[English] 日本語
Yorodumi
- PDB-4asx: Crystal structure of Activin receptor type-IIA (ACVR2A) kinase do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4asx
TitleCrystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dihydro-Bauerine C
ComponentsACTIVIN RECEPTOR TYPE-2A
KeywordsTRANSFERASE / PROTEIN KINASE
Function / homology
Function and homology information


Regulation of signaling by NODAL / inhibin-betaglycan-ActRII complex / inhibin binding / penile erection / positive regulation of activin receptor signaling pathway / activin receptor activity / Sertoli cell proliferation / sperm ejaculation / BMP receptor activity / embryonic skeletal system development ...Regulation of signaling by NODAL / inhibin-betaglycan-ActRII complex / inhibin binding / penile erection / positive regulation of activin receptor signaling pathway / activin receptor activity / Sertoli cell proliferation / sperm ejaculation / BMP receptor activity / embryonic skeletal system development / activin receptor complex / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / activin binding / cellular response to BMP stimulus / activin receptor signaling pathway / Signaling by Activin / Signaling by NODAL / gastrulation with mouth forming second / regulation of nitric oxide biosynthetic process / determination of left/right symmetry / anterior/posterior pattern specification / cell surface receptor protein serine/threonine kinase signaling pathway / odontogenesis of dentin-containing tooth / growth factor binding / mesoderm development / positive regulation of SMAD protein signal transduction / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of erythrocyte differentiation / PDZ domain binding / cellular response to growth factor stimulus / : / spermatogenesis / receptor complex / positive regulation of protein phosphorylation / phosphorylation / protein serine/threonine kinase activity / cell surface / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / 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. ...Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / 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. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / 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-6OJ / Activin receptor type-2A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWilliams, E. / Chaikuad, A. / Canning, P. / Kochan, G. / Mahajan, P. / Cooper, C.D.O. / Beltrami, A. / Krojer, T. / Pohl, B. / Bracher, F. ...Williams, E. / Chaikuad, A. / Canning, P. / Kochan, G. / Mahajan, P. / Cooper, C.D.O. / Beltrami, A. / Krojer, T. / Pohl, B. / Bracher, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Bullock, A.
CitationJournal: To be Published
Title: Crystal Structure of Activin Receptor Type-Iia (Acvr2A) Kinase Domain in Complex with a Beta- Carboline Inhibitor
Authors: Williams, E. / Chaikuad, A. / Canning, P. / Mahajan, P. / Cooper, C.D.O. / Beltrami, A. / Krojer, T. / Huber, K. / Bracher, F. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
History
DepositionMay 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Jun 20, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: ACTIVIN RECEPTOR TYPE-2A
B: ACTIVIN RECEPTOR TYPE-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,19413
Polymers73,0982
Non-polymers1,09711
Water5,783321
1
A: ACTIVIN RECEPTOR TYPE-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0666
Polymers36,5491
Non-polymers5175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ACTIVIN RECEPTOR TYPE-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1287
Polymers36,5491
Non-polymers5796
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.426, 110.426, 208.848
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2059-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYILEILE5BB-9 - 25015 - 84
21GLYGLYILEILE5AA-9 - 25015 - 84
12SERSERALAALA5BB274 - 349108 - 183
22SERSERALAALA5AA274 - 349108 - 183
13VALVALARGARG5BB360 - 484194 - 318
23VALVALARGARG5AA360 - 484194 - 318
14GLYGLYVALVAL6BB251 - 26185 - 95
24GLYGLYVALVAL6AA251 - 26185 - 95
15ASPASPGLYGLY5BB262 - 27396 - 107
25ASPASPGLYGLY5AA262 - 27396 - 107

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999578, 0.000187, 0.029032), (0.029032, -0.012558, -0.9995), (0.000178, 0.999921, -0.012558)27.43262, 49.4078, -46.51868

-
Components

#1: Protein ACTIVIN RECEPTOR TYPE-2A / ACTIVIN RECEPTOR TYPE IIA / ACTR-IIA / ACTRIIA


Mass: 36548.766 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 191-488
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P27037, receptor protein serine/threonine kinase
#2: Chemical ChemComp-6OJ / 7,8-bis(chloranyl)-9-methyl-3,4-dihydro-2H-pyrido[3,4-b]indol-1-one / Dihydro-Bauerine C


Mass: 269.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10Cl2N2O
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.62 Å3/Da / Density % sol: 53.07 % / Description: NONE
Crystal growDetails: 20 % PEG 3350 0.20 M NA(MALONATE)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9611
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 2.05→19.99 Å / Num. obs: 47777 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q4T

3q4t


Resolution: 2.05→19.99 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.666 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 2414 5.1 %RANDOM
Rwork0.18652 ---
obs0.18844 45307 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.745 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4872 0 70 321 5263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195115
X-RAY DIFFRACTIONr_bond_other_d0.0040.023486
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9596905
X-RAY DIFFRACTIONr_angle_other_deg1.46638486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1885628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90424.393239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17915889
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1231529
X-RAY DIFFRACTIONr_chiral_restr0.0880.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025703
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021042
X-RAY DIFFRACTIONr_nbd_refined0.2620.21412
X-RAY DIFFRACTIONr_nbd_other0.2210.23331
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22463
X-RAY DIFFRACTIONr_nbtor_other0.1150.22316
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2125
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0930.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.253
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7742.9835115
X-RAY DIFFRACTIONr_mcbond_other0.0033.0043486
X-RAY DIFFRACTIONr_mcangle_it2.9124.4276905
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 179 -
Rwork0.27 2921 -
obs--99.65 %
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)
10.41890.2926-0.15630.5027-0.08460.09480.0053-0.0175-0.00750.01170.0178-0.0445-0.0224-0.0092-0.0230.027-0.01180.01260.0563-0.00220.0446-39.323554.999511.4716
20.9466-0.31770.03790.11920.03980.4234-0.146-0.2036-0.00540.04290.08770.0041-0.00420.00170.05830.03630.0215-0.00430.1079-0.02620.029-11.514536.02478.0689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-9 - 484
2X-RAY DIFFRACTION1A349 - 484
3X-RAY DIFFRACTION2B-9 - 348
4X-RAY DIFFRACTION2B349 - 484

+
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