|Entry||Database: PDB / ID: 4o3u|
|Title||Zymogen HGF-beta/MET with Zymogen Activator Peptide ZAP2.3|
|Keywords||transferase/growth factor / trypsin homoloy / receptor activation / transferase-growth factor complex|
|Function / homology|
Function and homology information
positive regulation of neuron projection regeneration / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / regulation of p38MAPK cascade / skeletal muscle cell proliferation / hepatocyte growth factor receptor activity / myoblast proliferation / Drug-mediated inhibition of MET activation / MET activates STAT3 / positive regulation of myelination / endothelial cell morphogenesis ...positive regulation of neuron projection regeneration / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / regulation of p38MAPK cascade / skeletal muscle cell proliferation / hepatocyte growth factor receptor activity / myoblast proliferation / Drug-mediated inhibition of MET activation / MET activates STAT3 / positive regulation of myelination / endothelial cell morphogenesis / negative regulation of hydrogen peroxide-mediated programmed cell death / negative regulation of guanyl-nucleotide exchange factor activity / MET interacts with TNS proteins / MET Receptor Activation / regulation of tau-protein kinase activity / positive regulation of endothelial cell chemotaxis / semaphorin receptor activity / hepatocyte growth factor receptor signaling pathway / Sema4D mediated inhibition of cell attachment and migration / MET receptor recycling / pancreas development / MET activates PTPN11 / negative regulation of Rho protein signal transduction / MET activates PI3K/AKT signaling / MET activates RAP1 and RAC1 / negative regulation of stress fiber assembly / negative regulation of thrombin-activated receptor signaling pathway / positive regulation of DNA biosynthetic process / semaphorin-plexin signaling pathway / MET activates PTK2 signaling / branching morphogenesis of an epithelial tube / positive chemotaxis / cellular response to hepatocyte growth factor stimulus / negative regulation of release of cytochrome c from mitochondria / positive regulation of interleukin-10 production / establishment of skin barrier / epithelial to mesenchymal transition / negative regulation of interleukin-6 production / MECP2 regulates neuronal receptors and channels / chemoattractant activity / positive regulation of osteoblast differentiation / positive regulation of microtubule polymerization / MET activates RAS signaling / phagocytosis / animal organ regeneration / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of peptidyl-serine phosphorylation / Interleukin-7 signaling / negative regulation of autophagy / cell chemotaxis / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / liver development / epithelial cell proliferation / platelet alpha granule lumen / Negative regulation of MET activity / growth factor activity / neuron differentiation / cell morphogenesis / receptor protein-tyrosine kinase / transmembrane receptor protein tyrosine kinase activity / negative regulation of inflammatory response / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of kinase activity / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / Platelet degranulation / PIP3 activates AKT signaling / nervous system development / positive regulation of phosphatidylinositol 3-kinase signaling / transmembrane receptor protein tyrosine kinase signaling pathway / cell migration / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / positive regulation of protein kinase B signaling / positive regulation of MAPK cascade / protein phosphatase binding / cell surface receptor signaling pathway / receptor complex / positive regulation of cell migration / positive regulation of protein phosphorylation / signaling receptor binding / protein-containing complex binding / negative regulation of apoptotic process / cell surface / signal transduction / plasma membrane => GO:0005886 / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane => GO:0016020 / membrane / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / divergent subfamily of APPLE domains / Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain ...Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / divergent subfamily of APPLE domains / Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / IPT/TIG domain / ig-like, plexins, transcription factors / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / Kringle domain / Kringle domain profile. / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain / Kringle / 7 Propeller / Methylamine Dehydrogenase; Chain H / Kringle-like fold / Immunoglobulin E-set / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Serine proteases, trypsin domain / Trypsin / Tyrosine-protein kinase, active site / Trypsin-like serine proteases / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Thrombin, subunit H / WD40/YVTN repeat-like-containing domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Protein kinases ATP-binding region signature. / Protein kinase, ATP binding site / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor receptor / Hepatocyte growth factor
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å|
|Authors||Eigenbrot, C. / Landgraf, K.E. / Steffek, M.|
|Citation||Journal: Nat.Chem.Biol. / Year: 2014|
Title: An allosteric switch for pro-HGF/Met signaling using zymogen activator peptides.
Authors: Landgraf, K.E. / Steffek, M. / Quan, C. / Tom, J. / Yu, C. / Santell, L. / Maun, H.R. / Eigenbrot, C. / Lazarus, R.A.
|Structure viewer||Molecule: |
Downloads & links
A: Hepatocyte growth factor
B: Hepatocyte growth factor receptor
P: ZAP 2.3
|#1: Protein|| |
Mass: 26800.920 Da / Num. of mol.: 1 / Fragment: HGF-beta (UNP Residues 25-567) / Mutation: V495G/C604S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGF, HPTA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14210
|#2: Protein|| |
Mass: 62714.141 Da / Num. of mol.: 1 / Fragment: Sema-PSI (UNP Residues 496-728) / Mutation: L303K/V304R/P305K/R306K/G307R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P08581, receptor protein-tyrosine kinase
|#3: Protein/peptide|| |
Mass: 1786.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide library displayed on phage / Source: (synth.) synthetic (unknown)
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 3.44 Å3/Da / Density % sol: 64.26 %|
|Crystal grow||Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 |
Details: 8% PEG8000, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|Diffraction||Mean temperature: 110 K|
|Diffraction source||Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 Å|
|Detector||Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 23, 2012|
|Radiation||Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.9794 Å / Relative weight: 1|
|Reflection||Resolution: 3.04→34.76 Å / Num. all: 24419 / Num. obs: 24340 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 102.77 Å2 / Rsym value: 0.056 / Net I/σ(I): 23|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: PDB ENTRY 1SHY
Resolution: 3.04→34.76 Å / Cor.coef. Fo:Fc: 0.8969 / Cor.coef. Fo:Fc free: 0.8574 / SU R Cruickshank DPI: 1.39 / Isotropic thermal model: individual atom isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
|Displacement parameters||Biso mean: 94.12 Å2|
|Refine analyze||Luzzati coordinate error obs: 0.593 Å|
|Refinement step||Cycle: LAST / Resolution: 3.04→34.76 Å|
|Refine LS restraints|
|LS refinement shell||Resolution: 3.04→3.17 Å / Total num. of bins used: 12 |
-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
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
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- 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.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+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
+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.
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