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- PDB-3hvq: Crystal structure of a complex between Protein Phosphatase 1 alph... -

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Basic information

Entry
Database: PDB / ID: 3hvq
TitleCrystal structure of a complex between Protein Phosphatase 1 alpha (PP1) and the PP1 binding and PDZ domains of Neurabin
Components
  • Neurabin-1
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE/HYDROLASE REGULATOR / PP1 / NEURABIN / SERINE/THREONINE PHOSPHATASE / POST SYNAPTIC DENSITY / GLUTAMETERGIC RECEPTORS / CARBOHYDRATE METABOLISM / CELL CYCLE / CELL DIVISION / GLYCOGEN METABOLISM / HYDROLASE / IRON / MANGANESE / METAL-BINDING / PHOSPHOPROTEIN / PROTEIN PHOSPHATASE / ACTIN-BINDING / CELL JUNCTION / CELL PROJECTION / CYTOSKELETON / DEVELOPMENTAL PROTEIN / DIFFERENTIATION / NEUROGENESIS / NUCLEUS / SYNAPSE / Synaptosome / HYDROLASE-HYDROLASE REGULATOR COMPLEX
Function / homology
Function and homology information


negative regulation of spontaneous neurotransmitter secretion / regulation of synapse structural plasticity / postsynaptic actin cytoskeleton organization / regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / positive regulation of long-term synaptic depression / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance ...negative regulation of spontaneous neurotransmitter secretion / regulation of synapse structural plasticity / postsynaptic actin cytoskeleton organization / regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / positive regulation of long-term synaptic depression / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding / regulation of filopodium assembly / regulation of translational initiation in response to stress / regulation of actin filament polymerization / regulation of dendritic spine morphogenesis / postsynaptic actin cytoskeleton / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / cellular response to toxic substance / growth cone lamellipodium / dephosphorylation / regulation of canonical Wnt signaling pathway / negative regulation of stress fiber assembly / dendritic spine neck / glycogen metabolic process / cortical actin cytoskeleton / protein-serine/threonine phosphatase / branching morphogenesis of an epithelial tube / regulation of synapse assembly / Triglyceride catabolism / entrainment of circadian clock by photoperiod / positive regulation of dendritic spine development / Maturation of hRSV A proteins / protein serine/threonine phosphatase activity / phosphatase activity / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / negative regulation of long-term synaptic potentiation / negative regulation of transcription elongation by RNA polymerase II / transition metal ion binding / DARPP-32 events / positive regulation of glycogen biosynthetic process / neuron development / ribonucleoprotein complex binding / protein dephosphorylation / lung development / actin filament organization / Downregulation of TGF-beta receptor signaling / excitatory postsynaptic potential / adherens junction / filopodium / neuromuscular junction / circadian regulation of gene expression / positive regulation of transcription elongation by RNA polymerase II / calcium-mediated signaling / positive regulation of neuron projection development / regulation of circadian rhythm / modulation of chemical synaptic transmission / response to lead ion / neuron projection development / actin filament binding / : / presynapse / lamellipodium / actin cytoskeleton / growth cone / GTPase binding / perikaryon / dendritic spine / transmembrane transporter binding / cytoskeleton / postsynaptic density / protein stabilization / iron ion binding / protein domain specific binding / cell division / neuronal cell body / dendrite / protein kinase binding / protein-containing complex binding / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Neurabin-1/2, PDZ domain / Neurabin-like family / PDZ domain / 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 ...Neurabin-1/2, PDZ domain / Neurabin-like family / PDZ domain / 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 / SAM domain (Sterile alpha motif) / Metallo-dependent phosphatase-like / PDZ domain / Pdz3 Domain / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / 4-Layer Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Neurabin-1 / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCritton, D.A. / Ragusa, M.J. / Page, R. / Peti, W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Spinophilin directs protein phosphatase 1 specificity by blocking substrate binding sites.
Authors: Ragusa, M.J. / Dancheck, B. / Critton, D.A. / Nairn, A.C. / Page, R. / Peti, W.
History
DepositionJun 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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_ncs_dom_lim / 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_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_conn.ptnr2_label_seq_id / _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 / _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: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Neurabin-1
D: Neurabin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,08513
Polymers112,3994
Non-polymers6869
Water10,088560
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-76 kcal/mol
Surface area33750 Å2
MethodPISA
2
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Neurabin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4055
Polymers56,2002
Non-polymers2053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-35 kcal/mol
Surface area19990 Å2
MethodPISA
3
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Neurabin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6818
Polymers56,2002
Non-polymers4816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-40 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.864, 83.655, 108.797
Angle α, β, γ (deg.)90.00, 93.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-460-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLUGLUCC436 - 49914 - 77
21PROPROGLUGLUDD436 - 49914 - 77
12LEULEUASPASPAA7 - 3006 - 299
22LEULEUASPASPBB7 - 3006 - 299

