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- PDB-7kdc: The complex between RhoD and the Plexin B2 RBD -

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Basic information

Entry
Database: PDB / ID: 7kdc
TitleThe complex between RhoD and the Plexin B2 RBD
Components
  • Plexin-B2
  • Rho-related GTP-binding protein RhoD
KeywordsSIGNALING PROTEIN / Plexin / RhoD / GTPase / axon guidance
Function / homology
Function and homology information


excitatory synapse assembly / regulation of neuron migration / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor activity / negative regulation of cell adhesion / focal adhesion assembly / RHOD GTPase cycle / semaphorin receptor complex / regulation of small GTPase mediated signal transduction / lamellipodium assembly ...excitatory synapse assembly / regulation of neuron migration / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor activity / negative regulation of cell adhesion / focal adhesion assembly / RHOD GTPase cycle / semaphorin receptor complex / regulation of small GTPase mediated signal transduction / lamellipodium assembly / positive regulation of axonogenesis / regulation of GTPase activity / homophilic cell adhesion via plasma membrane adhesion molecules / actin filament bundle assembly / semaphorin-plexin signaling pathway / Rho protein signal transduction / positive regulation of cell adhesion / neuroblast proliferation / regulation of cell migration / guanyl-nucleotide exchange factor activity / neural tube closure / positive regulation of translation / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / actin filament organization / regulation of protein phosphorylation / brain development / positive regulation of neuron projection development / cell migration / regulation of cell shape / collagen-containing extracellular matrix / mitochondrial outer membrane / early endosome / endosome membrane / positive regulation of cell migration / Golgi membrane / GTPase activity / GTP binding / protein kinase binding / signal transduction / plasma membrane / cytosol
Similarity search - Function
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 ...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 / Small GTPase Rho / small GTPase Rho family profile. / ig-like, plexins, transcription factors / Rho GTPase activation protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Plexin-B2 / Rho-related GTP-binding protein RhoD
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKuo, Y. / Wang, Y. / Zhang, x.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationI-1702 United States
CitationJournal: Elife / Year: 2021
Title: A putative structural mechanism underlying the antithetic effect of homologous RND1 and RhoD GTPases in mammalian plexin regulation.
Authors: Liu, Y. / Ke, P. / Kuo, Y.C. / Wang, Y. / Zhang, X. / Song, C. / Shan, Y.
History
DepositionOct 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.2Aug 11, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho-related GTP-binding protein RhoD
B: Rho-related GTP-binding protein RhoD
C: Plexin-B2
D: Plexin-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,14710
Polymers66,0064
Non-polymers1,1426
Water1448
1
A: Rho-related GTP-binding protein RhoD
C: Plexin-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5745
Polymers33,0032
Non-polymers5713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-27 kcal/mol
Surface area16270 Å2
MethodPISA
2
B: Rho-related GTP-binding protein RhoD
D: Plexin-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5745
Polymers33,0032
Non-polymers5713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-27 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.810, 82.810, 136.761
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein Rho-related GTP-binding protein RhoD / Rho-related protein HP1 / RhoHP1


Mass: 21335.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOD, ARHD / Production host: Escherichia coli (E. coli) / References: UniProt: O00212
#2: Protein Plexin-B2


Mass: 11667.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxnb2 / Production host: Escherichia coli (E. coli) / References: UniProt: B2RXS4
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThe original sequence for chains C and D included residues 1274 to 1842 of UNP PLXB2_MOUSE B2RXS4, ...The original sequence for chains C and D included residues 1274 to 1842 of UNP PLXB2_MOUSE B2RXS4, however, proteolytic cleavage occurs during incubation at an unknown site. Thus, the reported sequence corresponds to the portion observed in the coordinates, which is residues 1463 to 1565 of UNP PLXB2_MOUSE B2RXS4.

