[English] 日本語
Yorodumi
- PDB-8p1h: Crystal structure of the chimera of human 14-3-3 zeta and phospho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p1h
TitleCrystal structure of the chimera of human 14-3-3 zeta and phosphorylated cytoplasmic loop fragment of the alpha7 acetylcholine receptor
ComponentsTyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta,Neuronal acetylcholine receptor subunit alpha-7
KeywordsSIGNALING PROTEIN / 14-3-3 / acetylcholine receptor / PROTEIN BINDING
Function / homology
Function and homology information


sensory processing / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity / acetylcholine receptor activity / dendritic spine organization ...sensory processing / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity / acetylcholine receptor activity / dendritic spine organization / acetylcholine binding / chloride channel regulator activity / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / acetylcholine-gated monoatomic cation-selective channel activity / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / plasma membrane raft / modulation of excitatory postsynaptic potential / positive regulation of excitatory postsynaptic potential / response to amyloid-beta / negative regulation of tumor necrosis factor production / toxic substance binding / monoatomic ion transport / monoatomic ion transmembrane transport / positive regulation of protein metabolic process / positive regulation of long-term synaptic potentiation / synapse organization / response to nicotine / calcium channel activity / memory / cognition / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / monoatomic ion channel activity / amyloid-beta binding / postsynapse / postsynaptic membrane / positive regulation of MAPK cascade / learning or memory / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / neuron projection / positive regulation of protein phosphorylation / synapse / positive regulation of cell population proliferation / signal transduction / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
Nicotinic acetylcholine receptor / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues ...Nicotinic acetylcholine receptor / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
AZIDE ION / BENZOIC ACID / DI(HYDROXYETHYL)ETHER / Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta / Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBoyko, K.M. / Kapitonova, A.A. / Tugaeva, K.V. / Varfolomeeva, L.A. / Lyukmanova, E.N. / Sluchanko, N.N.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Crystal structure reveals canonical recognition of the phosphorylated cytoplasmic loop of human alpha7 nicotinic acetylcholine receptor by 14-3-3 protein.
Authors: Sluchanko, N.N. / Kapitonova, A.A. / Shulepko, M.A. / Kukushkin, I.D. / Kulbatskii, D.S. / Tugaeva, K.V. / Varfolomeeva, L.A. / Minyaev, M.E. / Boyko, K.M. / Popov, V.O. / Kirpichnikov, M.P. / Lyukmanova, E.N.
History
DepositionMay 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta,Neuronal acetylcholine receptor subunit alpha-7
B: Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta,Neuronal acetylcholine receptor subunit alpha-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,23511
Polymers55,6332
Non-polymers6039
Water6,648369
1
A: Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta,Neuronal acetylcholine receptor subunit alpha-7
hetero molecules

B: Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta,Neuronal acetylcholine receptor subunit alpha-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,23511
Polymers55,6332
Non-polymers6039
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area3180 Å2
ΔGint6 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.628, 103.118, 112.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta,Neuronal acetylcholine receptor subunit alpha-7


Mass: 27816.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ, CHRNA7, NACHRA7 / Production host: Escherichia coli (E. coli) / References: UniProt: E7EX29, UniProt: P36544

-
Non-polymers , 5 types, 378 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N3
#4: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium acetate tetrahydrate; 0.1 M Sodium cacodylate trihydrate pH 6.5; 20% w/v Polyethylene glycol 8,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.95→21.06 Å / Num. obs: 60333 / % possible obs: 98.1 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.056 / Rrim(I) all: 0.17 / Χ2: 1.03 / Net I/σ(I): 14.1 / Num. measured all: 525966
Reflection shellResolution: 1.95→2 Å / % possible obs: 96.5 % / Redundancy: 9.2 % / Rmerge(I) obs: 2.857 / Num. measured all: 38225 / Num. unique obs: 4146 / CC1/2: 0.49 / Rpim(I) all: 0.975 / Rrim(I) all: 3.023 / Χ2: 0.9 / Net I/σ(I) obs: 0.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→21.06 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.41 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25325 2965 4.9 %RANDOM
Rwork0.20886 ---
obs0.21099 57226 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.712 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å2-0 Å20 Å2
2--2.39 Å2-0 Å2
3----0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.95→21.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 41 369 4144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123895
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163699
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.6415249
X-RAY DIFFRACTIONr_angle_other_deg0.6551.5678507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7185494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.152530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22510705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024638
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02902
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_it3.2252.7941943
X-RAY DIFFRACTIONr_mcbond_other3.2252.7941943
X-RAY DIFFRACTIONr_mcangle_it4.555.0192430
X-RAY DIFFRACTIONr_mcangle_other4.5495.0192431
X-RAY DIFFRACTIONr_scbond_it4.0793.0251952
X-RAY DIFFRACTIONr_scbond_other4.0783.0251953
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0755.3782814
X-RAY DIFFRACTIONr_long_range_B_refined7.81229.54751
X-RAY DIFFRACTIONr_long_range_B_other7.7927.574624
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 221 -
Rwork0.329 4070 -
obs--96.17 %
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)
10.77820.2526-0.15840.81390.13720.634-0.0636-0.0036-0.0955-0.06010.0573-0.15550.0429-0.02390.00630.02450.004-0.00840.0141-0.02730.0748-4.672-45.903-9.548
20.99120.1440.17490.58040.15570.7523-0.0604-0.04930.1267-0.0585-0.00170.0926-0.0912-0.09280.0620.03590.02180.01290.01850.00680.0684-2.866-3.19-6.812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 241
2X-RAY DIFFRACTION2B1 - 240

+
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://pdbjlvh1.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