[English] 日本語
Yorodumi
- PDB-7ag0: Complex between the bone morphogenetic protein 2 and its antagoni... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ag0
TitleComplex between the bone morphogenetic protein 2 and its antagonist Noggin
Components
  • Bone morphogenetic protein 2
  • Noggin
KeywordsCYTOKINE / Bmp-2 / TGF-beta superfamily / cysteine-knot
Function / homology
Function and homology information


neural plate anterior/posterior regionalization / negative regulation of cardiac epithelial to mesenchymal transition / neural plate morphogenesis / cell differentiation in hindbrain / notochord morphogenesis / negative regulation of cytokine activity / regulation of fibroblast growth factor receptor signaling pathway / ureteric bud formation / cardiac atrium formation / cardiocyte differentiation ...neural plate anterior/posterior regionalization / negative regulation of cardiac epithelial to mesenchymal transition / neural plate morphogenesis / cell differentiation in hindbrain / notochord morphogenesis / negative regulation of cytokine activity / regulation of fibroblast growth factor receptor signaling pathway / ureteric bud formation / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / positive regulation of phosphatase activity / cardiac jelly development / positive regulation of extracellular matrix constituent secretion / negative regulation of aldosterone biosynthetic process / embryonic skeletal joint morphogenesis / negative regulation of cortisol biosynthetic process / atrioventricular canal morphogenesis / negative regulation of steroid biosynthetic process / embryonic heart tube anterior/posterior pattern specification / mesenchymal cell proliferation involved in ureteric bud development / prostatic bud formation / positive regulation of glomerulus development / nodal signaling pathway / enzyme activator complex / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / negative regulation of cardiac muscle cell differentiation / corticotropin hormone secreting cell differentiation / atrial cardiac muscle tissue morphogenesis / thyroid-stimulating hormone-secreting cell differentiation / endoderm formation / mesenchyme development / ameloblast differentiation / negative regulation of insulin-like growth factor receptor signaling pathway / aortic valve development / pericardium development / telencephalon regionalization / pharyngeal arch artery morphogenesis / short-term synaptic potentiation / heart induction / positive regulation of cartilage development / positive regulation of odontogenesis / positive regulation of peroxisome proliferator activated receptor signaling pathway / pituitary gland development / BMP receptor complex / proteoglycan metabolic process / embryonic skeletal system development / ventricular compact myocardium morphogenesis / negative regulation of cardiac muscle cell proliferation / co-receptor binding / membranous septum morphogenesis / lung vasculature development / negative regulation of cartilage development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / somite development / telencephalon development / BMP receptor binding / positive regulation of bone mineralization involved in bone maturation / positive regulation of odontoblast differentiation / phosphatase activator activity / Transcriptional regulation by RUNX2 / endocardial cushion formation / positive regulation of astrocyte differentiation / positive regulation of branching involved in ureteric bud morphogenesis / cranial skeletal system development / heart trabecula morphogenesis / cellular response to BMP stimulus / Signaling by BMP / cardiac muscle cell differentiation / astrocyte differentiation / axial mesoderm development / cardiac muscle tissue morphogenesis / positive regulation of ossification / motor neuron axon guidance / dorsal/ventral pattern formation / positive regulation of p38MAPK cascade / cartilage development / limb development / atrioventricular valve morphogenesis / face morphogenesis / endocardial cushion morphogenesis / Molecules associated with elastic fibres / middle ear morphogenesis / embryonic digit morphogenesis / branching involved in ureteric bud morphogenesis / smoothened signaling pathway / positive regulation of osteoblast proliferation / ventricular septum morphogenesis / spinal cord development / negative regulation of fat cell differentiation / Formation of paraxial mesoderm / negative regulation of astrocyte differentiation / cytokine binding / bone mineralization / exploration behavior / negative regulation of SMAD protein signal transduction / lung morphogenesis / odontogenesis of dentin-containing tooth
Similarity search - Function
Noggin / Noggin / : / 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 ...Noggin / Noggin / : / 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 cytokine
Similarity search - Domain/homology
Bone morphogenetic protein 2 / Noggin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.104 Å
AuthorsRobert, C. / Bruck, F. / Herman, R. / Vandevenne, M. / Filee, P. / Kerff, F. / Matagne, A.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Walloon Region#16100518 AUTOBMP-2 Belgium
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural analysis of the interaction between human cytokine BMP-2 and the antagonist Noggin reveals molecular details of cell chondrogenesis inhibition.
Authors: Robert, C. / Kerff, F. / Bouillenne, F. / Gavage, M. / Vandevenne, M. / Filee, P. / Matagne, A.
History
DepositionSep 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Noggin
B: Bone morphogenetic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5056
Polymers36,1372
Non-polymers3684
Water55831
1
A: Noggin
B: Bone morphogenetic protein 2
hetero molecules

A: Noggin
B: Bone morphogenetic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,01012
Polymers72,2734
Non-polymers7378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area10920 Å2
ΔGint-83 kcal/mol
Surface area25540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.310, 103.310, 170.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

-
Components

#1: Protein Noggin


Mass: 23212.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOG / Plasmid: pET17(b) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13253
#2: Protein Bone morphogenetic protein 2 / BMP-2 / Bone morphogenetic protein 2A / BMP-2A


Mass: 12923.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2, BMP2A / Plasmid: pET17(b) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12643
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 1.4 M NaKPO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 3.1→49.427 Å / Num. obs: 10331 / % possible obs: 99.9 % / Redundancy: 56.6 % / Biso Wilson estimate: 103.29 Å2 / CC1/2: 0.977 / Net I/σ(I): 9.5
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 49.3 % / Mean I/σ(I) obs: 0.69 / Num. unique obs: 733 / CC1/2: 0.32 / % possible all: 99.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M4U

1m4u


Resolution: 3.104→49.427 Å / SU ML: 0.65 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 514 5.03 %
Rwork0.2321 17448 -
obs0.2345 10266 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 227.82 Å2 / Biso mean: 101.9559 Å2 / Biso min: 52.18 Å2
Refinement stepCycle: final / Resolution: 3.104→49.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 56 31 2044
Biso mean--114.57 86.67 -
Num. residues----245
LS refinement shellResolution: 3.104→3.2672 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3891 133 -
Rwork0.3844 2481 -
obs--100 %

+
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