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- PDB-3q3j: Crystal structure of plexin A2 RBD in complex with Rnd1 -

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Basic information

Entry
Database: PDB / ID: 3q3j
TitleCrystal structure of plexin A2 RBD in complex with Rnd1
Components
  • Plexin-A2
  • Rho-related GTP-binding protein Rho6
KeywordsMembrane protein/protein binding / Ras-binding domain / plexin / small gtpase / structural genomics consortium / SGC / Membrane protein-protein binding complex
Function / homology
Function and homology information


cerebellar granule cell precursor tangential migration / Other semaphorin interactions / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor complex / limb bud formation / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / pharyngeal system development / Sema4D induced cell migration and growth-cone collapse / semaphorin receptor activity / cortical cytoskeleton organization ...cerebellar granule cell precursor tangential migration / Other semaphorin interactions / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor complex / limb bud formation / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / pharyngeal system development / Sema4D induced cell migration and growth-cone collapse / semaphorin receptor activity / cortical cytoskeleton organization / CRMPs in Sema3A signaling / negative regulation of cell adhesion / Sema4D mediated inhibition of cell attachment and migration / RND1 GTPase cycle / neural tube development / centrosome localization / neuron remodeling / semaphorin-plexin signaling pathway / positive regulation of axonogenesis / small GTPase mediated signal transduction / establishment or maintenance of cell polarity / Sema3A PAK dependent Axon repulsion / somitogenesis / regulation of GTPase activity / regulation of actin cytoskeleton organization / regulation of cell migration / actin filament organization / cell projection / adherens junction / cell cortex / actin cytoskeleton / cell migration / regulation of cell shape / cytoplasmic vesicle / cytoskeleton / GTPase activity / signaling receptor binding / intracellular membrane-bounded organelle / GTP binding / protein kinase binding / plasma membrane => GO:0005886 / identical protein binding / plasma membrane
Similarity search - Function
Plexin-A2, 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-A2, 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 superfamily / Sema domain profile. / Sema domain / small GTPase Rho family profile. / Small GTPase Rho / IPT/TIG domain / Rho GTPase activation protein / ig-like, plexins, transcription factors / domain found in Plexins, Semaphorins and Integrins / PSI domain / IPT domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Immunoglobulin-like fold / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Plexin-A2 / Rho-related GTP-binding protein Rho6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.971 Å
AuthorsWang, H. / Tempel, W. / Tong, Y. / Guan, X. / Shen, L. / Buren, L. / Zhang, N. / Wernimont, A.K. / Crombet, L. / Arrowsmith, C.H. ...Wang, H. / Tempel, W. / Tong, Y. / Guan, X. / Shen, L. / Buren, L. / Zhang, N. / Wernimont, A.K. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of plexin A2 RBD in complex with Rnd1
Authors: Wang, H. / Tempel, W. / Tong, Y. / Guan, X. / Shen, L. / Buren, L. / Zhang, N. / Wernimont, A.K. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
History
DepositionDec 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plexin-A2
B: Rho-related GTP-binding protein Rho6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,64413
Polymers37,0972
Non-polymers54711
Water68538
1
A: Plexin-A2
B: Rho-related GTP-binding protein Rho6
hetero molecules

A: Plexin-A2
B: Rho-related GTP-binding protein Rho6
hetero molecules

A: Plexin-A2
B: Rho-related GTP-binding protein Rho6
hetero molecules

A: Plexin-A2
B: Rho-related GTP-binding protein Rho6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,57652
Polymers148,3908
Non-polymers2,18644
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area12370 Å2
ΔGint-138 kcal/mol
Surface area51980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.022, 67.129, 145.291
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-203-

UNX

21B-204-

UNX

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Plexin-A2 / Semaphorin receptor OCT


Mass: 13007.935 Da / Num. of mol.: 1 / Fragment: UNP residues 1490-1600
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNA2, KIAA0463, OCT, PLXN2, UNQ209/PRO235 / Plasmid: pET28-mhl (GI:134105571) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O75051
#2: Protein Rho-related GTP-binding protein Rho6 / Rho family GTPase 1 / Rnd1


Mass: 24089.500 Da / Num. of mol.: 1 / Fragment: UNP residues 5-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RND1, RHO6 / Plasmid: pET28-mhl (GI:134105571) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q92730

