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- PDB-2rex: Crystal structure of the effector domain of PLXNB1 bound with Rnd... -

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Basic information

Entry
Database: PDB / ID: 2rex
TitleCrystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase
Components
  • Plexin-B1
  • Rho-related GTP-binding protein Rho6
KeywordsSIGNALING PROTEIN/LIPOPROTEIN / complex / Structural Genomics Consortium / SGC / gtpase / gnp / Plexin / effector domain / Glycoprotein / Membrane / Phosphorylation / Receptor / Secreted / Transmembrane / Cytoskeleton / GTP-binding / Lipoprotein / Methylation / Nucleotide-binding / Prenylation / SIGNALING PROTEIN-LIPOPROTEIN COMPLEX
Function / homology
Function and homology information


semaphorin receptor binding / negative regulation of osteoblast proliferation / semaphorin receptor complex / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / inhibitory synapse assembly / negative regulation of cell adhesion / semaphorin receptor activity / GTPase activating protein binding / Sema4D induced cell migration and growth-cone collapse / RHOD GTPase cycle ...semaphorin receptor binding / negative regulation of osteoblast proliferation / semaphorin receptor complex / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / inhibitory synapse assembly / negative regulation of cell adhesion / semaphorin receptor activity / GTPase activating protein binding / Sema4D induced cell migration and growth-cone collapse / RHOD GTPase cycle / positive regulation of axonogenesis / Sema4D mediated inhibition of cell attachment and migration / RND1 GTPase cycle / ossification involved in bone maturation / small GTPase-mediated signal transduction / neuron remodeling / positive regulation of Rho protein signal transduction / regulation of cytoskeleton organization / semaphorin-plexin signaling pathway / synapse assembly / GTPase activator activity / positive regulation of GTPase activity / neuron projection morphogenesis / regulation of cell migration / actin filament organization / adherens junction / regulation of actin cytoskeleton organization / cell migration / transmembrane signaling receptor activity / actin cytoskeleton / G alpha (12/13) signalling events / regulation of cell shape / postsynaptic membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / signaling receptor binding / intracellular membrane-bounded organelle / GTPase activity / protein kinase binding / GTP binding / glutamatergic synapse / signal transduction / extracellular region / plasma membrane / cytosol
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 / Small GTPase Rho / small GTPase Rho family profile. / ig-like, plexins, transcription factors / Rho GTPase activation protein / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / Immunoglobulin E-set / P-loop containing nucleotide triphosphate hydrolases / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Plexin-B1 / Rho-related GTP-binding protein Rho6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsTong, Y. / Tempel, W. / Shen, L. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase.
Authors: Tong, Y. / Tempel, W. / Shen, L. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionSep 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plexin-B1
B: Rho-related GTP-binding protein Rho6
C: Plexin-B1
D: Rho-related GTP-binding protein Rho6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,66040
Polymers70,4874
Non-polymers1,17336
Water1,35175
1
A: Plexin-B1
B: Rho-related GTP-binding protein Rho6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,83020
Polymers35,2432
Non-polymers58718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
MethodPISA
2
C: Plexin-B1
D: Rho-related GTP-binding protein Rho6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,83020
Polymers35,2432
Non-polymers58718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
MethodPISA
3
A: Plexin-B1
B: Rho-related GTP-binding protein Rho6
hetero molecules

C: Plexin-B1
D: Rho-related GTP-binding protein Rho6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,66040
Polymers70,4874
Non-polymers1,17336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area4850 Å2
MethodPISA
4
A: Plexin-B1
B: Rho-related GTP-binding protein Rho6
hetero molecules

A: Plexin-B1
B: Rho-related GTP-binding protein Rho6
hetero molecules

C: Plexin-B1
D: Rho-related GTP-binding protein Rho6
hetero molecules

C: Plexin-B1
D: Rho-related GTP-binding protein Rho6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,32080
Polymers140,9738
Non-polymers2,34672
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_545-x,y-1,-z1
Buried area11120 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.136, 71.653, 101.885
Angle α, β, γ (deg.)90.000, 128.360, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe authors state that the relationships between chains A and B and between chains C and D of the asymmetric unit reflect the biologically relevant interface between the plexin effector domain and RND1 gtpase.

