[English] 日本語
Yorodumi
- PDB-1reu: Structure of the bone morphogenetic protein 2 mutant L51P -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1reu
TitleStructure of the bone morphogenetic protein 2 mutant L51P
Componentsbone morphogenetic protein 2
KeywordsHORMONE/GROWTH FACTOR / TGF-beta fold / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / embryonic heart tube anterior/posterior pattern specification / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / negative regulation of steroid biosynthetic process ...cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / embryonic heart tube anterior/posterior pattern specification / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / negative regulation of steroid biosynthetic process / ameloblast differentiation / positive regulation of extracellular matrix constituent secretion / negative regulation of cardiac muscle cell differentiation / positive regulation of odontogenesis / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / corticotropin hormone secreting cell differentiation / lung vasculature development / negative regulation of insulin-like growth factor receptor signaling pathway / mesenchyme development / thyroid-stimulating hormone-secreting cell differentiation / aortic valve development / telencephalon regionalization / positive regulation of phosphatase activity / positive regulation of cartilage development / proteoglycan metabolic process / heart induction / positive regulation of peroxisome proliferator activated receptor signaling pathway / pericardium development / BMP receptor complex / co-receptor binding / telencephalon development / cardiac epithelial to mesenchymal transition / BMP receptor binding / positive regulation of odontoblast differentiation / mesenchymal cell differentiation / endocardial cushion formation / positive regulation of bone mineralization involved in bone maturation / Transcriptional regulation by RUNX2 / phosphatase activator activity / positive regulation of astrocyte differentiation / Signaling by BMP / cardiac muscle cell differentiation / cellular response to BMP stimulus / cardiac muscle tissue morphogenesis / positive regulation of ossification / astrocyte differentiation / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / positive regulation of p38MAPK cascade / endocardial cushion morphogenesis / negative regulation of fat cell differentiation / branching involved in ureteric bud morphogenesis / bone mineralization / odontogenesis of dentin-containing tooth / positive regulation of osteoblast proliferation / inner ear development / positive regulation of SMAD protein signal transduction / positive regulation of Wnt signaling pathway / cellular response to organic cyclic compound / negative regulation of cell cycle / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / positive regulation of fat cell differentiation / positive regulation of osteoblast differentiation / cell fate commitment / chondrocyte differentiation / BMP signaling pathway / positive regulation of bone mineralization / Notch signaling pathway / positive regulation of neuron differentiation / protein serine/threonine kinase activator activity / osteoclast differentiation / negative regulation of MAP kinase activity / skeletal system development / cytokine activity / negative regulation of smooth muscle cell proliferation / response to bacterium / animal organ morphogenesis / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of canonical Wnt signaling pathway / growth factor activity / protein destabilization / bone development / osteoblast differentiation / positive regulation of miRNA transcription / Regulation of RUNX2 expression and activity / positive regulation of DNA-binding transcription factor activity / cell-cell signaling / heart development / positive regulation of protein binding / in utero embryonic development / positive regulation of MAPK cascade / transcription by RNA polymerase II / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / positive regulation of apoptotic process
Similarity search - Function
: / 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. ...: / 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
Bone morphogenetic protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKeller, S. / Nickel, J. / Zhang, J.-L. / Sebald, W. / Mueller, T.D.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Molecular recognition of BMP-2 and BMP receptor IA.
Authors: Keller, S. / Nickel, J. / Zhang, J.L. / Sebald, W. / Mueller, T.D.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of human bone morphogenetic protein-2 at 2.7 A resolution
Authors: Scheufler, C. / Sebald, W. / Huelsmeyer, M.
#2: Journal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of the BMP-2-BRIA ectodomain complex
Authors: Kirsch, T. / Sebald, W. / Dreyer, M.K.
History
DepositionNov 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: bone morphogenetic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7343
Polymers11,4981
Non-polymers2362
Water23413
1
A: bone morphogenetic protein 2
hetero molecules

A: bone morphogenetic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4696
Polymers22,9962
Non-polymers4734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_444x-y-1/3,-y-2/3,-z-2/31
Buried area3640 Å2
ΔGint-64 kcal/mol
Surface area11210 Å2
MethodPISA, PQS
2
A: bone morphogenetic protein 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)70,40618
Polymers68,9886
Non-polymers1,41812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_554y,x,-z-11
crystal symmetry operation5_554x-y,-y,-z-11
crystal symmetry operation6_554-x,-x+y,-z-11
Buried area9410 Å2
ΔGint-163 kcal/mol
Surface area35140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.292, 94.292, 102.882
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settingtrigonal
Space group name H-MH32
DetailsThe biological assembly is a dimer generated by the two fold axis (disulfide bonded homodimer): 2/3+x-y, 1/3-y, 1/3-z

-
Components

#1: Protein bone morphogenetic protein 2 /


Mass: 11498.064 Da / Num. of mol.: 1 / Fragment: mature part / Mutation: L51P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pN25c109 / Production host: Escherichia coli (E. coli) / References: UniProt: P12643
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: lithium sulfate, tert-butanol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 10, 2003 / Details: Osmic ConfocalBlue
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→19.76 Å / Num. all: 5624 / Num. obs: 5624 / % possible obs: 93.5 % / Observed criterion σ(I): 1.2 / Redundancy: 3.4 % / Biso Wilson estimate: 101.2 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.65→2.82 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.293 / % possible all: 72.3

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNS1.1refinement
CCP4(SCALA)data scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BMP

3bmp


Resolution: 2.65→19.76 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 1489344.52 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 259 5.3 %RANDOM
Rwork0.215 ---
all0.216 5624 --
obs0.2151 4918 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.4107 Å2 / ksol: 0.310865 e/Å3
Displacement parametersBiso mean: 64.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.21 Å24.25 Å20 Å2
2--4.21 Å20 Å2
3----8.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.65→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms804 0 16 13 833
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.331
X-RAY DIFFRACTIONc_mcangle_it2.461.5
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.057 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 35 5.6 %
Rwork0.332 587 -
obs-377 72.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3MPD_XPLOR_PAR.PROMPD_XPLOR_TOP.PAR

+
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