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- PDB-4o3t: Zymogen HGF-beta/MET with Zymogen Activator Peptide ZAP.14 -

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Basic information

Entry
Database: PDB / ID: 4o3t
TitleZymogen HGF-beta/MET with Zymogen Activator Peptide ZAP.14
Components
  • Hepatocyte growth factor
  • Hepatocyte growth factor receptor
  • ZAP.14
Keywordstransferase/growth factor / trypsin homology / receptor activation / transferase-growth factor complex
Function / homology
Function and homology information


regulation of p38MAPK cascade / skeletal muscle cell proliferation / negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor activity / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET Receptor Activation / MET interacts with TNS proteins ...regulation of p38MAPK cascade / skeletal muscle cell proliferation / negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor activity / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET Receptor Activation / MET interacts with TNS proteins / endothelial cell morphogenesis / hepatocyte growth factor receptor signaling pathway / semaphorin receptor activity / MET receptor recycling / pancreas development / MET activates PTPN11 / MET activates RAP1 and RAC1 / Sema4D mediated inhibition of cell attachment and migration / MET activates PI3K/AKT signaling / positive regulation of endothelial cell chemotaxis / negative regulation of stress fiber assembly / MET activates PTK2 signaling / positive regulation of DNA biosynthetic process / cellular response to hepatocyte growth factor stimulus / branching morphogenesis of an epithelial tube / positive chemotaxis / negative regulation of Rho protein signal transduction / negative regulation of release of cytochrome c from mitochondria / chemoattractant activity / negative regulation of thrombin-activated receptor signaling pathway / negative regulation of interleukin-6 production / semaphorin-plexin signaling pathway / myoblast proliferation / positive regulation of interleukin-10 production / epithelial to mesenchymal transition / establishment of skin barrier / positive regulation of osteoblast differentiation / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / MET activates RAS signaling / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / Interleukin-7 signaling / negative regulation of autophagy / cell surface receptor protein tyrosine kinase signaling pathway / basal plasma membrane / platelet alpha granule lumen / molecular function activator activity / InlB-mediated entry of Listeria monocytogenes into host cell / epithelial cell proliferation / cell chemotaxis / excitatory postsynaptic potential / growth factor activity / liver development / Negative regulation of MET activity / receptor protein-tyrosine kinase / negative regulation of inflammatory response / cell morphogenesis / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / Platelet degranulation / PIP3 activates AKT signaling / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / protein phosphatase binding / Interleukin-4 and Interleukin-13 signaling / cell surface receptor signaling pathway / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynapse / positive regulation of MAPK cascade / positive regulation of cell migration / signaling receptor binding / negative regulation of apoptotic process / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / ATP binding / identical protein binding / membrane / 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 ...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 / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin E-set / Trypsin-like serine proteases / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Thrombin, subunit H / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Protein kinase domain profile. / Protein kinase domain / Peptidase S1, PA clan / 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)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsEigenbrot, C. / Landgraf, K.E. / Steffek, M.
CitationJournal: 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.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hepatocyte growth factor
B: Hepatocyte growth factor receptor
P: ZAP.14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6465
Polymers90,8383
Non-polymers8092
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.789, 121.467, 137.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hepatocyte growth factor / Hepatopoietin-A / Scatter factor / SF / Hepatocyte growth factor alpha chain / Hepatocyte growth ...Hepatopoietin-A / Scatter factor / SF / Hepatocyte growth factor alpha chain / Hepatocyte growth factor beta chain


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 Hepatocyte growth factor receptor / HGF receptor / HGF/SF receptor / Proto-oncogene c-Met / Scatter factor receptor / SF receptor / ...HGF receptor / HGF/SF receptor / Proto-oncogene c-Met / Scatter factor receptor / SF receptor / Tyrosine-protein kinase Met


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 ZAP.14


Mass: 1322.530 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: derived from synthetic peptide library displayed on phage particles
Source: (synth.) synthetic (others)
#4: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG6000, 800 mM NaCl, 400 mM trimethylammonium oxide, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 4, 2011
RadiationMonochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.99→45.54 Å / Num. all: 20873 / Num. obs: 20853 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 73.84 Å2 / Rsym value: 0.112 / Net I/σ(I): 15

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
BUSTER2.11.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHY

1shy


Resolution: 2.99→45.54 Å / Cor.coef. Fo:Fc: 0.8641 / Cor.coef. Fo:Fc free: 0.8233 / Isotropic thermal model: individual atom isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2758 877 4.21 %RANDOM
Rwork0.2315 ---
all0.235 20873 --
obs0.2334 20853 99.53 %-
Displacement parametersBiso mean: 66.81 Å2
Baniso -1Baniso -2Baniso -3
1-14.6371 Å20 Å20 Å2
2---31.6373 Å20 Å2
3---17.0002 Å2
Refine analyzeLuzzati coordinate error obs: 0.442 Å
Refinement stepCycle: LAST / Resolution: 2.99→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5750 0 54 0 5804
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095968HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.088102HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2032SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes139HARMONIC2
X-RAY DIFFRACTIONt_gen_planes860HARMONIC5
X-RAY DIFFRACTIONt_it5968HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion22.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion775SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6348SEMIHARMONIC4
LS refinement shellResolution: 2.99→3.15 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3265 118 4 %
Rwork0.2558 2831 -
all0.2588 2949 -
obs-2949 99.53 %

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