[English] 日本語
Yorodumi
- PDB-3hvq: Crystal structure of a complex between Protein Phosphatase 1 alph... -

+
Open data


ID or keywords:

Loading...

-
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


growth cone lamellipodium / negative regulation of spontaneous neurotransmitter secretion / regulation of synapse structural plasticity / positive regulation of long-term synaptic depression / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / cellular response to toxic substance / postsynaptic actin cytoskeleton organization ...growth cone lamellipodium / negative regulation of spontaneous neurotransmitter secretion / regulation of synapse structural plasticity / positive regulation of long-term synaptic depression / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / cellular response to toxic substance / postsynaptic actin cytoskeleton organization / postsynaptic actin cytoskeleton / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of filopodium assembly / regulation of actin filament polymerization / regulation of dendritic spine morphogenesis / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation / positive regulation of dendritic spine development / negative regulation of stress fiber assembly / regulation of synapse assembly / myosin phosphatase activity / protein serine/threonine phosphatase activity / cortical actin cytoskeleton / branching morphogenesis of an epithelial tube / glycogen metabolic process / dendritic spine neck / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / Triglyceride catabolism / phosphatase activity / phosphoprotein phosphatase activity / negative regulation of long-term synaptic potentiation / DARPP-32 events / neuron development / ribonucleoprotein complex binding / dephosphorylation / excitatory postsynaptic potential / Downregulation of TGF-beta receptor signaling / protein dephosphorylation / filopodium / actin filament organization / calcium-mediated signaling / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / modulation of chemical synaptic transmission / neuromuscular junction / regulation of circadian rhythm / positive regulation of neuron projection development / neuron projection development / actin filament binding / actin cytoskeleton / Circadian Clock / presynapse / GTPase binding / lamellipodium / growth cone / perikaryon / transmembrane transporter binding / dendritic spine / postsynaptic density / cytoskeleton / cell cycle / cell division / protein domain specific binding / dendrite / neuronal cell body / glutamatergic synapse / protein-containing complex binding / nucleolus / protein kinase binding / extracellular exosome / nucleoplasm / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / Purple Acid Phosphatase; chain A, domain 2 ...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 / Metallo-dependent phosphatase-like / PDZ domain / Pdz3 Domain / SAM domain (Sterile alpha motif) / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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 / Phosphate


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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more