[English] 日本語
Yorodumi
- PDB-1bmp: BONE MORPHOGENETIC PROTEIN-7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bmp
TitleBONE MORPHOGENETIC PROTEIN-7
ComponentsBONE MORPHOGENETIC PROTEIN-7
KeywordsTRANSFORMING GROWTH FACTOR / MORPHOGEN / CYTOKINE / BONE / CARTILAGE / GLYCOPROTEIN
Function / homology
Function and homology information


negative regulation of prostatic bud formation / negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis / negative regulation of glomerular mesangial cell proliferation / mesenchymal cell apoptotic process involved in nephron morphogenesis / positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of hyaluranon cable assembly / chorio-allantoic fusion / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / negative regulation of striated muscle cell apoptotic process ...negative regulation of prostatic bud formation / negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis / negative regulation of glomerular mesangial cell proliferation / mesenchymal cell apoptotic process involved in nephron morphogenesis / positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of hyaluranon cable assembly / chorio-allantoic fusion / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / negative regulation of striated muscle cell apoptotic process / embryonic skeletal joint morphogenesis / neural fold elevation formation / ameloblast differentiation / positive regulation of epithelial cell differentiation / metanephric mesenchymal cell proliferation involved in metanephros development / embryonic camera-type eye morphogenesis / mesenchyme development / monocyte aggregation / allantois development / mesonephros development / regulation of removal of superoxide radicals / hindbrain development / mesenchymal cell differentiation / BMP receptor binding / pericardium morphogenesis / endocardial cushion formation / pharyngeal system development / heart trabecula morphogenesis / cellular response to BMP stimulus / embryonic pattern specification / branching involved in salivary gland morphogenesis / regulation of phosphorylation / response to vitamin D / metanephros development / negative regulation of mitotic nuclear division / cardiac muscle tissue development / positive regulation of heterotypic cell-cell adhesion / cartilage development / positive regulation of dendrite development / negative regulation of non-canonical NF-kappaB signal transduction / embryonic limb morphogenesis / Molecules associated with elastic fibres / ureteric bud development / regulation of branching involved in prostate gland morphogenesis / branching morphogenesis of an epithelial tube / negative regulation of NF-kappaB transcription factor activity / negative regulation of Notch signaling pathway / dendrite development / cardiac septum morphogenesis / odontogenesis of dentin-containing tooth / positive regulation of SMAD protein signal transduction / mesoderm formation / negative regulation of cell cycle / negative regulation of neuron differentiation / epithelial to mesenchymal transition / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / positive regulation of neuron differentiation / positive regulation of brown fat cell differentiation / ossification / neuron projection morphogenesis / skeletal system development / cytokine activity / axon guidance / growth factor activity / response to peptide hormone / negative regulation of neurogenesis / response to estradiol / heparin binding / cellular response to hypoxia / collagen-containing extracellular matrix / vesicle / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
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. / Cystine Knot Cytokines, subunit B ...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 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsGriffith, D.L. / Scott, D.L.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Three-dimensional structure of recombinant human osteogenic protein 1: structural paradigm for the transforming growth factor beta superfamily.
Authors: Griffith, D.L. / Keck, P.C. / Sampath, T.K. / Rueger, D.C. / Carlson, W.D.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary Crystallographic Data of Recombinant Human Osteogenic Protein-1 (Hop-1)
Authors: Griffith, D.L. / Oppermann, H. / Rueger, D.C. / Sampath, T.K. / Tucker, R.F. / Carlson, W.D.
History
DepositionDec 14, 1995Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BONE MORPHOGENETIC PROTEIN-7


Theoretical massNumber of molelcules
Total (without water)15,7001
Polymers15,7001
Non-polymers00
Water00
1
A: BONE MORPHOGENETIC PROTEIN-7

A: BONE MORPHOGENETIC PROTEIN-7


Theoretical massNumber of molelcules
Total (without water)31,3992
Polymers31,3992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2370 Å2
ΔGint-26 kcal/mol
Surface area11690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.460, 99.460, 42.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein BONE MORPHOGENETIC PROTEIN-7 / OSTEOGENIC PROTEIN-1 / HOP-1 / BMP-7


Mass: 15699.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: REFERENCE, T.K. SAMPATH, ET AL. (1992) J. BIOL. CHEM. 267, 20452-20362
Gene: HOP-1 CDNA / Organ: OVARY / Gene (production host): HOP-1 CDNA / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P18075

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 60 %
Crystal
*PLUS
Density % sol: 62 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
24 %satammonium sulfate1drop
325 mMsodium acetate1drop
48 %satammonium sulfate1reservoir
550 mMsodium acetate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 30, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 5502 / % possible obs: 87 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.067
Reflection
*PLUS
Highest resolution: 2.8 Å

-
Processing

Software
NameVersionClassification
R-AXISSOFTWAREdata collection
R-AXISSOFTWAREdata reduction
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
R-AXISdata scaling
X-PLORphasing
RefinementResolution: 2.8→10 Å / σ(F): 2
Details: LOOP REGION (RESIDUES 118 - 122) IS DISORDERED AND MODELED STEREOCHEMICALLY. NOTE THAT RESIDUE 59 IS DESCRIBED AS TRANS IN THE PAPER CITED ON JRNL RECORDS ABOVE BUT THE CURRENT MODEL ...Details: LOOP REGION (RESIDUES 118 - 122) IS DISORDERED AND MODELED STEREOCHEMICALLY. NOTE THAT RESIDUE 59 IS DESCRIBED AS TRANS IN THE PAPER CITED ON JRNL RECORDS ABOVE BUT THE CURRENT MODEL PRESENTED IN THIS ENTRY HAS RESIDUE 59 AS CIS.
RfactorNum. reflection
Rfree0.308 -
Rwork0.227 -
obs-5418
Displacement parametersBiso mean: 28.48 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 0 0 828
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.03
X-RAY DIFFRACTIONp_angle_d0.0250.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.1380.1
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0450.1
X-RAY DIFFRACTIONp_chiral_restr0.2111
X-RAY DIFFRACTIONp_singtor_nbd0.1851
X-RAY DIFFRACTIONp_multtor_nbd0.251
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1941
X-RAY DIFFRACTIONp_planar_tor23.230
X-RAY DIFFRACTIONp_staggered_tor25.950
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor35.150
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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://pdbjlvh1.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