[English] 日本語
Yorodumi
- PDB-4fww: Crystal structure of the Sema-PSI extracellular domains of human ... -

+
Open data


ID or keywords:

Loading...

-
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 / single fertilization / phagocytosis / stress fiber / transmembrane receptor protein tyrosine kinase activity / response to virus / positive regulation of MAP kinase activity / defense response ...Signaling by MST1 / macrophage colony-stimulating factor receptor activity / vacuole / single fertilization / phagocytosis / stress fiber / transmembrane receptor protein tyrosine kinase activity / response to virus / positive regulation of MAP kinase activity / defense response / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / cell migration / nervous system development / 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 / 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 / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin E-set / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 6 types, 374 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


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 / Glycerol


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


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


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


Mass: 18.015 Da / Num. of mol.: 358 / 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: 3.03 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

-
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

-
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

+
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