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

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


Mass: 37349.844 Da / Num. of mol.: 2 / Fragment: CATALYTIC SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1A, PPP1CA / Plasmid: RP1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein Neurabin-1 / Neurabin-I / Neural tissue-specific F-actin-binding protein I / Protein phosphatase 1 regulatory ...Neurabin-I / Neural tissue-specific F-actin-binding protein I / Protein phosphatase 1 regulatory subunit 9A / p180 / PP1bp175


Mass: 18849.867 Da / Num. of mol.: 2 / Fragment: PP1 BINDING AND PDZ DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ppp1r9a / Plasmid: RP1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O35867

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Non-polymers , 4 types, 569 molecules

#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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 0.2 M (NH4)2HPO4, 20% PEG 3350, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2008
Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING
RadiationMonochromator: SI(111) CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 54834 / Num. obs: 53709 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 25.5 Å2 / Rsym value: 0.103 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5 / Num. unique all: 2731 / Rsym value: 0.263 / % possible all: 97.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EGG

3egg


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.339 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22128 2704 5 %RANDOM
Rwork0.16083 ---
all0.16386 51001 --
obs0.16386 51001 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.592 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å21.49 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6413 0 32 560 7005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226614
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9758935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3995806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78924.451328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.436151150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0971543
X-RAY DIFFRACTIONr_chiral_restr0.0930.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025049
X-RAY DIFFRACTIONr_nbd_refined0.1960.23061
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24482
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2581
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.221
X-RAY DIFFRACTIONr_mcbond_it1.82434163
X-RAY DIFFRACTIONr_mcangle_it2.89356495
X-RAY DIFFRACTIONr_scbond_it5.13582780
X-RAY DIFFRACTIONr_scangle_it7.027112440
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1C256medium positional0.420.5
2A1176medium positional0.110.5
1C245loose positional0.655
2A1144loose positional0.345
1C256medium thermal0.982
2A1176medium thermal0.952
1C245loose thermal2.6210
2A1144loose thermal2.5810
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 200 -
Rwork0.167 3616 -
obs--96.19 %
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)
10.44590.0314-0.1750.2392-0.09910.3498-0.01220.03020.0106-0.01960.02290.00440.0288-0.054-0.0107-0.0199-0.0089-0.01-0.0151-0.0028-0.0106-20.390617.901444.6702
20.3577-0.0381-0.3890.4443-0.05890.4782-0.01660.00720.0006-0.00050.0088-0.01830.00010.00010.0077-0.01590.0039-0.0051-0.0106-0.002-0.019717.835418.160810.7803
31.1536-0.2715-0.62281.24830.01221.50260.0103-0.02830.2448-0.05140.08650.0519-0.1409-0.0749-0.0967-0.07040.0135-0.0051-0.0520.0068-0.003-26.53934.679646.0824
43.116-4.5235-1.90188.50531.48612.546-0.16120.1215-0.2789-0.0388-0.1840.5745-0.1167-0.19350.34520.0072-0.0453-0.036-0.0152-0.0459-0.072-19.18731.182725.2167
52.51530.4449-0.62840.8676-0.47110.3744-0.21430.2629-0.3266-0.01870.0829-0.1079-0.0175-0.05210.13140.0299-0.06340.0149-0.0239-0.0603-0.0149-6.6949-6.293513.3418
60.68890.4494-0.34321.0266-0.23211.350.09080.00210.20280.01640.071-0.0587-0.1260.0391-0.1617-0.02120.00140.016-0.04350.0082-0.018824.770934.686310.3273
73.05534.52781.01918.01930.37876.8596-0.2076-0.1899-0.50550.31320.1205-0.29950.4351-0.08240.08710.0520.0786-0.0411-0.0260.0569-0.026418.22531.106929.2866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 300
2X-RAY DIFFRACTION2B7 - 300
3X-RAY DIFFRACTION3C436 - 481
4X-RAY DIFFRACTION4C482 - 501
5X-RAY DIFFRACTION5C502 - 592
6X-RAY DIFFRACTION6D435 - 481
7X-RAY DIFFRACTION7D482 - 499

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