[English] 日本語
Yorodumi
- PDB-5oy6: Crystal structure of the ACVR1 (ALK2) kinase in complex with cycl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oy6
TitleCrystal structure of the ACVR1 (ALK2) kinase in complex with cyclical inhibitor OD36.
ComponentsActivin receptor type-1
KeywordsSIGNALING PROTEIN / Kinase / ALK2 / Receptor / BMP / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


endocardial cushion cell fate commitment / mitral valve morphogenesis / endocardial cushion fusion / BMP receptor complex / atrial septum primum morphogenesis / BMP receptor activity / cardiac muscle cell fate commitment / acute inflammatory response / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition ...endocardial cushion cell fate commitment / mitral valve morphogenesis / endocardial cushion fusion / BMP receptor complex / atrial septum primum morphogenesis / BMP receptor activity / cardiac muscle cell fate commitment / acute inflammatory response / activin receptor activity, type I / positive regulation of cardiac epithelial to mesenchymal transition / positive regulation of determination of dorsal identity / transforming growth factor beta receptor activity, type I / activin receptor complex / endocardial cushion formation / smooth muscle cell differentiation / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / cellular response to BMP stimulus / activin receptor signaling pathway / negative regulation of activin receptor signaling pathway / transforming growth factor beta binding / embryonic heart tube morphogenesis / gastrulation with mouth forming second / dorsal/ventral pattern formation / determination of left/right symmetry / neural crest cell migration / atrioventricular valve morphogenesis / branching involved in blood vessel morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / ventricular septum morphogenesis / SMAD binding / germ cell development / peptide hormone binding / positive regulation of SMAD protein signal transduction / mesoderm formation / regulation of ossification / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / negative regulation of signal transduction / transforming growth factor beta receptor signaling pathway / protein tyrosine kinase binding / negative regulation of extrinsic apoptotic signaling pathway / cellular response to growth factor stimulus / positive regulation of peptidyl-tyrosine phosphorylation / apical part of cell / heart development / in utero embryonic development / protein kinase activity / positive regulation of cell migration / cadherin binding / phosphorylation / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP binding / 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 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain ...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 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / 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 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
cyclical inhibitor OD36 / Activin receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsWilliams, E.P. / Pinkas, D.M. / Krojer, T. / Kupinska, K. / Mahajan, P. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N.
CitationJournal: To Be Published
Title: Establishment and characterization of endothelial colony forming cells as a surrogate model for Fibrodysplasia Ossificans Progressiva
Authors: Sanchez-Duffhues, G. / Orlova, V. / Benderitter, P. / Williams, E.P. / Garcia de Vinuesa, A. / Caradec, J. / van Wijhe, M. / de Boer, H. / Goumans, M.J. / Eeckhoff, M. / Morales Piga, A. / ...Authors: Sanchez-Duffhues, G. / Orlova, V. / Benderitter, P. / Williams, E.P. / Garcia de Vinuesa, A. / Caradec, J. / van Wijhe, M. / de Boer, H. / Goumans, M.J. / Eeckhoff, M. / Morales Piga, A. / Bachiller, J. / Koolwijk, P. / Bullock, A. / Hoflack, J. / ten Dijke, P.
History
DepositionSep 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Activin receptor type-1
B: Activin receptor type-1
C: Activin receptor type-1
D: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,59810
Polymers138,1514
Non-polymers1,4476
Water1,26170
1
A: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9934
Polymers34,5381
Non-polymers4553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8682
Polymers34,5381
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8682
Polymers34,5381
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Activin receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8682
Polymers34,5381
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.260, 103.530, 84.840
Angle α, β, γ (deg.)90.00, 116.52, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Activin receptor type-1 / Activin receptor type I / ACTR-I / Activin receptor-like kinase 2 / ALK-2 / Serine/threonine- ...Activin receptor type I / ACTR-I / Activin receptor-like kinase 2 / ALK-2 / Serine/threonine-protein kinase receptor R1 / SKR1 / TGF-B superfamily receptor type I / TSR-I


Mass: 34537.633 Da / Num. of mol.: 4 / Mutation: Q207D
Source method: isolated from a genetically manipulated source
Details: Contains a Q207D mutation compared to the wt gene - Q04771
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR1, ACVRLK2 / Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): Sf9
References: UniProt: Q04771, receptor protein serine/threonine kinase
#2: Chemical
ChemComp-B4E / cyclical inhibitor OD36


Mass: 330.769 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H15ClN4O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.3M magnesium formate, 0.1M bis-tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 9, 2014 / Details: Compound Refractive Lenses
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.56→75.39 Å / Num. obs: 42050 / % possible obs: 99.91 % / Observed criterion σ(F): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 63.101 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.076 / Net I/σ(I): 8.7
Reflection shellResolution: 2.56→2.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4176 / CC1/2: 0.904 / Rrim(I) all: 0.578 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLM7.2.1data reduction
Aimless7.0.044data scaling
PHASER7.0.044phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H9R