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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: 4.1 Å3/Da / Density % sol: 70.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M MgCl2, 22 % (w/v) PEG 3350, and 100 mM MIB (pH 6.8, sodium malonate, imidazole, and boric acid mixed at 2:3:3 molar ratio).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 19325 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 107.05 Å2 / Rpim(I) all: 0.059 / Rsym value: 0.075 / Net I/σ(I): 23.2
Reflection shellResolution: 3.1→3.15 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 857 / CC1/2: 0.843 / Rpim(I) all: 0.465 / Rsym value: 0.514 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2REX

2rex


Resolution: 3.1→39.63 Å / SU ML: 0.4476 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 37.7234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2664 951 5.07 %
Rwork0.2151 17812 -
obs0.2178 18763 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 123.4 Å2
Refinement stepCycle: LAST / Resolution: 3.1→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 68 8 4458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244546
X-RAY DIFFRACTIONf_angle_d0.48216217
X-RAY DIFFRACTIONf_chiral_restr0.0428720
X-RAY DIFFRACTIONf_plane_restr0.005787
X-RAY DIFFRACTIONf_dihedral_angle_d18.4906621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.260.37621350.35892431X-RAY DIFFRACTION94.55
3.26-3.470.37741390.27942574X-RAY DIFFRACTION99.3
3.47-3.740.3631280.25712548X-RAY DIFFRACTION98.6
3.74-4.110.27571310.23392595X-RAY DIFFRACTION99.42
4.11-4.710.29461400.22972548X-RAY DIFFRACTION99.56
4.71-5.930.23111440.21762570X-RAY DIFFRACTION99.82
5.93-39.630.22271340.16662546X-RAY DIFFRACTION99.19
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.196023313091.04834450438-0.3084937528143.06984101017-1.798150249062.369813493970.2391071946920.07228675160790.05998720348990.169877358213-0.392430756276-0.00914654373522-0.562421891159-0.05962310027180.2045706472431.3027068540.1018208123570.1406713878241.20199351840.07549875223240.779959144812-9.7887309760152.02948128254.05022005745
22.69174651651.511398485371.371038277183.477954947870.6901067073252.09782202869-0.302972733877-0.3009271155460.108381277082-0.1607083453070.2350156870150.023836981191-0.2822136081790.6006213127130.1117443823211.009568575190.0103124067259-0.01707726191741.23772990541-0.1812261354330.652037026972-32.858298758365.3283911708-80.1342770533
34.229019430431.562232592481.311430518832.798033373160.18214793670.160713332090.004533774448130.659602709478-0.293154774458-0.2186097770610.12906049043-0.1248575170970.2337577607960.425443519467-0.2209922995321.071850350110.114034769795-0.03551990042331.23118033804-0.1548739947420.764994474893-19.780556143866.0915369572-51.818047837
41.211122942270.277706620120.844899318638.25759210829-2.050279497941.38849956159-0.170858028592-0.110581145780.06775495174190.7838450361310.2737827946730.611722708988-0.471507959998-0.367491007815-0.2078420949610.9569748205560.1468258898570.1157362771121.100441443620.09470054748810.772116401304-15.559916960363.8307896514-24.3155397241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 15:194 OR RESID 201:202 ) )A15 - 194
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 15:194 OR RESID 201:202 ) )A201 - 202
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 15:194 OR RESID 201:202 ) )B15 - 194
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 15:194 OR RESID 201:202 ) )B201 - 202
5X-RAY DIFFRACTION3( CHAIN C AND RESID 1463:1508 ) OR ( CHAIN D AND RESID 1509:1565 )C1463 - 1508
6X-RAY DIFFRACTION3( CHAIN C AND RESID 1463:1508 ) OR ( CHAIN D AND RESID 1509:1565 )D1509 - 1565
7X-RAY DIFFRACTION4( CHAIN C AND RESID 1509:1565 ) OR ( CHAIN D AND RESID 1463:1508 )C1509 - 1565
8X-RAY DIFFRACTION4( CHAIN C AND RESID 1509:1565 ) OR ( CHAIN D AND RESID 1463:1508 )D1463 - 1508

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