[English] 日本語
Yorodumi
- PDB-1s4y: Crystal structure of the activin/actrIIb extracellular domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s4y
TitleCrystal structure of the activin/actrIIb extracellular domain
Components
  • Activin receptor type IIB precursor
  • Inhibin beta A chain
KeywordsTRANSFERASE / structural genomics / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


Signaling by Activin / activin A complex / inhibin A complex / cardiac fibroblast cell development / androst-4-ene-3,17-dione biosynthetic process / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / negative regulation of follicle-stimulating hormone secretion / GABAergic neuron differentiation ...Signaling by Activin / activin A complex / inhibin A complex / cardiac fibroblast cell development / androst-4-ene-3,17-dione biosynthetic process / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / negative regulation of follicle-stimulating hormone secretion / GABAergic neuron differentiation / Signaling by BMP / Antagonism of Activin by Follistatin / TGFBR3 regulates activin signaling / type II activin receptor binding / progesterone secretion / lymphatic endothelial cell differentiation / Sertoli cell differentiation / striatal medium spiny neuron differentiation / positive regulation of activin receptor signaling pathway / enzyme activator complex / Glycoprotein hormones / negative regulation of macrophage differentiation / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / venous blood vessel development / hemoglobin biosynthetic process / lymphangiogenesis / negative regulation of phosphorylation / testosterone biosynthetic process / retina vasculature development in camera-type eye / embryonic foregut morphogenesis / cellular response to follicle-stimulating hormone stimulus / artery development / cellular response to cholesterol / transforming growth factor beta receptor activity, type I / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transforming growth factor beta receptor activity, type II / transforming growth factor beta receptor activity, type III / activin binding / pattern specification process / SMAD protein signal transduction / Signaling by BMP / Signaling by Activin / activin receptor signaling pathway / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / mesodermal cell differentiation / gastrulation with mouth forming second / pancreas development / kinase activator activity / determination of left/right symmetry / negative regulation of ossification / insulin secretion / negative regulation of cold-induced thermogenesis / anterior/posterior pattern specification / skeletal system morphogenesis / odontogenesis / positive regulation of transcription by RNA polymerase III / organ growth / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / growth factor binding / endodermal cell differentiation / eyelid development in camera-type eye / mesoderm development / odontogenesis of dentin-containing tooth / roof of mouth development / negative regulation of type II interferon production / peptide hormone binding / positive regulation of protein metabolic process / androgen metabolic process / positive regulation of collagen biosynthetic process / positive regulation of SMAD protein signal transduction / cellular response to angiotensin / blood vessel remodeling / hair follicle development / regulation of signal transduction / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / hematopoietic progenitor cell differentiation / response to glucose / ovarian follicle development / extrinsic apoptotic signaling pathway / protein serine/threonine/tyrosine kinase activity / erythrocyte differentiation / positive regulation of erythrocyte differentiation / post-embryonic development / cytokine activity / kidney development / skeletal system development / growth factor activity / lung development / defense response / negative regulation of cell growth / cytokine-mediated signaling pathway / hormone activity / autophagy / male gonad development
Similarity search - Function
Inhibin, beta A subunit / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal ...Inhibin, beta A subunit / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / 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 / 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-2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGreenwald, J. / Vega, M.E. / Allendorph, G.P. / Fischer, W.H. / Vale, W. / Choe, S. / Joint Center for Structural Genomics (JCSG)
CitationJournal: Mol.Cell / Year: 2004
Title: A Flexible Activin Explains the Membrane-Dependent Cooperative Assembly of TGF-beta Family Receptors.
Authors: Greenwald, J. / Vega, M.E. / Allendorph, G.P. / Fischer, W.H. / Vale, W. / Choe, S.
History
DepositionJan 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 IIB precursor
B: Inhibin beta A chain
C: Activin receptor type IIB precursor
D: Inhibin beta A chain


Theoretical massNumber of molelcules
Total (without water)49,1314
Polymers49,1314
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.290, 120.627, 43.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Activin receptor type IIB precursor / ACTR-IIB


Mass: 11573.676 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ACVR2B / Production host: Escherichia coli (E. coli) / References: UniProt: P27040, EC: 2.7.1.37
#2: Protein Inhibin beta A chain / Activin beta-A chain / Erythroid differentiation protein / EDF


Mass: 12991.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INHBA / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08476
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG 3350, magnesium chloride, bis tris, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 21, 2003
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 19028 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.047
Reflection shellResolution: 2.3→2.38 Å / Rsym value: 0.213 / % possible all: 94.4

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→70.71 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.898 / SU B: 8.367 / SU ML: 0.206 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28615 988 5.2 %RANDOM
Rwork0.20611 ---
obs0.21021 18101 91.58 %-
all-18101 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.082 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.3→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3102 0 0 177 3279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0213195
X-RAY DIFFRACTIONr_bond_other_d0.0060.022606
X-RAY DIFFRACTIONr_angle_refined_deg2.3851.9284326
X-RAY DIFFRACTIONr_angle_other_deg1.10936090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2645385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1330.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023603
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02675
X-RAY DIFFRACTIONr_nbd_refined0.2190.2626
X-RAY DIFFRACTIONr_nbd_other0.2540.23072
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1030.21908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.251
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.2133
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3780.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.171.51946
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.08623099
X-RAY DIFFRACTIONr_scbond_it3.37831249
X-RAY DIFFRACTIONr_scangle_it5.0374.51227
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.303→2.363 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 69
Rwork0.222 1262
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)
14.58250.8426-0.96676.798-1.30695.70080.1324-0.4428-0.15570.2414-0.195-0.49410.11040.7250.06270.03920.05420.05160.28760.05760.096330.719127.3673-1.8856
21.33980.1686-1.63450.19930.070910.48590.1986-0.20730.1110.2048-0.07310.0726-0.3839-0.1986-0.12540.1624-0.03690.02420.1430.0230.121612.859232.050217.3911
37.6593-0.16981.5677.89980.09464.43530.04690.4369-0.4348-0.23610.079-0.2023-0.0837-0.0132-0.12590.105-0.07540.03550.0762-0.0330.174731.341261.816327.092
410.80687.57384.86587.62293.24542.77520.0842-0.0390.2878-0.2309-0.0510.3190.0779-0.3463-0.03310.2827-0.0882-0.02310.28710.04670.234711.214547.615723.9236
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 955 - 95
2X-RAY DIFFRACTION2BB2 - 1162 - 116
3X-RAY DIFFRACTION3CC4 - 984 - 98
4X-RAY DIFFRACTION4DD4 - 1164 - 116

+
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