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- PDB-5xqz: Structure of the MOB1-NDR2 complex -

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Basic information

Entry
Database: PDB / ID: 5xqz
TitleStructure of the MOB1-NDR2 complex
Components
  • MOB kinase activator 1A
  • Serine/threonine-protein kinase 38-like
KeywordsSIGNALING PROTEIN/TRANSFERASE / SIGNALING PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


regulation of cellular component organization / postsynapse organization / hippo signaling / Signaling by Hippo / protein kinase activator activity / negative regulation of autophagy / protein serine/threonine kinase activator activity / actin cytoskeleton / actin binding / protein phosphorylation ...regulation of cellular component organization / postsynapse organization / hippo signaling / Signaling by Hippo / protein kinase activator activity / negative regulation of autophagy / protein serine/threonine kinase activator activity / actin cytoskeleton / actin binding / protein phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / magnesium ion binding / extracellular exosome / ATP binding / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / : / Protein kinase, C-terminal / Protein kinase C terminal domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Extension to Ser/Thr-type protein kinases ...MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / : / Protein kinase, C-terminal / Protein kinase C terminal domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
MOB kinase activator 1A / Serine/threonine-protein kinase 38-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsWu, G. / Lin, K.
CitationJournal: Nat Commun / Year: 2017
Title: Stable MOB1 interaction with Hippo/MST is not essential for development and tissue growth control.
Authors: Kulaberoglu, Y. / Lin, K. / Holder, M. / Gai, Z. / Gomez, M. / Assefa Shifa, B. / Mavis, M. / Hoa, L. / Sharif, A.A.D. / Lujan, C. / Smith, E.S.J. / Bjedov, I. / Tapon, N. / Wu, G. / Hergovich, A.
History
DepositionJun 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MOB kinase activator 1A
C: Serine/threonine-protein kinase 38-like
B: MOB kinase activator 1A
D: Serine/threonine-protein kinase 38-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4119
Polymers61,0044
Non-polymers4075
Water4,468248
1
A: MOB kinase activator 1A
C: Serine/threonine-protein kinase 38-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7515
Polymers30,5022
Non-polymers2503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-18 kcal/mol
Surface area13280 Å2
MethodPISA
2
B: MOB kinase activator 1A
D: Serine/threonine-protein kinase 38-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6594
Polymers30,5022
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-18 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.519, 94.424, 102.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUAA33 - 21110 - 188
21GLUGLULEULEUBC33 - 21110 - 188
12SERSERARGARGCB21 - 842 - 65
22SERSERARGARGDD21 - 842 - 65

NCS ensembles :
ID
1
2

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Components

#1: Protein MOB kinase activator 1A / Mob1 alpha / Mob1A / Mob1 homolog 1B / Mps one binder kinase activator-like 1B


Mass: 22316.445 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 33-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOB1A, C2orf6, MOB4B, MOBK1B, MOBKL1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8S9
#2: Protein Serine/threonine-protein kinase 38-like / NDR2 protein kinase / Nuclear Dbf2-related kinase 2


Mass: 8185.360 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-87
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK38L, KIAA0965, NDR2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y2H1, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, HEPES, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 32723 / % possible obs: 99.6 % / Redundancy: 6.9 % / Net I/σ(I): 16.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.748 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R Free: 0.198 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24374 1665 5.1 %RANDOM
Rwork0.15631 ---
obs0.16084 31004 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.202 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.91 Å20 Å2
3---0.68 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4147 0 20 248 4415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024254
X-RAY DIFFRACTIONr_bond_other_d0.0020.022971
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9535723
X-RAY DIFFRACTIONr_angle_other_deg3.84537212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7365499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3224.045220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.76615782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3291529
X-RAY DIFFRACTIONr_chiral_restr0.0890.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024652
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02889
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.17437225
X-RAY DIFFRACTIONr_sphericity_free44.204575
X-RAY DIFFRACTIONr_sphericity_bonded17.257311
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A64060.16
12B64060.16
21C24690.23
22D24690.23
LS refinement shellResolution: 2.104→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 102 -
Rwork0.17 1877 -
obs--89.22 %

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