[English] 日本語
Yorodumi
- PDB-1nys: Crystal Structure of Activin A Bound to the ECD of ActRIIB P41 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nys
TitleCrystal Structure of Activin A Bound to the ECD of ActRIIB P41
Components
  • Inhibin beta A chain
  • activin receptor
KeywordsMEMBRANE PROTEIN/HORMONE/GROWTH FACTOR / ACTIVIN / TYPE II / TGF BETA / ACTRIIB / EXTRACELLULAR DOMAIN / MEMBRANE PROTEIN-HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


TGFBR3 regulates activin signaling / Signaling by BMP / inhibin-betaglycan-ActRII complex / activin A complex / inhibin A complex / cardiac fibroblast cell development / enzyme activator complex / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / inhibin binding ...TGFBR3 regulates activin signaling / Signaling by BMP / inhibin-betaglycan-ActRII complex / activin A complex / inhibin A complex / cardiac fibroblast cell development / enzyme activator complex / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / inhibin binding / positive regulation of ovulation / GABAergic neuron differentiation / activin receptor activity, type II / Antagonism of Activin by Follistatin / TGFBR3 regulates activin signaling / negative regulation of follicle-stimulating hormone secretion / penile erection / type II activin receptor binding / progesterone secretion / lymphatic endothelial cell differentiation / striatal medium spiny neuron differentiation / positive regulation of activin receptor signaling pathway / Glycoprotein hormones / activin receptor activity / negative regulation of macrophage differentiation / venous blood vessel development / cellular response to oxygen-glucose deprivation / positive regulation of follicle-stimulating hormone secretion / Signaling by Activin / Sertoli cell proliferation / hemoglobin biosynthetic process / lymphangiogenesis / sperm ejaculation / retina vasculature development in camera-type eye / BMP receptor activity / sexual reproduction / embryonic skeletal system development / activin receptor complex / embryonic foregut morphogenesis / negative regulation of phosphorylation / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / pattern specification process / artery development / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / activin binding / cellular response to BMP stimulus / Signaling by BMP / mesodermal cell differentiation / activin receptor signaling pathway / SMAD protein signal transduction / Signaling by Activin / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / kinase activator activity / gastrulation with mouth forming second / cellular response to angiotensin / pancreas development / odontogenesis / regulation of nitric oxide biosynthetic process / skeletal system morphogenesis / determination of left/right symmetry / insulin secretion / negative regulation of cold-induced thermogenesis / positive regulation of transcription by RNA polymerase III / anterior/posterior pattern specification / organ growth / adrenal gland development / response to aldosterone / negative regulation of G1/S transition of mitotic cell cycle / roof of mouth development / odontogenesis of dentin-containing tooth / eyelid development in camera-type eye / endodermal cell differentiation / mesoderm development / growth factor binding / positive regulation of SMAD protein signal transduction / peptide hormone binding / negative regulation of type II interferon production / hair follicle development / blood vessel remodeling / positive regulation of collagen biosynthetic process / regulation of signal transduction / BMP signaling pathway / positive regulation of osteoblast differentiation / hematopoietic progenitor cell differentiation / response to glucose / positive regulation of bone mineralization / coreceptor activity / ovarian follicle development / extrinsic apoptotic signaling pathway / protein serine/threonine/tyrosine kinase activity / positive regulation of protein metabolic process / positive regulation of erythrocyte differentiation / post-embryonic development / erythrocyte differentiation / kidney development / skeletal system development / cytokine activity / response to activity
Similarity search - Function
Inhibin, beta A subunit / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal ...Inhibin, beta A subunit / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Ribbon / 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 / Mainly Beta
Similarity search - Domain/homology
Inhibin beta A chain / Activin receptor type-2A / Activin receptor type-2B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsThompson, T.B. / Woodruff, T.K. / Jardetzky, T.S.
CitationJournal: EMBO J. / Year: 2003
Title: Structures of an ActRIIB:activin A complex reveal a novel binding mode for TGF-beta ligand:receptor interactions
Authors: Thompson, T.B. / Woodruff, T.K. / Jardetzky, T.S.
History
DepositionFeb 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 16, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE According to the depositor, Pro64 is a DNA sequence error in the database (PIR JQ1484). ...SEQUENCE According to the depositor, Pro64 is a DNA sequence error in the database (PIR JQ1484). The correct residue is Arg64. This has been confirmed by sequence alignment of orthologous proteins.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: activin receptor
B: Inhibin beta A chain
C: activin receptor
D: Inhibin beta A chain


Theoretical massNumber of molelcules
Total (without water)50,6674
Polymers50,6674
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.954, 104.954, 46.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein activin receptor


Mass: 12341.596 Da / Num. of mol.: 2 / Fragment: N-terminal Extracellular Domain (residues 19-119)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: actrIIb / Plasmid: pvl1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF+ / References: UniProt: P38444, UniProt: P38445*PLUS
#2: Protein Inhibin beta A chain / Activin beta-A chain / Erythroid differentiation protein / EDF


Mass: 12991.865 Da / Num. of mol.: 2 / Fragment: Mature Domain (residues 311-426)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INHBA / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): BA83.6-02 / References: UniProt: P08476

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, sodium chloride, hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17-10 mg/mlprotein1drop
220 mMHEPES1drop
3150 mM1droppH7.5NaCl
427 %PEG40001reservoir
5250 mM1reservoirNaCl
6100 mMHEPES1reservoirpH7.0

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→25 Å / Num. obs: 9789 / % possible obs: 93.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 77 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.14
Reflection shellResolution: 3.05→3.1 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.9
Reflection
*PLUS
Num. measured all: 44194
Reflection shell
*PLUS
% possible obs: 87 %

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
BRUTEphasing
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BTE

1bte


Resolution: 3.05→24.74 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 484 5.2 %RANDOM
Rwork0.252 ---
all0.28 ---
obs0.252 9254 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.6845 Å2 / ksol: 0.270069 e/Å3
Displacement parametersBiso mean: 77 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å20 Å2
2--2.51 Å20 Å2
3----5.03 Å2
Refine analyzeLuzzati coordinate error free: 0.52 Å / Luzzati sigma a free: 0.72 Å
Refinement stepCycle: LAST / Resolution: 3.05→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 0 0 2635
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 3.05→3.24 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.435 61 4.3 %
Rwork0.357 1346 -
obs--87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.251 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.84
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
LS refinement shell
*PLUS
Lowest resolution: 3.1 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