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- PDB-2h7v: Co-crystal structure of YpkA-Rac1 -

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Basic information

Entry
Database: PDB / ID: 2h7v
TitleCo-crystal structure of YpkA-Rac1
Components
  • Migration-inducing protein 5
  • Protein kinase ypkA
KeywordsSIGNALING PROTEIN / YpkA / YopO / Rac1 / GDI / GTPase / Yersinia
Function / homology
Function and homology information


regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 ...regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / respiratory burst / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / Activation of RAC1 downstream of NMDARs / Rho GDP-dissociation inhibitor binding / small GTPase-mediated signal transduction / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RHO GTPases activate IQGAPs / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / cell chemotaxis / substrate adhesion-dependent cell spreading / cell-matrix adhesion / small monomeric GTPase / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament organization / cell motility / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network / Signaling by SCF-KIT / cytoplasmic ribonucleoprotein granule / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / VEGFA-VEGFR2 Pathway / response to wounding / recycling endosome membrane / Constitutive Signaling by Aberrant PI3K in Cancer / melanosome
Similarity search - Function
Rac1-binding domain, N-terminal GTPase binding subdomain / Rac1-binding domain, C-terminal subdomain / Serine/threonine protein kinase, yersinia-type / YpkA, Rac1-binding domain / Rac1-binding domain, C-terminal / Rac1-binding domain, N-terminal / Rac1-binding domain / Small GTPase Rho / small GTPase Rho family profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Rac1-binding domain, N-terminal GTPase binding subdomain / Rac1-binding domain, C-terminal subdomain / Serine/threonine protein kinase, yersinia-type / YpkA, Rac1-binding domain / Rac1-binding domain, C-terminal / Rac1-binding domain, N-terminal / Rac1-binding domain / Small GTPase Rho / small GTPase Rho family profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, 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 / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related C3 botulinum toxin substrate 1 / Protein kinase YpkA
Similarity search - Component
Biological speciesHomo sapiens (human)
Yersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPrehna, G. / Ivanov, M. / Bliska, J.B. / Stebbins, C.E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Yersinia virulence depends on mimicry of host rho-family nucleotide dissociation inhibitors.
Authors: Prehna, G. / Ivanov, M.I. / Bliska, J.B. / Stebbins, C.E.
History
DepositionJun 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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 1.4Aug 30, 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: Migration-inducing protein 5
B: Migration-inducing protein 5
C: Protein kinase ypkA
D: Protein kinase ypkA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4118
Polymers110,4764
Non-polymers9354
Water1,35175
1
A: Migration-inducing protein 5
C: Protein kinase ypkA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7064
Polymers55,2382
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Migration-inducing protein 5
D: Protein kinase ypkA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7064
Polymers55,2382
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.398, 75.519, 99.772
Angle α, β, γ (deg.)92.08, 103.38, 115.79
Int Tables number1
Space group name H-MP1
DetailsDimer consisting of one YpkA molecule and one Rac1 molecule. Biological contact is residues 574 to 601 of YpkA.

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Components

#1: Protein Migration-inducing protein 5 / Ras-related C3 botulinum toxin substrate 1 / isoform Rac1


Mass: 20789.117 Da / Num. of mol.: 2 / Mutation: F78S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIG5, RAC1 / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P63000
#2: Protein Protein kinase ypkA / Protein kinase A / Targeted effector protein kinase


Mass: 34449.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: ypkA / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q05608
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM HEPES pH 6.5-7.5, 5%-8% PEGMME2000 micro seeding, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1801
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.1
SYNCHROTRONNSLS X29A21.1
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDApr 21, 2005Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror
ADSC QUANTUM 3152CCDApr 21, 2005Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21
ReflectionResolution: 2.6→95.78 Å / Num. obs: 51987 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rsym value: 0.09 / Net I/σ(I): 11.8
Reflection shellResolution: 2.6→2.667 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.418 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2H7O, 1MH1

2h7o

1mh1


Resolution: 2.6→95.78 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 26.265 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.354 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2552 5 %RANDOM
Rwork0.222 ---
all0.224 ---
obs0.222 51262 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.645 Å2
Baniso -1Baniso -2Baniso -3
1-7.3 Å24.77 Å2-3.29 Å2
2--0.97 Å2-0.77 Å2
3----5.7 Å2
Refinement stepCycle: LAST / Resolution: 2.6→95.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7058 0 58 75 7191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227223
X-RAY DIFFRACTIONr_bond_other_d0.0020.026710
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9879775
X-RAY DIFFRACTIONr_angle_other_deg0.866315624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0395883
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49224.308318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.171151340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9511553
X-RAY DIFFRACTIONr_chiral_restr0.0840.21147
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021367
X-RAY DIFFRACTIONr_nbd_refined0.2420.21914
X-RAY DIFFRACTIONr_nbd_other0.1850.27111
X-RAY DIFFRACTIONr_nbtor_refined0.190.23697
X-RAY DIFFRACTIONr_nbtor_other0.0930.24635
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2203
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0590.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0340.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.2109
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.24
X-RAY DIFFRACTIONr_mcbond_it0.8741.55686
X-RAY DIFFRACTIONr_mcbond_other0.1361.51803
X-RAY DIFFRACTIONr_mcangle_it1.09127200
X-RAY DIFFRACTIONr_scbond_it1.57933128
X-RAY DIFFRACTIONr_scangle_it2.5044.52575
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 162 -
Rwork0.373 3649 -
obs-3811 99.5 %
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)
12.6988-2.522.4136.4001-2.47134.5338-0.2353-0.01950.3198-0.1464-0.1275-0.5774-0.41920.34430.3628-0.08370.0965-0.0052-0.3251-0.0404-0.12392.325-13.915-34.124
28.0317-1.5123.24961.3848-0.50973.3601-0.230.11220.9175-0.0668-0.2511-0.1441-0.71570.01970.4811-0.0516-0.0576-0.0191-0.08910.0372-0.0465-9.406-13.538-98.915
30.14460.4021-0.92441.1338-2.67896.6549-0.13050.15750.0637-0.04240.34160.02890.70010.0917-0.2111-0.0359-0.0392-0.0016-0.11760.0044-0.021111.268-37.541-71.343
40.54540.0415-0.0444.16275.66657.7321-0.01160.2689-0.21430.6369-0.32750.27540.7133-1.23130.33920.2540.0858-0.09010.08450.04050.0071-25.968-4.697-56.522
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 1785 - 182
22BB1 - 1795 - 183
33CC439 - 51410 - 85
43CC532 - 648103 - 219
53CC657 - 702228 - 273
63CC704 - 732275 - 303
74DD441 - 48612 - 57
84DD489 - 51260 - 83
94DD533 - 647104 - 218
104DD658 - 732229 - 303

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