[English] 日本語
Yorodumi
- PDB-1si5: Protease-like domain from 2-chain hepatocyte growth factor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1si5
TitleProtease-like domain from 2-chain hepatocyte growth factor
Componentshepatocyte growth factor
KeywordsHORMONE/GROWTH FACTOR / chymotrypsin homology / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / hepatocyte growth factor receptor signaling pathway / MET receptor recycling ...regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / hepatocyte growth factor receptor signaling pathway / MET receptor recycling / MET activates PTPN11 / MET activates RAP1 and RAC1 / myoblast proliferation / MET activates PI3K/AKT signaling / MET activates PTK2 signaling / positive regulation of DNA biosynthetic process / cellular response to hepatocyte growth factor stimulus / negative regulation of release of cytochrome c from mitochondria / chemoattractant activity / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / epithelial to mesenchymal transition / positive regulation of osteoblast differentiation / MET activates RAS signaling / negative regulation of peptidyl-serine phosphorylation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Interleukin-7 signaling / cell chemotaxis / negative regulation of autophagy / liver development / platelet alpha granule lumen / epithelial cell proliferation / growth factor activity / cell morphogenesis / Negative regulation of MET activity / negative regulation of inflammatory response / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of peptidyl-tyrosine phosphorylation / Platelet degranulation / PIP3 activates AKT signaling / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / positive regulation of protein phosphorylation / signaling receptor binding / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / identical protein binding
Similarity search - Function
Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily ...Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Hepatocyte growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsKirchhofer, D. / Yao, X. / Peek, M. / Eigenbrot, C. / Lipari, M.T. / Billeci, K.L. / Maun, H.R. / Moran, P. / Santell, L. / Lazarus, R.A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural and functional basis of the serine protease-like hepatocyte growth factor beta-chain in Met binding and signaling
Authors: Kirchhofer, D. / Yao, X. / Peek, M. / Eigenbrot, C. / Lipari, M.T. / Billeci, K.L. / Maun, H.R. / Moran, P. / Santell, L. / Wiesmann, C. / Lazarus, R.A.
History
DepositionFeb 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing
Revision 1.6Oct 27, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: hepatocyte growth factor


Theoretical massNumber of molelcules
Total (without water)26,8431
Polymers26,8431
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.700, 63.700, 135.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

-
Components

#1: Protein hepatocyte growth factor / / Scatter factor / SF / Hepatopoeitin A / lung fibroblast-derived mitogen


Mass: 26842.998 Da / Num. of mol.: 1 / Fragment: protease-like domain / Mutation: Cys604Ser
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14210
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: NaCl, CaCl2, PEG 1500, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 6, 2003
RadiationMonochromator: front end, vertically collimating premirror, double-crystal silicon (111) monochromator with a fixed-height exit beam, toroidal focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. all: 10933 / Num. obs: 10933 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.246 / Net I/σ(I): 24
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 4 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.7 / Num. unique all: 886 / % possible all: 83

-
Processing

Software
NameVersionClassification
REFMAC5.1refinement
TRUNCATEdata reduction
AMoREphasing
X-PLOR5.1refinement
HKL-2000data collection
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→42.64 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.874 / SU B: 10.678 / SU ML: 0.229 / Isotropic thermal model: restrained atomic / Cross valid method: THROUGHOUT / σ(F): 0.02 / ESU R: 0.432 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.301 531 4.9 %RANDOM
Rwork0.246 ---
all0.248 10933 --
obs0.248 10399 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.703 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.36 Å20 Å2
2--0.73 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.53→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 0 33 1798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211701
X-RAY DIFFRACTIONr_angle_refined_deg1.481.962317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8465219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.60622.92365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10115261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7071511
X-RAY DIFFRACTIONr_chiral_restr0.1070.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021284
X-RAY DIFFRACTIONr_nbd_refined0.2440.2753
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.26
X-RAY DIFFRACTIONr_mcbond_it4.0992.51089
X-RAY DIFFRACTIONr_mcangle_it6.5251737
X-RAY DIFFRACTIONr_scbond_it4.112.5612
X-RAY DIFFRACTIONr_scangle_it5.6925580
LS refinement shellResolution: 2.53→2.62 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.385 --
Rwork0.323 1341 -
obs-886 83 %

+
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