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- PDB-4fww: Crystal structure of the Sema-PSI extracellular domains of human ... -

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Basic information

Entry
Database: PDB / ID: 4fww
TitleCrystal structure of the Sema-PSI extracellular domains of human RON receptor tyrosine kinase
ComponentsMacrophage-stimulating protein receptor
KeywordsTRANSFERASE / beta-propeller / cysteine-knot / receptor tyrosine kinase / macrophage stimulating protein / N-glycosylation / extracellular
Function / homology
Function and homology information


Signaling by MST1 / macrophage colony-stimulating factor receptor activity / vacuole / positive regulation of MAP kinase activity / phagocytosis / single fertilization / stress fiber / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / defense response ...Signaling by MST1 / macrophage colony-stimulating factor receptor activity / vacuole / positive regulation of MAP kinase activity / phagocytosis / single fertilization / stress fiber / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / defense response / receptor protein-tyrosine kinase / response to virus / cell migration / nervous system development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / innate immune response / positive regulation of cell population proliferation / enzyme binding / cell surface / signal transduction / ATP binding / plasma membrane
Similarity search - Function
RON, Sema domain / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / Tyrosine-protein kinase, HGF/MSP receptor / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily ...RON, Sema domain / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / Tyrosine-protein kinase, HGF/MSP receptor / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / YVTN repeat-like/Quinoprotein amine dehydrogenase / : / 7 Propeller / Methylamine Dehydrogenase; Chain H / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin E-set / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Macrophage-stimulating protein receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChao, K.L. / Herzberg, O.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structure of the Sema-PSI Extracellular Domain of Human RON Receptor Tyrosine Kinase.
Authors: Chao, K.L. / Tsai, I.W. / Chen, C. / Herzberg, O.
History
DepositionJul 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage-stimulating protein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,09118
Polymers56,1331
Non-polymers1,95917
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.400, 73.300, 87.900
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Macrophage-stimulating protein receptor / MSP receptor / CDw136 / Protein-tyrosine kinase 8 / p185-Ron / Macrophage-stimulating protein ...MSP receptor / CDw136 / Protein-tyrosine kinase 8 / p185-Ron / Macrophage-stimulating protein receptor alpha chain / Macrophage-stimulating protein receptor beta chain


Mass: 56132.543 Da / Num. of mol.: 1
Fragment: extracellular Sema and PSI domains (UNP Residues 42-568)
Source method: isolated from a genetically manipulated source
Details: The furin consensus cleavage sequence was mutated to a thrombin cleavage sequence. The recombinant protein contained the 115 amino acid residues IPT1 domain. However, proteolytic degradation ...Details: The furin consensus cleavage sequence was mutated to a thrombin cleavage sequence. The recombinant protein contained the 115 amino acid residues IPT1 domain. However, proteolytic degradation during crystallization removed ~75 amino acid residues of the domain and the remaining 40 residues are disordered and are not listed in the sequence record. Proteolytic degradation also removed N-terminal residues 23-41. These are not included in the sequence.
Source: (gene. exp.) Homo sapiens (human) / Gene: MST1R, PTK8, RON / Plasmid: pMT/BiP-V5-HisA / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2
References: UniProt: Q04912, receptor protein-tyrosine kinase
#2: Polysaccharide beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 374 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 19% PEG 4000, 0.1 M Sodium Acetate, pH 4.6, 0.2 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 24, 2010 / Details: mirrors
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.85→19.32 Å / Num. all: 57269 / Num. obs: 51510 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.46
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.47 / % possible all: 63.7

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2UZX chain B

2uzx


Resolution: 1.85→19.32 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.857 / SU ML: 0.11 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23245 2627 5.1 %RANDOM
Rwork0.19091 ---
obs0.19311 48882 89.95 %-
all-51510 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.634 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3845 0 127 358 4330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024031
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.995497
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0485510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48323.688160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24915548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9981521
X-RAY DIFFRACTIONr_chiral_restr0.1250.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0223080
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.21829
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22733
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2340
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3070.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0321.52657
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6924174
X-RAY DIFFRACTIONr_scbond_it2.7231600
X-RAY DIFFRACTIONr_scangle_it4.1594.51430
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 133 -
Rwork0.362 2504 -
obs--63.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.25360.8368-0.1811.2007-0.43061.6772-0.12370.1117-0.2665-0.17630.1255-0.31910.08620.313-0.00180.0794-0.00730.01370.1137-0.06860.114310.319-12.33224.53
21.67390.3156-0.37532.9013-1.99033.4434-0.03540.27450.0011-0.2530.19820.27640.0666-0.4128-0.16290.0299-0.0089-0.02810.102-0.00830.0771-14.822-6.60623.506
31.27330.9331-0.60722.373-1.17631.94810.03120.2260.12860.02540.1020.1927-0.1702-0.0291-0.13320.0562-0.0146-0.0230.1224-0.00720.0609-8.219-2.71119.885
41.9577-1.5380.143822.01791.83624.7498-0.09560.2675-0.3962-0.6213-0.0502-0.08070.40870.08940.14590.5032-0.07590.0760.167-0.05670.3795-1.48230.215.856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 266
2X-RAY DIFFRACTION2A267 - 391
3X-RAY DIFFRACTION3A392 - 522
4X-RAY DIFFRACTION4A523 - 568

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