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- PDB-4qt8: Crystal Structure of RON Sema-PSI-IPT1 extracellular domains in c... -

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Basic information

Entry
Database: PDB / ID: 4qt8
TitleCrystal Structure of RON Sema-PSI-IPT1 extracellular domains in complex with MSP beta-chain
Components
  • Hepatocyte growth factor-like protein
  • Macrophage-stimulating protein receptor
KeywordsHYDROLASE/SIGNALING PROTEIN / Growth Factor receptor/Growth factor / Receptor-ligand complex / RON receptor tyrosine kinase / Macrophage Stimulating Protein / HYDROLASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Signaling by MST1 / macrophage colony-stimulating factor receptor activity / regulation of cAMP-dependent protein kinase activity / vacuole / regulation of receptor signaling pathway via JAK-STAT / single fertilization / negative regulation of gluconeogenesis / phagocytosis / stress fiber / transmembrane receptor protein tyrosine kinase activity ...Signaling by MST1 / macrophage colony-stimulating factor receptor activity / regulation of cAMP-dependent protein kinase activity / vacuole / regulation of receptor signaling pathway via JAK-STAT / single fertilization / negative regulation of gluconeogenesis / phagocytosis / stress fiber / transmembrane receptor protein tyrosine kinase activity / response to virus / positive regulation of MAP kinase activity / defense response / receptor tyrosine kinase binding / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / cell migration / nervous system development / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / phosphorylation / innate immune response / positive regulation of cell population proliferation / enzyme binding / cell surface / signal transduction / proteolysis / extracellular space / extracellular region / ATP binding / plasma membrane
Similarity search - Function
Macrophage stimulating protein / RON, Sema domain / Hepatocyte growth factor/Macrophage stimulatory protein / divergent subfamily of APPLE domains / Tyrosine-protein kinase, HGF/MSP receptor / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain ...Macrophage stimulating protein / RON, Sema domain / Hepatocyte growth factor/Macrophage stimulatory protein / divergent subfamily of APPLE domains / Tyrosine-protein kinase, HGF/MSP receptor / 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 / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / 7 Propeller / Methylamine Dehydrogenase; Chain H / Kringle-like fold / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Immunoglobulin E-set / Trypsin / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Trypsin-like serine proteases / Tyrosine-protein kinase, active site / Thrombin, subunit H / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Peptidase S1, PA clan / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Hepatocyte growth factor-like protein / Macrophage-stimulating protein receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHerzberg, O. / Chao, K.L.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural basis for the binding specificity of human Recepteur d'Origine Nantais (RON) receptor tyrosine kinase to macrophage-stimulating protein.
Authors: Chao, K.L. / Gorlatova, N.V. / Eisenstein, E. / Herzberg, O.
History
DepositionJul 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Macrophage-stimulating protein receptor
A: Macrophage-stimulating protein receptor
C: Hepatocyte growth factor-like protein
D: Hepatocyte growth factor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,6596
Polymers200,6484
Non-polymers1,0112
Water0
1
A: Macrophage-stimulating protein receptor
C: Hepatocyte growth factor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7493
Polymers100,3242
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Macrophage-stimulating protein receptor
D: Hepatocyte growth factor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9113
Polymers100,3242
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.585, 63.775, 146.049
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLUGLUBA28 - 6836 - 661
21GLNGLNGLUGLUAB28 - 6836 - 661
12CYSCYSLEULEUCC468 - 7104 - 246
22CYSCYSLEULEUDD468 - 7104 - 246

NCS ensembles :
ID
1
2

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Components

#1: Protein Macrophage-stimulating protein receptor / MSP receptor / CDw136 / Protein-tyrosine kinase 8 / p185-Ron / RON receptor tyrosine kinase


Mass: 71987.438 Da / Num. of mol.: 2
Fragment: extracellular Sema-PSI-IPT1 domains (UNP residues 25-683)
Mutation: R306L, R307V, R308P, A311S, R322Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MST1R, PTK8, RON / Plasmid: pMT/BiP/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2
References: UniProt: Q04912, receptor protein-tyrosine kinase
#2: Protein Hepatocyte growth factor-like protein / Macrophage stimulatory protein / Macrophage-stimulating protein / MSP


Mass: 28336.740 Da / Num. of mol.: 2 / Fragment: beta chain (UNP residues 465-711) / Mutation: C672S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: D3F15S2, DNF15S2, HGFL, MSI1, MST1 / Plasmid: pMT/BiP/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P26927
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 20% w/v PEG4000, 8% v/v isopropanol, 4% v/v polypropylene glycol 400, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2010 / Details: mirrors
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.577
11-h,-k,l20.423
ReflectionResolution: 2.996→146.96 Å / Num. all: 39670 / Num. obs: 38960 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.202 / Net I/σ(I): 4.4
Reflection shellHighest resolution: 2.996 Å

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4FWW & 2ASU

4fww

2asu


Resolution: 3→19.98 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.818 / SU B: 13.688 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29077 1889 5.1 %RANDOM
Rwork0.23381 ---
obs0.23677 35063 92.37 %-
all-37299 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.191 Å2
Baniso -1Baniso -2Baniso -3
1-12.43 Å2-0 Å2-30.05 Å2
2---18.97 Å2-0 Å2
3---6.54 Å2
Refinement stepCycle: LAST / Resolution: 3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12550 0 67 0 12617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912982
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211846
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.96717769
X-RAY DIFFRACTIONr_angle_other_deg0.866327179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.53451701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95722.946482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.75151769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9251581
X-RAY DIFFRACTIONr_chiral_restr0.0740.22023
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114862
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022923
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.475.3276858
X-RAY DIFFRACTIONr_mcbond_other3.4665.3276857
X-RAY DIFFRACTIONr_mcangle_it5.9427.9768541
X-RAY DIFFRACTIONr_mcangle_other3.8156.9838501
X-RAY DIFFRACTIONr_scbond_it2.595.3716124
X-RAY DIFFRACTIONr_scbond_other1.6644.6566263
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8426.9939415
X-RAY DIFFRACTIONr_long_range_B_refined6.35636.97513931
X-RAY DIFFRACTIONr_long_range_B_other6.35536.97513932
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B328110.05
12A328110.05
21C130870.03
22D130870.03
LS refinement shellResolution: 2.997→3.075 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 118 -
Rwork0.305 2220 -
obs--79.77 %

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