[English] 日本語
Yorodumi
- PDB-2arv: Structure of human Activin A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2arv
TitleStructure of human Activin A
ComponentsInhibin beta A chain
KeywordsHORMONE/GROWTH FACTOR / homodimer / cystine knot / disulfide linked / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


activin A complex / inhibin A complex / cardiac fibroblast cell development / regulation of follicle-stimulating hormone secretion / negative regulation of B cell differentiation / positive regulation of ovulation / GABAergic neuron differentiation / Antagonism of Activin by Follistatin / negative regulation of follicle-stimulating hormone secretion / progesterone secretion ...activin A complex / inhibin A complex / cardiac fibroblast cell development / regulation of follicle-stimulating hormone secretion / negative regulation of B cell differentiation / positive regulation of ovulation / GABAergic neuron differentiation / Antagonism of Activin by Follistatin / negative regulation of follicle-stimulating hormone secretion / progesterone secretion / type II activin receptor binding / striatal medium spiny neuron differentiation / negative regulation of macrophage differentiation / Glycoprotein hormones / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / hemoglobin biosynthetic process / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / Signaling by BMP / negative regulation of phosphorylation / activin receptor signaling pathway / Signaling by Activin / mesodermal cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / SMAD protein signal transduction / cellular response to angiotensin / positive regulation of transcription by RNA polymerase III / odontogenesis / response to aldosterone / negative regulation of G1/S transition of mitotic cell cycle / roof of mouth development / eyelid development in camera-type eye / endodermal cell differentiation / peptide hormone binding / positive regulation of SMAD protein signal transduction / negative regulation of type II interferon production / hair follicle development / positive regulation of collagen biosynthetic process / hematopoietic progenitor cell differentiation / extrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of protein metabolic process / erythrocyte differentiation / positive regulation of erythrocyte differentiation / cytokine activity / growth factor activity / defense response / hormone activity / negative regulation of cell growth / autophagy / cytokine-mediated signaling pathway / male gonad development / cell-cell signaling / nervous system development / cellular response to hypoxia / transcription by RNA polymerase II / cell differentiation / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / protein-containing complex binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding
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 / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. ...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 / 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 / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Chem-1PG / Inhibin beta A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHarrington, A.E. / Morris-Triggs, S.A. / Ruotolo, B.T. / Robinson, C.V. / Ohnuma, S. / Hyvonen, M.
CitationJournal: Embo J. / Year: 2006
Title: Structural basis for the inhibition of activin signalling by follistatin
Authors: Harrington, A.E. / Morris-Triggs, S.A. / Ruotolo, B.T. / Robinson, C.V. / Ohnuma, S. / Hyvonen, M.
History
DepositionAug 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Inhibin beta A chain
B: Inhibin beta A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,89710
Polymers25,9842
Non-polymers9138
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-65 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.572, 96.247, 118.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 1 - 116 / Label seq-ID: 1 - 116

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA
DetailsThe biological unit is a homodimer as found in the asymmetric unit

-
Components

#1: 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 / Plasmid: pBAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08476
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / Polyethylene glycol


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.5 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulphate, PEG300, Na-Hepes, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978847 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 23, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978847 Å / Relative weight: 1
ReflectionResolution: 2→29.2 Å / Num. obs: 24229 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.065

-
Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1S4Y

1s4y


Resolution: 2→29.2 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.949 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 1151 4.9 %RANDOM
Rwork0.2159 ---
all0.21802 22157 --
obs0.21802 22157 93.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.624 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20 Å2
2---0.07 Å20 Å2
3---1.39 Å2
Refinement stepCycle: LAST / Resolution: 2→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 55 54 1853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211858
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9562503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7035221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93124.3982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.98315308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.176156
X-RAY DIFFRACTIONr_chiral_restr0.1350.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021380
X-RAY DIFFRACTIONr_nbd_refined0.2710.2704
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21241
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.26
X-RAY DIFFRACTIONr_mcbond_it6.51121134
X-RAY DIFFRACTIONr_mcangle_it7.93531780
X-RAY DIFFRACTIONr_scbond_it7.9662833
X-RAY DIFFRACTIONr_scangle_it10.0483722
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 829 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.880.5
medium thermal8.372
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 64 -
Rwork0.255 1350 -
obs--78.56 %

+
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