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Non-polymers , 4 types, 49 molecules

#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 9 / Source method: obtained synthetically
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.94 Å3/Da / Density % sol: 36.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The complex sample (2.7 mg/mL) was incubated with 5mM Gpp(NH)p. Crystallization cocktail: 25.5% PEG3350, 0.2 M magnesium chloride, 0.1M Hepes. Seeding was applied in the production of the ...Details: The complex sample (2.7 mg/mL) was incubated with 5mM Gpp(NH)p. Crystallization cocktail: 25.5% PEG3350, 0.2 M magnesium chloride, 0.1M Hepes. Seeding was applied in the production of the diffraction-quality crystal., pH 7.5, vapor diffusion, sitting drops, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98322 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98322 Å / Relative weight: 1
ReflectionResolution: 1.97→40 Å / Num. obs: 20734 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Χ2: 1.567 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.97-27.20.96410181.276100
2-2.047.30.77210191.312100
2.04-2.087.30.67710281.397100
2.08-2.127.30.5410291.333100
2.12-2.177.30.41810101.354100
2.17-2.227.30.33510091.346100
2.22-2.277.20.31910361.427100
2.27-2.347.30.26310121.363100
2.34-2.47.30.21710301.361100
2.4-2.487.30.17110331.336100
2.48-2.577.30.14310341.319100
2.57-2.677.30.11310311.386100
2.67-2.87.20.08910311.31899.9
2.8-2.947.20.07310351.444100
2.94-3.137.20.06310331.686100
3.13-3.377.10.05510432.15100
3.37-3.717.10.05310602.519100
3.71-4.246.90.04210572.328100
4.24-5.346.80.03210631.724100
5.34-406.60.03511232.00199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2REX, 3ig3
Resolution: 1.971→39.276 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.979 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. The programs chainsaw (CCP4) and Coot and the Molprobity server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 1072 5.187 %RANDOM
Rwork0.211 ---
obs0.213 20667 99.284 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso max: 93.31 Å2 / Biso mean: 30.452 Å2 / Biso min: 20.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.595 Å20 Å20 Å2
2--0.241 Å20 Å2
3---0.354 Å2
Refinement stepCycle: LAST / Resolution: 1.971→39.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 42 38 2145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222140
X-RAY DIFFRACTIONr_bond_other_d0.0010.021352
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9962927
X-RAY DIFFRACTIONr_angle_other_deg0.87333338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5935274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94924.59574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19515340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.304159
X-RAY DIFFRACTIONr_chiral_restr0.070.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02387
X-RAY DIFFRACTIONr_mcbond_it0.4911.51390
X-RAY DIFFRACTIONr_mcbond_other0.1181.5550
X-RAY DIFFRACTIONr_mcangle_it0.93822239
X-RAY DIFFRACTIONr_scbond_it1.5123750
X-RAY DIFFRACTIONr_scangle_it2.3834.5688
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 (%)
1.971-2.0220.334660.2521367151094.901
2.022-2.0770.239750.2391392147199.728
2.077-2.1370.261850.2281344143599.582
2.137-2.2030.239710.2151311138999.496
2.203-2.2750.259790.2051273135699.705
2.275-2.3550.298650.2171243131399.619
2.355-2.4430.244610.21195126299.525
2.443-2.5430.272580.2211158122399.428
2.543-2.6550.258660.2161112118199.746
2.655-2.7840.242540.2071056111599.552
2.784-2.9340.263590.221015107799.721
2.934-3.1110.254670.227953102199.902
3.111-3.3240.209520.20790595999.791
3.324-3.5880.23380.201855893100
3.588-3.9270.206350.19279483199.759
3.927-4.3850.226360.18272175899.868
4.385-5.0530.252360.18664568299.853
5.053-6.1640.246320.22155058499.658
6.164-8.6110.2210.24843946399.352
8.611-39.2760.416160.24126729396.587
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)
16.50090.6347-1.62013.78630.89774.9229-0.07720.2227-0.0837-0.1597-0.22150.33660.0296-0.44430.29870.1051-0.00760.01020.10560.03060.1367-7.543912.288231.4727
23.40371.3583-0.51282.5825-0.61952.0134-0.14140.3181-0.014-0.22920.21460.12090.0824-0.136-0.07320.1158-0.0499-0.02260.09920.0340.021714.651222.616514.0516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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