- PDB-5hlz: Structure of Pro-Activin A Complex at 2.85 A resolution -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 5hlz
Title
Structure of Pro-Activin A Complex at 2.85 A resolution
Components
(Inhibin beta A chain) x 2
Keywords
SIGNALING PROTEIN / Growth factor / Precursor / Signalling
Function / homology
Function and homology information
activin A complex / inhibin A complex / cardiac fibroblast cell development / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / 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 / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / 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 / Glycoprotein hormones / negative regulation of macrophage differentiation / 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 / activin receptor signaling pathway / negative regulation of phosphorylation / Signaling by Activin / SMAD protein signal transduction / mesodermal cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / cellular response to angiotensin / odontogenesis / positive regulation of transcription by RNA polymerase III / response to aldosterone / negative regulation of G1/S transition of mitotic cell cycle / roof of mouth development / endodermal cell differentiation / eyelid development in camera-type eye / 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 / hormone activity / negative regulation of cell growth / defense response / 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 / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / 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
A: Inhibin beta A chain B: Inhibin beta A chain D: Inhibin beta A chain F: Inhibin beta A chain H: Inhibin beta A chain C: Inhibin beta A chain E: Inhibin beta A chain G: Inhibin beta A chain
Mass: 30272.439 Da / Num. of mol.: 4 / Fragment: Pro domain, UNP Residues 30-305 Mutation: C35S, C38S, deletion of K259-D282, furin cleavage site (RRRRR) replaced by HRV 3C protease cleavage site (LEVLFQGP),C35S, C38S, deletion of K259-D282, furin cleavage site replaced by HRV 3C ...Mutation: C35S, C38S, deletion of K259-D282, furin cleavage site (RRRRR) replaced by HRV 3C protease cleavage site (LEVLFQGP),C35S, C38S, deletion of K259-D282, furin cleavage site replaced by HRV 3C protease cleavage site (LEVLFQGP),C35S, C38S, deletion of K259-D282, furin cleavage site (RRRRR) replaced by HRV 3C protease cleavage site (LEVLFQGP),C35S, C38S, deletion of K259-D282, furin cleavage site replaced by HRV 3C protease cleavage site (LEVLFQGP) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INHBA / Details (production host): N-terminal His6-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08476
Resolution: 2.85→3.01 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.948 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8
-
Processing
Software
Name
Version
Classification
PHENIX
(1.10pre_2084: ???)
refinement
XDS
datareduction
Aimless
datascaling
PHASER
phasing
Coot
modelbuilding
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: Structure of the uncleaved growth factor Resolution: 2.851→40.9 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.41 / Details: NCS restraint was included in the refinement.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2736
1331
5.14 %
Random selection
Rwork
0.2197
-
-
-
obs
0.2225
25879
99.67 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parameters
Biso mean: 69.62 Å2
Refinement step
Cycle: LAST / Resolution: 2.851→40.9 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9153
0
0
10
9163
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
9318
X-RAY DIFFRACTION
f_angle_d
0.81
12536
X-RAY DIFFRACTION
f_dihedral_angle_d
15.107
5828
X-RAY DIFFRACTION
f_chiral_restr
0.038
1396
X-RAY DIFFRACTION
f_plane_restr
0.003
1605
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.8508-2.9527
0.3902
138
0.3258
2541
X-RAY DIFFRACTION
100
2.9527-3.0709
0.3451
144
0.2835
2326
X-RAY DIFFRACTION
100
3.0709-3.2106
0.3166
139
0.2714
2518
X-RAY DIFFRACTION
100
3.2106-3.3798
0.3059
140
0.244
2516
X-RAY DIFFRACTION
100
3.3798-3.5914
0.2927
123
0.2283
2408
X-RAY DIFFRACTION
100
3.5914-3.8685
0.2912
131
0.2018
2446
X-RAY DIFFRACTION
100
3.8685-4.2575
0.229
124
0.1923
2486
X-RAY DIFFRACTION
100
4.2575-4.8727
0.2287
131
0.1769
2418
X-RAY DIFFRACTION
100
4.8727-6.1357
0.2541
139
0.2065
2438
X-RAY DIFFRACTION
100
6.1357-40.904
0.2763
122
0.2345
2451
X-RAY DIFFRACTION
98
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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