[English] 日本語
Yorodumi
- PDB-5fm3: Crystal structure of hyper-phosphorylated RET kinase domain with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fm3
TitleCrystal structure of hyper-phosphorylated RET kinase domain with (proximal) juxtamembrane segment
ComponentsPROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET
KeywordsTRANSFERASE
Function / homology
Function and homology information


Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / posterior midgut development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / membrane protein proteolysis / positive regulation of peptidyl-serine phosphorylation of STAT protein / Formation of the ureteric bud ...Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / posterior midgut development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / membrane protein proteolysis / positive regulation of peptidyl-serine phosphorylation of STAT protein / Formation of the ureteric bud / positive regulation of neuron maturation / Formation of the nephric duct / enteric nervous system development / neuron cell-cell adhesion / innervation / plasma membrane protein complex / neuron maturation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of cell adhesion mediated by integrin / neural crest cell migration / ureteric bud development / response to pain / regulation of axonogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / positive regulation of cell size / RET signaling / regulation of cell adhesion / cellular response to retinoic acid / NPAS4 regulates expression of target genes / transmembrane receptor protein tyrosine kinase activity / axon guidance / receptor protein-tyrosine kinase / positive regulation of neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process / MAPK cascade / retina development in camera-type eye / signaling receptor activity / RAF/MAP kinase cascade / protein tyrosine kinase activity / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / receptor complex / endosome membrane / positive regulation of cell migration / response to xenobiotic stimulus / axon / protein phosphorylation / neuronal cell body / calcium ion binding / dendrite / positive regulation of gene expression / positive regulation of DNA-templated transcription / signal transduction / ATP binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, Ret receptor / Tyrosine-protein kinase receptor Ret, cadherin like domain 3 / Ret, cadherin like domain 1 / RET, cadherin-like domain 4 / RET Cadherin like domain 1 / RET Cadherin like domain 3 / RET Cadherin like domain 4 / Cadherin domain / Cadherins domain profile. / Cadherin-like ...Tyrosine-protein kinase, Ret receptor / Tyrosine-protein kinase receptor Ret, cadherin like domain 3 / Ret, cadherin like domain 1 / RET, cadherin-like domain 4 / RET Cadherin like domain 1 / RET Cadherin like domain 3 / RET Cadherin like domain 4 / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-PP1 / Proto-oncogene tyrosine-protein kinase receptor Ret
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsPlaza-Menacho, I. / Barnouin, K. / Barry, R. / Borg, A. / Orme, M. / Mouilleron, S. / Martinez-Torres, R.J. / Meier, P. / McDonald, N.Q.
CitationJournal: Cell Rep / Year: 2016
Title: RET Functions as a Dual-Specificity Kinase that Requires Allosteric Inputs from Juxtamembrane Elements.
Authors: Plaza-Menacho, I. / Barnouin, K. / Barry, R. / Borg, A. / Orme, M. / Chauhan, R. / Mouilleron, S. / Martinez-Torres, R.J. / Meier, P. / McDonald, N.Q.
History
DepositionOct 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Apr 24, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0032
Polymers40,7211
Non-polymers2811
Water905
1
A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET
hetero molecules

A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0064
Polymers81,4432
Non-polymers5632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3730 Å2
ΔGint-21.9 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.569, 98.569, 146.301
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET / CADHERIN FAMILY MEMBER 12 / PROTO-ONCOGENE C-RET


Mass: 40721.398 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 659-1013
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P07949, receptor protein-tyrosine kinase
#2: Chemical ChemComp-PP1 / 1-TER-BUTYL-3-P-TOLYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE


Mass: 281.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.17 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 9361 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Biso Wilson estimate: 77.33 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.9

-
Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.95→34.665 Å / SU ML: 0.35 / σ(F): 1.36 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 447 4.8 %
Rwork0.1991 --
obs0.2004 9360 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→34.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 21 5 2150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022196
X-RAY DIFFRACTIONf_angle_d0.6652992
X-RAY DIFFRACTIONf_dihedral_angle_d14.5321279
X-RAY DIFFRACTIONf_chiral_restr0.04333
X-RAY DIFFRACTIONf_plane_restr0.003372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.37660.28991340.25042885X-RAY DIFFRACTION100
3.3766-4.25290.25381650.20572905X-RAY DIFFRACTION100
4.2529-34.66740.19251480.18253123X-RAY DIFFRACTION100
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)
10.05730.01580.02780.0569-0.15110.2814-0.25470.0371-0.07040.11160.2914-0.83680.12520.42740.00990.39610.04220.01260.3078-0.01080.5892.7351-36.44371.2382
20.3405-0.1047-0.10770.666-0.27290.9298-0.0208-0.0354-0.2174-0.0044-0.1196-0.1354-0.03370.1096-0.12530.2930.00990.13090.2527-0.05530.47140.9601-35.3626-3.7082
30.2812-0.13230.19160.0735-0.16530.5648-0.16230.19810.1799-0.40640.01610.1371-0.13210.53790.08090.6291-0.11990.05620.34270.14850.6966-1.1722-21.731-13.8269
40.3192-0.12680.29370.5603-0.09440.22740.4580.8191-0.1333-0.1304-0.15020.2626-0.18250.03180.07990.59510.06940.11170.5604-0.09470.3892-5.6349-30.6124-20.8376
51.5271-0.74870.16780.6724-0.17070.25230.0836-0.109-0.28390.0173-0.01380.75590.0922-0.20920.10910.57720.0762-0.02030.4079-0.1180.434-19.101-33.3051-14.8279
60.35160.1218-0.10160.29730.02430.1518-0.36970.7884-0.1898-0.20530.22480.2991-0.1589-0.0741-0.18960.86210.3259-0.29460.925-0.10680.1989-23.6139-26.5208-26.5482
70.2882-0.0371-0.12530.245-0.11240.13330.55010.27750.1284-0.22240.0785-0.10330.0488-0.11370.15880.88440.07390.00841.0606-0.23540.5041-7.9419-30.3057-33.8916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 707 THROUGH 735 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 736 THROUGH 800 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 801 THROUGH 847 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 848 THROUGH 890 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 891 THROUGH 956 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 957 THROUGH 997 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 998 THROUGH 1011 )

+
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