+Open data
-Basic information
Entry | Database: PDB / ID: 5aej | ||||||
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Title | Crystal structure of human Gremlin-1 | ||||||
Components | GREMLIN-1 | ||||||
Keywords | SIGNALING PROTEIN / SIGNALING / GREMLIN / GROWTH FACTORS / INHIBITOR / CYSTINE KNOT / EXTRACELLULAR SIGNALLING / DAN FAMILY | ||||||
Function / homology | Function and homology information : / negative regulation of bone remodeling / : / sequestering of BMP from receptor via BMP binding / mesenchymal to epithelial transition involved in metanephros morphogenesis / positive regulation of peptidyl-tyrosine autophosphorylation / negative regulation of monocyte chemotaxis / determination of dorsal identity / ureteric bud formation / negative regulation of osteoclast proliferation ...: / negative regulation of bone remodeling / : / sequestering of BMP from receptor via BMP binding / mesenchymal to epithelial transition involved in metanephros morphogenesis / positive regulation of peptidyl-tyrosine autophosphorylation / negative regulation of monocyte chemotaxis / determination of dorsal identity / ureteric bud formation / negative regulation of osteoclast proliferation / morphogen activity / negative regulation of bone mineralization involved in bone maturation / BMP binding / positive regulation of cardiac muscle cell differentiation / negative regulation of bone trabecula formation / negative regulation of osteoblast proliferation / proximal/distal pattern formation / regulation of epithelial to mesenchymal transition / negative regulation of bone mineralization / positive regulation of branching involved in ureteric bud morphogenesis / vascular endothelial growth factor receptor 2 binding / cell migration involved in sprouting angiogenesis / collagen fibril organization / negative regulation of chondrocyte differentiation / positive regulation of signaling receptor activity / embryonic limb morphogenesis / limb development / regulation of focal adhesion assembly / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of receptor internalization / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / : / cytokine activity / animal organ morphogenesis / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / negative regulation of cell growth / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of angiogenesis / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / collagen-containing extracellular matrix / receptor ligand activity / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 Å | ||||||
Authors | Kisonaite, M. / Hyvonen, M. | ||||||
Citation | Journal: Biochem.J. / Year: 2016 Title: Structure of Gremlin-1 and Analysis of its Interaction with Bmp-2. Authors: Kisonaite, M. / Wang, X. / Hyvonen, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aej.cif.gz | 205.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aej.ent.gz | 166.2 KB | Display | PDB format |
PDBx/mmJSON format | 5aej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aej_validation.pdf.gz | 478.1 KB | Display | wwPDB validaton report |
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Full document | 5aej_full_validation.pdf.gz | 485.2 KB | Display | |
Data in XML | 5aej_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 5aej_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/5aej ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5aej | HTTPS FTP |
-Related structure data
Related structure data | 4jphS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 17535.152 Da / Num. of mol.: 4 / Fragment: CYSTINE-KNOT DOMAIN, RESIDUES 72-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PUBS520 / References: UniProt: O60565 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | CONTAINS N-TERMINAL HIS-TAG WITH TEV CLEAVAGE SITE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % / Description: NONE |
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Crystal grow | pH: 4.5 Details: 2.1 M NACL, 0.1 M NA ACETATE, 0.3 M LI SULFATE, PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97942 |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: May 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.63 Å / Num. obs: 47349 / % possible obs: 99.7 % / Observed criterion σ(I): 2.2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4JPH Resolution: 1.904→41.631 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 22.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.904→41.631 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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