[English] 日本語
Yorodumi
- PDB-1shy: The Crystal Structure of HGF beta-chain in Complex with the Sema ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1shy
TitleThe Crystal Structure of HGF beta-chain in Complex with the Sema Domain of the Met Receptor.
Components
  • Hepatocyte growth factor receptorC-Met
  • Hepatocyte growth factor
KeywordsGROWTH FACTOR/GROWTH FACTOR RECEPTOR / protease / sema domain / PSI domain / receptor ectodomain growth factor / GROWTH FACTOR-GROWTH FACTOR RECEPTOR 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsStamos, J. / Wiesmann, C.
Citation
Journal: Embo J. / Year: 2004
Title: Crystal structure of the HGF beta-chain in complex with the Sema domain of the Met receptor.
Authors: Stamos, J. / Lazarus, R.A. / Yao, X. / Kirchhofer, D. / Wiesmann, C.
#1: Journal: To be Published
Title: Structural and functional basis of the serine protease-like HGF b-chain in Met binding and signaling
Authors: Kirchhofer, D. / Xiaoyi, Y. / Peek, M. / Eigenbrot, C. / Lipari, M.T. / Billeci, K.L. / Maun, H.R. / Moran, P. / Santell, L. / Lazarus, R.A.
History
DepositionFeb 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED
Remark 700SHEET DETERMINATION METHOD: AUTHOR PROVIDED
Remark 999SEQUENCE IN CHAIN B, THE FURIN CLEAVAGE SITE WAS REPLACED WITH A THROMBIN CLEAVAGE SITE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hepatocyte growth factor
B: Hepatocyte growth factor receptor


Theoretical massNumber of molelcules
Total (without water)88,5502
Polymers88,5502
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.052, 186.352, 66.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Hepatocyte growth factor / / Scatter factor / SF / Hepatopoeitin A


Mass: 26014.117 Da / Num. of mol.: 1 / Fragment: HGF beta chain / Mutation: C604S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGF, HPTA / Production host: Escherichia coli (E. coli) / References: UniProt: P14210
#2: Protein Hepatocyte growth factor receptor / C-Met / Met proto-oncogene tyrosine kinase / c-met / HGF receptor / HGF-SF receptor


Mass: 62535.852 Da / Num. of mol.: 1 / Fragment: Met receptor Sema and PSI domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08581

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.8 Å3/Da / Density % sol: 74.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.928 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 7, 2003
RadiationMonochromator: monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 28312 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.058
Reflection shellResolution: 3.2→3.31 Å / Rsym value: 0.586 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HGF beta chain

Resolution: 3.22→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.889 / SU B: 17.302 / SU ML: 0.297 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.83 / ESU R Free: 0.409
RfactorNum. reflection% reflectionSelection details
Rfree0.26978 1417 5 %RANDOM
Rwork0.20904 ---
obs0.21206 26830 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.027 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å20 Å20 Å2
2---2.24 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.22→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5735 0 0 0 5735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215883
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9427991
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5675722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024482
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2460.22571
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3250.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it3.7312.53617
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.37755869
X-RAY DIFFRACTIONr_scbond_it3.682.52266
X-RAY DIFFRACTIONr_scangle_it6.01652122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.217→3.282 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rfree0.35 69
Rwork0.327 1448
Refinement TLS params.Method: refined / Origin x: -6.9404 Å / Origin y: 29.4231 Å / Origin z: 39.4854 Å
111213212223313233
T0.3008 Å20.009 Å2-0.1689 Å2-0.2576 Å20.1267 Å2--0.1623 Å2
L2.9671 °2-1.7139 °2-1.1851 °2-3.7827 °21.1785 °2--1.8934 °2
S-0.4129 Å °-0.2747 Å °0.264 Å °0.2786 Å °0.4647 Å °0.077 Å °-0.3013 Å °0.1519 Å °-0.0517 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA495 - 7221 - 228
2X-RAY DIFFRACTION1BB40 - 53016 - 506
3X-RAY DIFFRACTION1BB531 - 564507 - 540

+
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