[English] 日本語
Yorodumi
- PDB-2p6a: The structure of the Activin:Follistatin 315 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p6a
TitleThe structure of the Activin:Follistatin 315 complex
Components
  • Follistatin
  • Inhibin beta A chain
  • probable fragment of follistatin
KeywordsSIGNALING PROTEIN / Follistatin / Activin / Inhibin / TGF-beta
Function / homology
Function and homology information


activin receptor antagonist activity / 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 ...activin receptor antagonist activity / 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 / ameloblast differentiation / negative regulation of macrophage differentiation / Glycoprotein hormones / positive regulation of follicle-stimulating hormone secretion / cellular response to oxygen-glucose deprivation / hemoglobin biosynthetic process / positive regulation of hair follicle development / regulation of BMP signaling pathway / gamete generation / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / pattern specification process / Signaling by BMP / activin binding / negative regulation of phosphorylation / activin receptor signaling pathway / heparan sulfate proteoglycan binding / Signaling by Activin / negative regulation of activin receptor signaling pathway / 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 / negative regulation of epithelial cell differentiation / response to aldosterone / hair follicle morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / female gonad development / roof of mouth development / eyelid development in camera-type eye / endodermal cell differentiation / odontogenesis of dentin-containing tooth / peptide hormone binding / positive regulation of SMAD protein signal transduction / negative regulation of type II interferon production / keratinocyte proliferation / hair follicle development / positive regulation of collagen biosynthetic process / BMP signaling pathway / hematopoietic progenitor cell differentiation / extrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of protein metabolic process / erythrocyte differentiation / positive regulation of erythrocyte differentiation / skeletal system development / cytokine activity / growth factor activity / defense response / hormone activity / negative regulation of cell growth / response to organic cyclic compound / 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 / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Follistatin, N-terminal / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / Inhibin, beta A subunit / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Follistatin-like, N-terminal ...Follistatin, N-terminal / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / Inhibin, beta A subunit / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Kazal type serine protease inhibitors / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Cystine-knot cytokine / Ribbon / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Inhibin beta A chain / Follistatin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLerch, T.F. / Shimasaki, S. / Woodruff, T.K. / Jardetzky, T.S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and biophysical coupling of heparin and activin binding to follistatin isoform functions.
Authors: Lerch, T.F. / Shimasaki, S. / Woodruff, T.K. / Jardetzky, T.S.
History
DepositionMar 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 9, 2011Group: Structure summary
Revision 1.4Aug 30, 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_ncs_dom_lim
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inhibin beta A chain
D: Follistatin
B: Inhibin beta A chain
C: Follistatin
E: probable fragment of follistatin


Theoretical massNumber of molelcules
Total (without water)96,3055
Polymers96,3055
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.641, 106.584, 87.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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: 5 / Auth seq-ID: 1 - 116 / Label seq-ID: 1 - 116

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BC
DetailsThe biological assembly of these proteins is one activin A dimer in complex with 2 follistatin 315 molecules, which compose the activin:follistatin 315 complex. We observe one complex 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 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08476
#2: Protein Follistatin / / FS / Activin-binding protein


Mass: 34796.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FST / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P19883
#3: Protein/peptide probable fragment of follistatin