3h9r


Resolution: 2.56→71.903 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 2123 5.06 %Random selection
Rwork0.2111 ---
obs0.2129 41945 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→71.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8873 0 100 70 9043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069181
X-RAY DIFFRACTIONf_angle_d0.80312519
X-RAY DIFFRACTIONf_dihedral_angle_d13.4915401
X-RAY DIFFRACTIONf_chiral_restr0.0511431
X-RAY DIFFRACTIONf_plane_restr0.0051572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.61960.38171580.30542628X-RAY DIFFRACTION99
2.6196-2.68510.3111170.30822619X-RAY DIFFRACTION99
2.6851-2.75770.29841330.29372642X-RAY DIFFRACTION99
2.7577-2.83880.33481230.28272675X-RAY DIFFRACTION100
2.8388-2.93050.31461340.27552645X-RAY DIFFRACTION99
2.9305-3.03520.30311160.25592686X-RAY DIFFRACTION100
3.0352-3.15670.29871370.24882653X-RAY DIFFRACTION100
3.1567-3.30040.31891340.24552626X-RAY DIFFRACTION100
3.3004-3.47440.2991640.24872642X-RAY DIFFRACTION100
3.4744-3.69210.26531220.21752712X-RAY DIFFRACTION100
3.6921-3.97710.2271440.20012640X-RAY DIFFRACTION100
3.9771-4.37730.23041310.17752659X-RAY DIFFRACTION100
4.3773-5.01060.1871750.17152644X-RAY DIFFRACTION100
5.0106-6.31220.21391860.20042644X-RAY DIFFRACTION100
6.3122-71.93140.22991490.18472707X-RAY DIFFRACTION99
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)
15.35560.16383.05686.99123.45984.08430.02230.1237-0.26830.65730.7538-0.67540.48831.2812-0.73170.54390.08820.07050.59-0.06330.514922.6826-9.4934-21.2045
24.2241-2.9224-3.50854.65542.17578.7826-0.0965-0.61120.3709-0.04570.4095-0.26280.1040.2631-0.30780.4084-0.0504-0.05530.39490.04030.451416.0834-2.4397-20.3701
34.94970.46441.28772.68350.31175.482-0.1567-0.19540.2040.08970.27550.32050.1103-1.0285-0.13910.41740.06690.03640.49180.13160.3716-1.7868-2.7206-22.9829
47.484-1.1418-0.37945.0034-2.16987.39830.23-0.07910.2668-0.44760.15560.19870.1576-0.4781-0.36110.5103-0.08710.01140.45410.06240.39074.522338.5969-33.8684
53.4353-0.2388-1.51392.25370.22035.25250.0552-0.999-0.15950.21480.18350.03940.03840.376-0.22490.4829-0.0311-0.02270.95020.20980.487613.408435.1803-13.8881
63.40280.85710.48646.3427-0.06975.16550.48930.0354-0.70030.71680.20640.06110.72680.9406-0.55220.83640.20380.01281.47120.37740.714816.307125.1788-5.986
76.2925-0.79863.0149.168-2.83685.7940.36890.39030.2238-1.3696-0.92390.8138-0.4959-0.56560.32370.91260.3427-0.21090.9679-0.24640.817-28.59122.5573-67.6421
82.18031.83260.92649.26133.14141.47070.8313-0.1478-0.1025-1.1733-1.50280.9866-0.0236-0.74370.62050.80150.1847-0.18851.1095-0.10520.8288-27.81722.9601-60.7809
93.7992-0.25050.9917.04281.57132.26830.7442-0.5133-0.1443-0.0434-1.0628-0.4690.0802-0.34650.29480.5196-0.0384-0.01230.74710.18780.461-14.567214.5261-50.5021
107.6053-4.4875-3.47743.74651.22593.85560.36610.83560.15710.0256-0.6289-2.0814-0.1244-0.78360.40150.87870.11780.05081.41160.08361.3222-14.38427.3312-6.1809
113.20492.00290.30334.6842-0.85222.81610.1682-0.0477-0.23510.0086-0.5481-0.7432-0.10080.13640.34820.43910.0363-0.06170.70540.03310.7859-32.11722.5091-11.6682
121.24710.5386-1.00523.2013-0.47821.73560.24310.0319-0.0851-0.1148-0.39330.180.3504-0.60570.13560.7336-0.1527-0.08071.0223-0.14021.09-45.83079.2462-12.43
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 204 through 248 )
2X-RAY DIFFRACTION2chain 'A' and (resid 249 through 307 )
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 498 )
4X-RAY DIFFRACTION4chain 'B' and (resid 204 through 289 )
5X-RAY DIFFRACTION5chain 'B' and (resid 290 through 460 )
6X-RAY DIFFRACTION6chain 'B' and (resid 461 through 498 )
7X-RAY DIFFRACTION7chain 'C' and (resid 204 through 249 )
8X-RAY DIFFRACTION8chain 'C' and (resid 250 through 295 )
9X-RAY DIFFRACTION9chain 'C' and (resid 296 through 498 )
10X-RAY DIFFRACTION10chain 'D' and (resid 204 through 220 )
11X-RAY DIFFRACTION11chain 'D' and (resid 221 through 453 )
12X-RAY DIFFRACTION12chain 'D' and (resid 454 through 495 )

+
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