[English] 日本語
Yorodumi
- PDB-2iep: Crystal structure of immunoglobulin-like domains 1 and 2 of the r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2iep
TitleCrystal structure of immunoglobulin-like domains 1 and 2 of the receptor tyrosine kinase MuSK
ComponentsMuscle-specific kinase receptor
KeywordsSIGNALING PROTEIN / TRANSFERASE / beta-sandwich
Function / homology
Function and homology information


positive regulation of protein geranylgeranylation / regulation of synaptic assembly at neuromuscular junction / positive regulation of synaptic assembly at neuromuscular junction / positive regulation of motor neuron apoptotic process / skeletal muscle acetylcholine-gated channel clustering / positive regulation of synaptic transmission, cholinergic / positive regulation of skeletal muscle acetylcholine-gated channel clustering / Wnt-protein binding / response to muscle activity / motor neuron apoptotic process ...positive regulation of protein geranylgeranylation / regulation of synaptic assembly at neuromuscular junction / positive regulation of synaptic assembly at neuromuscular junction / positive regulation of motor neuron apoptotic process / skeletal muscle acetylcholine-gated channel clustering / positive regulation of synaptic transmission, cholinergic / positive regulation of skeletal muscle acetylcholine-gated channel clustering / Wnt-protein binding / response to muscle activity / motor neuron apoptotic process / neuromuscular junction development / cochlea development / enzyme-linked receptor protein signaling pathway / receptor clustering / positive regulation of Rac protein signal transduction / response to axon injury / response to electrical stimulus / transmembrane receptor protein tyrosine kinase activity / cell projection / PDZ domain binding / long-term synaptic potentiation / cell surface receptor protein tyrosine kinase signaling pathway / neuromuscular junction / receptor protein-tyrosine kinase / memory / positive regulation of neuron projection development / positive regulation of peptidyl-tyrosine phosphorylation / retina development in camera-type eye / postsynaptic membrane / protein tyrosine kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / receptor complex / positive regulation of protein phosphorylation / phosphorylation / external side of plasma membrane / negative regulation of gene expression / synapse / regulation of DNA-templated transcription / positive regulation of gene expression / protein kinase binding / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Muscle, skeletal receptor tyrosine protein kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.205 Å
AuthorsStiegler, A.L. / Burden, S.J. / Hubbard, S.R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of the Agrin-responsive Immunoglobulin-like Domains 1 and 2 of the Receptor Tyrosine Kinase MuSK
Authors: Stiegler, A.L. / Burden, S.J. / Hubbard, S.R.
History
DepositionSep 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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 / 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 / _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: Muscle-specific kinase receptor
B: Muscle-specific kinase receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1835
Polymers41,8942
Non-polymers2883
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Muscle-specific kinase receptor
hetero molecules

A: Muscle-specific kinase receptor
hetero molecules

A: Muscle-specific kinase receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2267
Polymers62,8423
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_654-x+1,-y,z-11
Buried area6090 Å2
ΔGint-111 kcal/mol
Surface area38170 Å2
MethodPISA
3
A: Muscle-specific kinase receptor
B: Muscle-specific kinase receptor
hetero molecules

A: Muscle-specific kinase receptor
B: Muscle-specific kinase receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,36510
Polymers83,7894
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.608, 118.004, 57.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Muscle-specific kinase receptor / E.C.2.7.10.1 / Muscle / skeletal receptor tyrosine protein kinase / MuSK


Mass: 20947.211 Da / Num. of mol.: 2 / Fragment: Ectodomain Ig1-2 (residues 22-212)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Musk / Plasmid: PACGP67 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q62838, receptor protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 8% PEG 4000, 0.2M Ammonium Sulfate, 0.1M Sodium Acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.92014 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92014 Å / Relative weight: 1
ReflectionResolution: 2.205→50 Å / Num. obs: 27127 / % possible obs: 98.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Χ2: 1.311 / Net I/σ(I): 15.9
Reflection shellResolution: 2.205→2.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.331 / Num. unique all: 2620 / Χ2: 1.631 / % possible all: 97.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FHG

1fhg


Resolution: 2.205→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.172 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1309 5 %RANDOM
Rwork0.216 ---
obs0.218 26130 95.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.626 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2---0.99 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.205→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 15 175 3020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222892
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9913932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23725104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83515517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3921516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022084
X-RAY DIFFRACTIONr_nbd_refined0.1920.21097
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21927
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.224
X-RAY DIFFRACTIONr_mcbond_it0.7541.51924
X-RAY DIFFRACTIONr_mcangle_it1.23323032
X-RAY DIFFRACTIONr_scbond_it1.73431095
X-RAY DIFFRACTIONr_scangle_it2.8964.5900
LS refinement shellResolution: 2.205→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 85 -
Rwork0.225 1631 -
obs-1716 86.4 %

+
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