[English] 日本語
Yorodumi
- PDB-2k3g: NMR structure analysis of a BMP receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k3g
TitleNMR structure analysis of a BMP receptor
ComponentsBone morphogenetic protein receptor type-1A
KeywordsSIGNALING PROTEIN / BMP / receptor / TGF-beta superfamily / ATP-binding / Disease mutation / Glycoprotein / Kinase / Magnesium / Manganese / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase / Transferase / Transmembrane
Function / homology
Function and homology information


positive regulation of transforming growth factor beta2 production / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / atrioventricular node cell development / anti-Mullerian hormone receptor signaling pathway / dorsal aorta morphogenesis / tricuspid valve morphogenesis / cardiac right ventricle morphogenesis / regulation of cardiac muscle cell proliferation / BMP binding ...positive regulation of transforming growth factor beta2 production / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / atrioventricular node cell development / anti-Mullerian hormone receptor signaling pathway / dorsal aorta morphogenesis / tricuspid valve morphogenesis / cardiac right ventricle morphogenesis / regulation of cardiac muscle cell proliferation / BMP binding / pharyngeal arch artery morphogenesis / atrioventricular valve development / mitral valve morphogenesis / BMP receptor activity / ventricular compact myocardium morphogenesis / cardiac conduction system development / negative regulation of smooth muscle cell migration / transforming growth factor beta receptor activity, type I / endocardial cushion formation / receptor protein serine/threonine kinase / cellular response to BMP stimulus / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / ventricular trabecula myocardium morphogenesis / dorsal/ventral pattern formation / outflow tract septum morphogenesis / endocardial cushion morphogenesis / chondrocyte differentiation / positive regulation of dendrite development / embryonic organ development / ventricular septum morphogenesis / positive regulation of bone mineralization / SMAD binding / outflow tract morphogenesis / positive regulation of cardiac muscle cell proliferation / positive regulation of osteoblast differentiation / positive regulation of SMAD protein signal transduction / BMP signaling pathway / transforming growth factor beta receptor signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / stem cell differentiation / HFE-transferrin receptor complex / cellular response to growth factor stimulus / positive regulation of miRNA transcription / osteoblast differentiation / angiogenesis / cell differentiation / signaling receptor complex / immune response / negative regulation of gene expression / external side of plasma membrane / protein serine/threonine kinase activity / neuronal cell body / positive regulation of gene expression / dendrite / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Bone morphogenetic protein receptor type-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsKlages, J. / Kotzsch, A. / Mueller, T. / Kessler, H.
CitationJournal: Biochemistry / Year: 2008
Title: The solution structure of BMPR-IA reveals a local disorder-to-order transition upon BMP-2 binding.
Authors: Klages, J. / Kotzsch, A. / Coles, M. / Sebald, W. / Nickel, J. / Muller, T. / Kessler, H.
History
DepositionMay 7, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bone morphogenetic protein receptor type-1A


Theoretical massNumber of molelcules
Total (without water)11,2791
Polymers11,2791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 50structures with the lowest energy
RepresentativeModel #1minimized average structure

-
Components

#1: Protein Bone morphogenetic protein receptor type-1A / Serine/threonine-protein kinase receptor R5 / SKR5 / Activin receptor-like kinase 3 / ALK-3 / CD292 antigen


Mass: 11278.693 Da / Num. of mol.: 1 / Fragment: Extracellular domain (UNP residues 51-152) / Mutation: A28G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMPR1A, ACVRLK3, ALK3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P36894, receptor protein serine/threonine kinase
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HNCO
1423D HNCA
1523D CBCA(CO)NH
1623D HBHA(CO)NH
1723D HN(CA)CB
1823D C(CO)NH
1923D (H)CCH-TOCSY
11013D HNHA
11122D 1H-1H NOESY
11223D 1H-15N NOESY
11323D 1H-13C NOESY
11413D HNHB
11523D (H)CCH-COSY
11623D 1H-15N-15N NOESY
11723D 1H-15N-13C NIOESY
11823D (H)CCH-TOCSY
11923D HN(CA)HA
12023D HN(CA)CO

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-99% 15N] Bone Morphogenetic Protein Receptor Type IA, 10 mM potassium phosphate, 0.2 w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-94% 13C; U-98% 15N] Bone Morphogenetic Protein Receptor Type IA, 10 mM potassium phosphate, 0.2 w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMBone Morphogenetic Protein Receptor Type IA[U-99% 15N]1
95 v/vH2O1
5 v/vD2O1
10 mMpotassium phosphate1
0.2 w/vsodium azide1
0.5 mMBone Morphogenetic Protein Receptor Type IA[U-94% 13C; U-98% 15N]2
95 v/vH2O2
5 v/vD2O2
10 mMpotassium phosphate2
0.2 w/vsodium azide2
Sample conditionspH: 6.3 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker DMXBrukerDMX7502
Bruker DMXBrukerDMX6003
Bruker DMXBrukerDMX6004

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.9.4aSchwieters, Kuszewski, Tjandra and Clorestructure solution
TopSpin1.3Bruker Biospinprocessing
TopSpin1.3Bruker Biospincollection
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
ProcheckNMRLaskowski and MacArthurgeometry optimization
AQUARullmann, Doreleijers and Kapteingeometry optimization
WHAT IFVriendgeometry optimization
X-PLOR NIH2.9.4aSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: standard protocols were used
NMR constraintsNOE constraints total: 699 / NOE intraresidue total count: 167 / NOE long range total count: 182 / NOE medium range total count: 57 / NOE sequential total count: 249
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 21
NMR ensemble rmsDistance rms dev: 0.022 Å / Distance rms dev error: 0.002 Å

+
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