Mass: 728.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Sequence detailsAUTHOR STATE THE FOLLOWING IN THE PUBLICATION: ON ONE FOLLISTATIN MOLECULE (CHAIN C AND ITS ...AUTHOR STATE THE FOLLOWING IN THE PUBLICATION: ON ONE FOLLISTATIN MOLECULE (CHAIN C AND ITS SYMMETRICALLY EQUIVALENT MOLECULES), ELECTRON DENSITY COULD BE SEEN FOR RESIDUES 289-299. ON THE SECOND FOLLISTATIN MOLECULE(CHAIN D AND ITS SYMMETRICALLY EQUIVALENT MOLECULES), CONTINUOUS ELECTRON DENSITY ALLOWED FOR THE BUILDING OF MAIN-CHAIN ATOMS OF 10 RESIDUES. SIDE CHAINS FOR THESE RESIDUES COULD NOT BE UNAMBIGUOUSLY MODELED, PREVENTING IDENTIFICATION OF THIS SEQUENCE IN THE C-TERMINAL EXTENSION. HOWEVER, BASED ON THE SYMMETRY OF THE TWO FOLLISTATIN MOLECULES, THIS STRETCH LIKELY CONSISTS OF RESIDUES 295-304, REPRESENTING THE MAJORITY OF THE CHARGED AMINO ACIDS IN THE C-TERMINAL EXTENSION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20-23% PEG 1000, 200mM MgCl2, 3% EtOH, 20mM Trimethyl-amine HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298 K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7.2 % / Av σ(I) over netI: 4 / Number: 100464 / Rmerge(I) obs: 0.16 / Rsym value: 0.16 / D res high: 3.4 Å / D res low: 34.344 Å / Num. obs: 13978 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
10.7540.3992.510.0720.0726
7.610.7599.510.0710.0716.8
6.217.610010.0990.0997
5.386.2110010.1230.1237.1
4.815.3810010.1350.1357.2
4.394.8110010.1460.1467.3
4.064.3910010.1930.1937.3
3.84.0610010.3030.3037.3
3.583.810010.4940.4947.3
3.43.5810010.7080.7087.3
ReflectionResolution: 3.4→34.344 Å / Num. obs: 13978 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.16 / Rsym value: 0.16 / Net I/σ(I): 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.4-3.587.30.70811461919940.708100
3.58-3.87.30.4941.41392819040.494100
3.8-4.067.30.3032.31299817810.303100
4.06-4.397.30.1933.81233216920.193100
4.39-4.817.30.1464.91127615530.146100
4.81-5.387.20.1354.81009714000.135100
5.38-6.217.10.1235.3905712690.123100
6.21-7.670.0996.4753810710.099100
7.6-10.756.80.0718.658338530.07199.5
10.75-40.3960.0728.827864610.07292.5

-
Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.4 Å34.34 Å
Translation3.4 Å34.34 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 13943
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
10.44-10037.90.768501
8.29-10.4440.20.87503
7.23-8.2945.50.844505
6.57-7.2345.40.838502
6.09-6.57430.844506
5.72-6.0946.20.842510
5.43-5.7241.70.863502
5.19-5.4336.20.881503
4.98-5.1937.30.891506
4.8-4.9834.90.883513
4.65-4.836.10.885516
4.51-4.6532.30.9539
4.38-4.5134.20.888532
4.26-4.3834.20.897552
4.15-4.2636.20.9575
4.05-4.1536.80.888581
3.95-4.0532.50.885605
3.87-3.9536.40.877620
3.78-3.8739.60.861618
3.71-3.7833.60.881643
3.63-3.7136.10.875650
3.56-3.6343.30.833663
3.5-3.5640.80.845658
3.4-3.542.90.8341140

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: one activin A monomer and ND, FSD1, and FSD2 of one follistatin 288 molecule (PDB 2B0U)

2b0u


Resolution: 3.4→31.01 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.811 / SU B: 90.513 / SU ML: 0.667 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.733 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.324 283 2 %RANDOM
Rwork0.223 ---
obs0.225 13955 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.862 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 3.4→31.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5952 0 0 0 5952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226090
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.9488262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8055804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34925.126238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.82115958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1241524
X-RAY DIFFRACTIONr_chiral_restr0.1280.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024582
X-RAY DIFFRACTIONr_nbd_refined0.4020.24068
X-RAY DIFFRACTIONr_nbtor_refined0.3670.24282
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3180.2385
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5240.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4780.26
X-RAY DIFFRACTIONr_mcbond_it16.71124123
X-RAY DIFFRACTIONr_mcangle_it21.07126399
X-RAY DIFFRACTIONr_scbond_it22.456122263
X-RAY DIFFRACTIONr_scangle_it25.907121863
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
463MEDIUM POSITIONAL0.520.5
419LOOSE POSITIONAL0.825
463MEDIUM THERMAL6.712
419LOOSE THERMAL13.110
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 25 -
Rwork0.25 984 -
obs-1009 99.9 %
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)
13.11183.4367-0.98886.7289-2.21375.79510.1140.71350.0724-0.003-0.1259-0.82310.32790.45590.0119-0.02330.00070.0815-0.0054-0.0105-0.028325.54524.651461.9862
27.6425-2.03930.21419.1209-5.102211.5611-0.14580.0574-0.42720.20910.11230.24371.27420.4170.03350.01820.0180.1118-0.02510.07130.000943.059533.53622.9732
30.28890.47460.110.8016-0.02161.88630.0321-0.06150.09380.0807-0.2016-0.0011-0.2747-0.10440.1695-0.1603-0.0422-0.0269-0.02940.01460.0922.289431.026635.169
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CD212 - 290212 - 290
21EE1 - 101 - 10
32DB212 - 299212 - 299
43AA1 - 1161 - 116
53BC1 - 1161 - 116
63CD1 - 2111 - 211
73DB1 - 2111 - 211

+
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