4A -

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Basic information

Entry
Database: PDB / ID: 4.0E+74
TitleCrystal structure of the RHO GTPASE BINDING DOMAIN of Plexin A4A
ComponentsPlexin-A4
KeywordsSIGNALING PROTEIN / plexin / rbd / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


glossopharyngeal nerve morphogenesis / chemorepulsion of branchiomotor axon / regulation of negative chemotaxis / vagus nerve morphogenesis / anterior commissure morphogenesis / regulation of axon extension involved in axon guidance / postganglionic parasympathetic fiber development / sympathetic neuron axon guidance / trigeminal nerve structural organization / facial nerve structural organization ...glossopharyngeal nerve morphogenesis / chemorepulsion of branchiomotor axon / regulation of negative chemotaxis / vagus nerve morphogenesis / anterior commissure morphogenesis / regulation of axon extension involved in axon guidance / postganglionic parasympathetic fiber development / sympathetic neuron axon guidance / trigeminal nerve structural organization / facial nerve structural organization / branchiomotor neuron axon guidance / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / maintenance of synapse structure / semaphorin receptor complex / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / sympathetic nervous system development / semaphorin receptor activity / CRMPs in Sema3A signaling / negative regulation of cell adhesion / embryonic heart tube development / motor neuron axon guidance / positive regulation of axonogenesis / Sema3A PAK dependent Axon repulsion / semaphorin-plexin signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / regulation of cell migration / 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 RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin family / Plexin repeat ...Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsGuan, X. / Wang, H. / Tempel, W. / Dong, A. / Tong, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the RHO GTPASE BINDING DOMAIN of Plexin A4A
Authors: Guan, X. / Wang, H. / Tempel, W. / Dong, A. / Tong, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
History
DepositionMar 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plexin-A4


Theoretical massNumber of molelcules
Total (without water)13,14912
Polymers13,1491
Non-polymers011
Water1,40578
1
A: Plexin-A4

A: Plexin-A4


Theoretical massNumber of molelcules
Total (without water)26,29824
Polymers26,2982
Non-polymers022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area690 Å2
ΔGint-6 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.790, 49.790, 124.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Plexin-A4


Mass: 13149.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNA4, KIAA1550, PLXNA4A, PLXNA4B, UNQ2820/PRO34003 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9HCM2
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.2M ammonium acetate, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.58→46.217 Å / Num. obs: 22346 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.208 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 24.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.58-1.620.9862.1812236161799.9
1.62-1.670.8212.7812104157199.9
1.67-1.710.6143.82120501540100
1.71-1.770.4774.83116761478100
1.77-1.820.3426.98115111432100
1.82-1.890.269.13113781396100
1.89-1.960.18112.4111292136399.9
1.96-2.040.1317.07110781304100
2.04-2.130.09821.93108111255100
2.13-2.230.07726.37105161205100
2.23-2.360.06529.74102891154100
2.36-2.50.05734.1999601098100
2.5-2.670.04738.0693091025100
2.67-2.880.04141.88697964100
2.88-3.160.05848.4812429903100
3.16-3.530.05259.2714626830100
3.53-4.080.0468.2112862738100
4.08-50.03274.410918638100
5-7.070.03570.218530511100
7.070.02969.33442232499.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2r2o

2r2o


Resolution: 1.58→46.217 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.197 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.227 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY ARP/WARP, COOT, the MOLPROBITY server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 1148 5.154 %RANDOM
Rwork0.2029 ---
obs0.204 22274 99.973 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 61.5 Å2 / Biso mean: 17.519 Å2 / Biso min: 11.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.269 Å20 Å20 Å2
2--0.269 Å20 Å2
3----0.538 Å2
Refinement stepCycle: LAST / Resolution: 1.58→46.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms761 0 11 78 850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02787
X-RAY DIFFRACTIONr_bond_other_d0.0010.02522
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9831073
X-RAY DIFFRACTIONr_angle_other_deg0.94431300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.235104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58125.55627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.82315142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.631153
X-RAY DIFFRACTIONr_chiral_restr0.0970.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021849
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.6210.33650.2991359142799.79
1.621-1.6650.301760.2731310138899.856
1.665-1.7140.258730.24712811354100
1.714-1.7660.286670.22312181285100
1.766-1.8240.222770.20311791256100
1.824-1.8880.241820.21111211203100
1.888-1.9590.24640.2011111117699.915
1.959-2.0390.209610.18610581119100
2.039-2.1290.194420.1910301072100
2.129-2.2330.204440.1869711015100
2.233-2.3540.253420.184929971100
2.354-2.4960.222440.19867911100
2.496-2.6680.219550.195784839100
2.668-2.8810.257320.21751783100
2.881-3.1550.199310.197683714100
3.155-3.5250.223410.198606647100
3.525-4.0660.204250.196522547100
4.066-4.970.162280.16426454100
4.97-6.9890.21990.239323332100
6.989-46.2170.17620.266147149100

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