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- PDB-4bsj: Crystal structure of VEGFR-3 extracellular domains D4-5 -

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Basic information

Entry
Database: PDB / ID: 4bsj
TitleCrystal structure of VEGFR-3 extracellular domains D4-5
ComponentsVASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3
KeywordsTRANSFERASE / LYMPHANGIOGENESIS / ANGIOGENESIS / VASCULAR / IG DOMAIN / GLYCOPROTEIN / RECEPTOR TYROSINE KINASE / DIMERIZATION
Function / homology
Function and homology information


regulation of blood vessel remodeling / positive regulation of protein kinase C signaling / lymphangiogenesis / VEGF binds to VEGFR leading to receptor dimerization / respiratory system process / vascular endothelial growth factor receptor activity / lymph vessel development / vasculature development / sprouting angiogenesis / blood vessel morphogenesis ...regulation of blood vessel remodeling / positive regulation of protein kinase C signaling / lymphangiogenesis / VEGF binds to VEGFR leading to receptor dimerization / respiratory system process / vascular endothelial growth factor receptor activity / lymph vessel development / vasculature development / sprouting angiogenesis / blood vessel morphogenesis / NOTCH4 Intracellular Domain Regulates Transcription / vascular endothelial growth factor signaling pathway / lung alveolus development / growth factor binding / regulation of MAPK cascade / positive regulation of vascular endothelial growth factor production / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / positive regulation of endothelial cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of endothelial cell migration / transmembrane receptor protein tyrosine kinase activity / positive regulation of JNK cascade / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / protein phosphatase binding / angiogenesis / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of ERK1 and ERK2 cascade / receptor complex / positive regulation of cell migration / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein homodimerization activity / extracellular region / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
VEGFR-2, transmembrane domain / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 ...VEGFR-2, transmembrane domain / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor receptor 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 Å
AuthorsLeppanen, V.-M. / Tvorogov, D. / Kisko, K. / Prota, A.E. / Jeltsch, M. / Anisimov, A. / Markovic-Mueller, S. / Stuttfeld, E. / Goldie, K.N. / Ballmer-Hofer, K. / Alitalo, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural and Mechanistic Insights Into Vegfr-3 Ligand Binding and Activation
Authors: Leppanen, V.-M. / Tvorogov, D. / Kisko, K. / Prota, A.E. / Jeltsch, M. / Anisimov, A. / Markovic-Mueller, S. / Stuttfeld, E. / Goldie, K.N. / Ballmer-Hofer, K. / Alitalo, K.
History
DepositionJun 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 2.0Apr 11, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site
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_seq_id / _atom_site.occupancy / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_special_symmetry.auth_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Jan 30, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 2.2Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 2.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9643
Polymers26,5211
Non-polymers4422
Water37821
1
A: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3
hetero molecules

A: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9276
Polymers53,0422
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.340, 133.340, 48.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-712-

HOH

21A-721-

HOH

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Components

#1: Protein VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3 / VEGFR-3 / FMS-LIKE TYROSINE KINASE 4 / FLT-4 / TYROSINE-PROTEIN KINASE RECEPTOR FLT4 / VEGFR-3


Mass: 26521.211 Da / Num. of mol.: 1
Fragment: EXTRACELLULAR DOMAINS 4 AND 5 (D4-5), RESIDUES 330-553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC1 / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P35916, receptor protein-tyrosine kinase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsN-ACETYL GLUCOSAMINE (NAG): THE NAG MOIETIES ARE COVALENTLY LINKED TO ASN411 AND ASN515.
Sequence detailsASP 328 AND HIS329 ARE A CLONING ARTEFACT AND HIS554 IS PART OF THE HIS-TAG. RESIDUES 470-483 WERE ...ASP 328 AND HIS329 ARE A CLONING ARTEFACT AND HIS554 IS PART OF THE HIS-TAG. RESIDUES 470-483 WERE OMITTED FROM THE MODEL DUE TO LACK OF ELECTRON DENSITY.

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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: 4.74 Å3/Da / Density % sol: 74.1 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 298 K, PHOSPHATE BUFFER 0.1 M, PH 7.5 - 8.5, PEG 400 25%.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2011
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 17532 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 73 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.1
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.32 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.5→38.492 Å / SU ML: 0.33 / σ(F): 1.99 / Phase error: 28.74 / Stereochemistry target values: ML
Details: AN INITIAL MODEL WAS BUILT WITH ARPWARP AND REFINED WITH REFMAC. RESIDUES 470-483 AND SIDECHAINS OF RESIDUES 328, 329, 469, 485 AND 487 ARE DISORDERED AND WERE OMITTED FROM THE FINAL MODEL.
RfactorNum. reflection% reflection
Rfree0.2533 878 5 %
Rwork0.2098 --
obs0.2118 17525 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 28 21 1722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061753
X-RAY DIFFRACTIONf_angle_d1.0212396
X-RAY DIFFRACTIONf_dihedral_angle_d13.566633
X-RAY DIFFRACTIONf_chiral_restr0.066274
X-RAY DIFFRACTIONf_plane_restr0.004297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.65670.3381420.31152746X-RAY DIFFRACTION100
2.6567-2.86170.30721350.29642746X-RAY DIFFRACTION100
2.8617-3.14960.31491550.26422746X-RAY DIFFRACTION100
3.1496-3.6050.26231720.22912738X-RAY DIFFRACTION100
3.605-4.54080.2191400.19252790X-RAY DIFFRACTION100
4.5408-38.49650.24211340.18252881X-RAY DIFFRACTION100

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