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- PDB-4mit: Crystal structure of E. histolytica RacC bound to the EhPAK4 PBD -

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Basic information

Entry
Database: PDB / ID: 4mit
TitleCrystal structure of E. histolytica RacC bound to the EhPAK4 PBD
Components
  • Rho family GTPase
  • Serine/threonine protein kinase PAK, putative
KeywordsSIGNALING PROTEIN / G domain / p21 binding domain / CRIB motif / hydrolase / kinase / GTP binding
Function / homology
Function and homology information


histone H4S1 kinase activity / : / histone H3S57 kinase activity / histone H2BS14 kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / histone H2BS36 kinase activity ...histone H4S1 kinase activity / : / histone H3S57 kinase activity / histone H2BS14 kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / histone H2BS36 kinase activity / Rho-dependent protein serine/threonine kinase activity / AMP-activated protein kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H3T3 kinase activity / 3-phosphoinositide-dependent protein kinase activity / histone H3T45 kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3T11 kinase activity / histone H3S10 kinase activity / small GTPase-mediated signal transduction / small monomeric GTPase / cytoskeleton / GTPase activity / GTP binding / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
SerineThreonine-protein kinase PAK-alpha; Chain A / CRIB domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain / Small GTPase Rho / Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase Ras domain profile. ...SerineThreonine-protein kinase PAK-alpha; Chain A / CRIB domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain / Small GTPase Rho / Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase Ras domain profile. / 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 / 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 / Alpha-Beta Complex / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Rho family GTPase / Serine/threonine protein kinase PAK, putative / Rho-related protein racC
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBosch, D.E. / Siderovski, D.P.
CitationJournal: Biochemistry / Year: 2015
Title: Entamoeba histolytica RacC Selectively Engages p21-Activated Kinase Effectors.
Authors: Bosch, D.E. / Siderovski, D.P.
History
DepositionSep 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Sep 20, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho family GTPase
B: Rho family GTPase
C: Rho family GTPase
D: Rho family GTPase
E: Serine/threonine protein kinase PAK, putative
F: Serine/threonine protein kinase PAK, putative
G: Serine/threonine protein kinase PAK, putative
H: Serine/threonine protein kinase PAK, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,98824
Polymers112,6048
Non-polymers2,38416
Water6,143341
1
A: Rho family GTPase
E: Serine/threonine protein kinase PAK, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7476
Polymers28,1512
Non-polymers5964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-43 kcal/mol
Surface area10990 Å2
MethodPISA
2
B: Rho family GTPase
F: Serine/threonine protein kinase PAK, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7476
Polymers28,1512
Non-polymers5964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-43 kcal/mol
Surface area10620 Å2
MethodPISA
3
C: Rho family GTPase
G: Serine/threonine protein kinase PAK, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7476
Polymers28,1512
Non-polymers5964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-44 kcal/mol
Surface area11360 Å2
MethodPISA
4
D: Rho family GTPase
H: Serine/threonine protein kinase PAK, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7476
Polymers28,1512
Non-polymers5964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-46 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.322, 211.957, 49.780
Angle α, β, γ (deg.)90.00, 102.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Rho family GTPase


Mass: 20645.807 Da / Num. of mol.: 4 / Mutation: Q65L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EhRacC, KM1_331620 / Plasmid: pLIC His / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: M7WE85, UniProt: Q24816*PLUS, small monomeric GTPase
#2: Protein
Serine/threonine protein kinase PAK, putative


Mass: 7505.105 Da / Num. of mol.: 4 / Fragment: EhPAK4 PBD, unp residues 33-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EHI7A_018700, EhPAK4 / Plasmid: pLIC His / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: N9UZ59
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: EhRacC-GTP/EhPAK4 PBD complex was mixed 1:1 with and equilibrated against crystallization solution containing 22% (w/v) PEG 4000, 200 mM magnesium chloride, and 100 mM MES, pH 6.5, VAPOR ...Details: EhRacC-GTP/EhPAK4 PBD complex was mixed 1:1 with and equilibrated against crystallization solution containing 22% (w/v) PEG 4000, 200 mM magnesium chloride, and 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 14, 2013 / Details: custom
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→46.9 Å / Num. all: 41369 / Num. obs: 36818 / % possible obs: 89 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 48.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 34.7
Reflection shellResolution: 2.35→2.37 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.8 / Num. unique all: 910 / % possible all: 85

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TH5

3th5


Resolution: 2.35→46.896 Å / SU ML: 0.28 / σ(F): 1.39 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2003 5.45 %RANDOM
Rwork0.1761 ---
obs0.1785 36744 86.95 %-
all-42234 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→46.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6874 0 140 341 7355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137165
X-RAY DIFFRACTIONf_angle_d1.2779766
X-RAY DIFFRACTIONf_dihedral_angle_d17.3932632
X-RAY DIFFRACTIONf_chiral_restr0.0731167
X-RAY DIFFRACTIONf_plane_restr0.0061185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3321-2.39050.3044980.24041656X-RAY DIFFRACTION58
2.3905-2.45510.3231470.23012394X-RAY DIFFRACTION84
2.4551-2.52730.27961430.22892433X-RAY DIFFRACTION87
2.5273-2.60890.28361350.22212442X-RAY DIFFRACTION84
2.6089-2.70210.28721400.21192413X-RAY DIFFRACTION86
2.7021-2.81030.33571420.22082406X-RAY DIFFRACTION85
2.8103-2.93820.26121330.21252464X-RAY DIFFRACTION85
2.9382-3.09310.2731440.2212406X-RAY DIFFRACTION85
3.0931-3.28680.25871370.20772451X-RAY DIFFRACTION86
3.2868-3.54050.20991460.18732544X-RAY DIFFRACTION89
3.5405-3.89670.24741540.17862686X-RAY DIFFRACTION94
3.8967-4.46010.18491620.15142753X-RAY DIFFRACTION96
4.4601-5.61780.16931560.14312843X-RAY DIFFRACTION99
5.6178-46.9050.18111660.15262850X-RAY DIFFRACTION99

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