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Plexin-B1 / Semaphorin receptor SEP


Mass: 13297.139 Da / Num. of mol.: 2 / Fragment: Residues 1743-1862
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, PLXN5, SEP / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O43157
#2: Protein Rho-related GTP-binding protein Rho6 / Rho family GTPase 1 / Rnd1


Mass: 21946.164 Da / Num. of mol.: 2 / Fragment: Residues 5-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RND1, RHO6 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q92730

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Non-polymers , 5 types, 111 molecules

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


Num. of mol.: 30 / Source method: obtained synthetically
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 36932 / % possible obs: 97.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Χ2: 1.503 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.383.20.23132320.661184.8
2.38-2.483.40.20534860.664193.1
2.48-2.593.60.1836870.711198.1
2.59-2.733.70.15737380.786199.8
2.73-2.93.80.10637940.7381100
2.9-3.123.80.08338090.8111100
3.12-3.433.80.05937770.951199.9
3.43-3.933.80.04837861.209199.8
3.93-4.953.80.03938091.307199.9
4.95-303.60.05338146.995197.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2CLS,2R2O

2cls

2r2o


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.214 / SU B: 11.089 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Atomic B factors are residuals of TLS refinement. Programs coot, molprobity have also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 999 2.71 %Thin shells
Rwork0.215 ---
all0.216 36863 --
obs0.216 36863 97.472 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.565 Å2
Baniso -1Baniso -2Baniso -3
1-5.87 Å20 Å22.92 Å2
2---2.831 Å20 Å2
3---0.585 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4279 0 98 75 4452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224457
X-RAY DIFFRACTIONr_bond_other_d0.0020.022906
X-RAY DIFFRACTIONr_angle_refined_deg1.4482.0046081
X-RAY DIFFRACTIONr_angle_other_deg0.9493.0017146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30324.25160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75215721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0821523
X-RAY DIFFRACTIONr_chiral_restr0.0810.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02811
X-RAY DIFFRACTIONr_nbd_refined0.1910.2781
X-RAY DIFFRACTIONr_nbd_other0.190.22988
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22071
X-RAY DIFFRACTIONr_nbtor_other0.0870.22304
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2156
X-RAY DIFFRACTIONr_metal_ion_refined0.1960.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.40.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.27
X-RAY DIFFRACTIONr_mcbond_it0.5951.52917
X-RAY DIFFRACTIONr_mcbond_other0.1281.51133
X-RAY DIFFRACTIONr_mcangle_it0.93624579
X-RAY DIFFRACTIONr_scbond_it1.50831801
X-RAY DIFFRACTIONr_scangle_it2.3274.51498
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 (%)
2.3-2.35900.2312305273884.186
2.359-2.42300.2312437268690.73
2.423-2.49200.2292480260395.275
2.492-2.5670.3172270.2212251252698.1
2.567-2.6500.2152448245499.756
2.65-2.7410.2621740.2212214239299.833
2.741-2.8430.252120.21322982310100
2.843-2.95600.21222252225100
2.956-3.0850.2311670.22519572124100
3.085-3.23100.2012022202399.951
3.231-3.4010.2411270.20218291956100
3.401-3.60100.21838184399.729
3.601-3.84100.2191745175099.714
3.841-4.1360.227900.2021517160899.938
4.136-4.5110.232780.1871425150599.867
4.511-5.01200.1921375137799.855
5.012-5.7280.209540.2171165122099.918
5.728-6.8760.246350.2561032106999.813
6.876-9.1950.256200.23481884399.407
9.195-200.368150.31448356787.831
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)
11.54830.56920.47484.45852.37884.6060.0260.31610.3174-0.4669-0.0062-0.0951-0.73670.0936-0.01980.0654-0.01480.0576-0.10030.0870.048619.6909-47.23496.9249
22.74361.0575-1.53525.0421-0.16063.10130.2623-0.10670.36460.3037-0.20330.513-0.3237-0.3247-0.059-0.1152-0.00010.0226-0.0854-0.0604-0.123.7864-62.834227.5641
34.6173-1.9355-0.42893.50440.2761.4222-0.0392-0.2648-0.67220.0956-0.03790.25210.3328-0.23630.0771-0.0753-0.0715-0.0654-0.09940.0476-0.09998.6767-21.862821.0376
42.32740.333-0.91363.8074-0.99333.39890.06770.3245-0.1831-0.5172-0.1417-0.25460.20750.02620.074-0.14340.0460.0033-0.091-0.0189-0.134524.4757-6.62410.0131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1746 - 1852
2X-RAY DIFFRACTION2B13 - 188
3X-RAY DIFFRACTION3C1746 - 1852
4X-RAY DIFFRACTION4D7 - 188

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