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- PDB-6czo: The KNL1-PP1 Holoenzyme -

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Basic information

Entry
Database: PDB / ID: 6czo
TitleThe KNL1-PP1 Holoenzyme
Components
  • CASC5 protein
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / PHOSPHATASE / REGULATOR / SLIM / Kinetochore
Function / homology
Function and homology information


regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / attachment of spindle microtubules to kinetochore / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein localization to kinetochore / regulation of canonical Wnt signaling pathway ...regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / attachment of spindle microtubules to kinetochore / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein localization to kinetochore / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity / protein serine/threonine phosphatase activity / branching morphogenesis of an epithelial tube / glycogen metabolic process / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / Triglyceride catabolism / phosphatase activity / phosphoprotein phosphatase activity / DARPP-32 events / ribonucleoprotein complex binding / dephosphorylation / Downregulation of TGF-beta receptor signaling / protein dephosphorylation / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / regulation of circadian rhythm / Circadian Clock / presynapse / perikaryon / dendritic spine / cell cycle / cell division / glutamatergic synapse / nucleolus / extracellular exosome / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Kinetochore scaffold 1 / KNL1 MELT repeat / MELT motif / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...Kinetochore scaffold 1 / KNL1 MELT repeat / MELT motif / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / CASC5 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsBajaj, R. / Peti, W. / Page, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098482 United States
CitationJournal: Structure / Year: 2018
Title: KNL1 Binding to PP1 and Microtubules Is Mutually Exclusive.
Authors: Bajaj, R. / Bollen, M. / Peti, W. / Page, R.
History
DepositionApr 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: CASC5 protein
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: CASC5 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,63210
Polymers82,2224
Non-polymers4106
Water1,08160
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: CASC5 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3165
Polymers41,1112
Non-polymers2053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-37 kcal/mol
Surface area12930 Å2
MethodPISA
2
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: CASC5 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3165
Polymers41,1112
Non-polymers2053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-32 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.049, 138.049, 118.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11C-525-

HOH

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Components

#1: Protein Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


Mass: 34162.148 Da / Num. of mol.: 2 / Fragment: residues 7-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein CASC5 protein


Mass: 6948.949 Da / Num. of mol.: 2 / Fragment: residues 23-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASC5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05C46
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.43 Å3/Da / Density % sol: 68.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 6000, 0.1 M HEPES, VAPOR DIFFUSION, TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.946→45.125 Å / Num. obs: 24812 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 29.2
Reflection shellResolution: 2.95→3 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1214 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MOV

4mov


Resolution: 2.95→45.125 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.43
RfactorNum. reflection% reflection
Rfree0.213 1259 5.08 %
Rwork0.169 --
obs0.172 24763 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.95→45.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4985 0 14 60 5059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045148
X-RAY DIFFRACTIONf_angle_d0.6156934
X-RAY DIFFRACTIONf_dihedral_angle_d12.2331893
X-RAY DIFFRACTIONf_chiral_restr0.024756
X-RAY DIFFRACTIONf_plane_restr0.003898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9463-3.06420.32161250.22992575X-RAY DIFFRACTION100
3.0642-3.20370.27011490.22922555X-RAY DIFFRACTION100
3.2037-3.37250.23011560.19752546X-RAY DIFFRACTION100
3.3725-3.58370.24151330.17782559X-RAY DIFFRACTION100
3.5837-3.86030.22151290.18622611X-RAY DIFFRACTION100
3.8603-4.24850.19191450.15082588X-RAY DIFFRACTION100
4.2485-4.86270.17341320.1312622X-RAY DIFFRACTION100
4.8627-6.1240.21141490.16722650X-RAY DIFFRACTION100
6.124-45.13060.20451410.16682798X-RAY DIFFRACTION100

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