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- PDB-5mya: Homodimerization of Tie2 Fibronectin-like domains 1-3 in space gr... -

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Basic information

Entry
Database: PDB / ID: 5mya
TitleHomodimerization of Tie2 Fibronectin-like domains 1-3 in space group C2
ComponentsAngiopoietin-1 receptor
KeywordsSIGNALING PROTEIN / receptor / fibronectin-like domains / dimerization / homotypic interactions
Function / homology
Function and homology information


Tie signaling pathway / regulation of establishment or maintenance of cell polarity / glomerulus vasculature development / regulation of endothelial cell apoptotic process / regulation of vascular permeability / endochondral ossification / heart trabecula formation / definitive hemopoiesis / sprouting angiogenesis / endothelial cell proliferation ...Tie signaling pathway / regulation of establishment or maintenance of cell polarity / glomerulus vasculature development / regulation of endothelial cell apoptotic process / regulation of vascular permeability / endochondral ossification / heart trabecula formation / definitive hemopoiesis / sprouting angiogenesis / endothelial cell proliferation / positive regulation of intracellular signal transduction / positive regulation of Rho protein signal transduction / growth factor binding / positive regulation of Rac protein signal transduction / positive regulation of focal adhesion assembly / microvillus / centriolar satellite / negative regulation of endothelial cell apoptotic process / cell surface receptor protein tyrosine kinase signaling pathway / Tie2 Signaling / response to cAMP / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / negative regulation of angiogenesis / basal plasma membrane / receptor protein-tyrosine kinase / response to peptide hormone / negative regulation of inflammatory response / response to estrogen / positive regulation of angiogenesis / cell-cell junction / cell-cell signaling / heart development / signaling receptor activity / RAF/MAP kinase cascade / basolateral plasma membrane / angiogenesis / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / response to hypoxia / protein kinase activity / positive regulation of protein phosphorylation / membrane raft / apical plasma membrane / focal adhesion / negative regulation of apoptotic process / cell surface / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tyrosine-protein kinase, receptor Tie-2, Ig-like domain 1, N-terminal / Tie-2 Ig-like domain 1 / Laminin-type EGF domain / Epidermal growth factor-like domain. / EGF-like domain profile. / : / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / EGF-like domain ...Tyrosine-protein kinase, receptor Tie-2, Ig-like domain 1, N-terminal / Tie-2 Ig-like domain 1 / Laminin-type EGF domain / Epidermal growth factor-like domain. / EGF-like domain profile. / : / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/Threonine protein kinases, catalytic domain / 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
Angiopoietin-1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.9 Å
AuthorsLeppanen, V.-M. / Saharinen, P. / Alitalo, K.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of Tie2 activation and Tie2/Tie1 heterodimerization.
Authors: Leppanen, V.M. / Saharinen, P. / Alitalo, K.
History
DepositionJan 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiopoietin-1 receptor
B: Angiopoietin-1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8119
Polymers75,1672
Non-polymers2,6447
Water1,13563
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint30 kcal/mol
Surface area28110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.160, 104.690, 79.520
Angle α, β, γ (deg.)90.00, 121.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Non-polymers , 2 types, 65 molecules AB

#1: Protein Angiopoietin-1 receptor / Endothelial tyrosine kinase / Tunica interna endothelial cell kinase / Tyrosine kinase with Ig and ...Endothelial tyrosine kinase / Tunica interna endothelial cell kinase / Tyrosine kinase with Ig and EGF homology domains-2 / Tyrosine-protein kinase receptor TEK / Tyrosine-protein kinase receptor TIE-2 / hTIE2 / p140 TEK


Mass: 37583.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: In addition to the Tie2 Fn-like domains, the entity includes mellitin signal peptide, a N-terminal cloning artefact (ADP), C-terminal Factor Xa cleavage site (IEGR) and His-tag. The first Fn- ...Details: In addition to the Tie2 Fn-like domains, the entity includes mellitin signal peptide, a N-terminal cloning artefact (ADP), C-terminal Factor Xa cleavage site (IEGR) and His-tag. The first Fn-like domain in chain B was disordered due to lack of crystal packing contacts and was omitted from model building.
Source: (gene. exp.) Homo sapiens (human) / Gene: TEK, TIE2, VMCM, VMCM1
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: Q02763, receptor protein-tyrosine kinase
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 7 molecules

#2: 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
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-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
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/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)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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

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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: 2.7 Å3/Da / Density % sol: 54 % / Description: Elongated rods
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris buffer at pH 7.0 - 8.5 and 14-20% PEG 3350 (w/v)
PH range: 7.0 - 8.5 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen cooling system
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 30, 2015
RadiationMonochromator: Standard ESRF channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 20882 / % possible obs: 99.4 % / Redundancy: 11.4 % / Biso Wilson estimate: 119.5 Å2 / Rsym value: 0.092 / Net I/σ(I): 16.1
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3444 / Rsym value: 1.869 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.9→29.419 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.75
Details: Maximum likelihood refinement of XYZ coordinates, TLS parameters and individual B-factors.
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 1074 5.14 %Random selection in XDS
Rwork0.2345 ---
obs0.2368 20878 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 139.9 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3736 0 173 63 3972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073999
X-RAY DIFFRACTIONf_angle_d1.1425479
X-RAY DIFFRACTIONf_dihedral_angle_d14.1771460
X-RAY DIFFRACTIONf_chiral_restr0.064665
X-RAY DIFFRACTIONf_plane_restr0.004692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.03190.3871290.37992489X-RAY DIFFRACTION100
3.0319-3.19160.38121410.33072448X-RAY DIFFRACTION100
3.1916-3.39130.44041170.29192467X-RAY DIFFRACTION100
3.3913-3.65270.32941320.26732458X-RAY DIFFRACTION100
3.6527-4.01940.28941160.26142488X-RAY DIFFRACTION100
4.0194-4.59910.30031400.21942469X-RAY DIFFRACTION100
4.5991-5.78720.21811440.19512478X-RAY DIFFRACTION100
5.7872-29.4210.25951550.22382507X-RAY DIFFRACTION100
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)
15.4914-2.1292-3.55150.95450.31714.0014-0.13480.58060.6845-0.1686-0.0075-0.2507-0.0124-0.32860.0290.8858-0.2441-0.0860.7986-0.14671.11582.7997-18.9401-44.8253
28.6517-2.7121-2.8353.01381.73353.1135-0.10880.74550.03450.04740.3091-0.4917-0.1373-0.3454-0.23410.68340.1271-0.02450.71320.03730.606458.074-10.1801-25.035
38.3147-3.486-1.39825.6784-0.11522.4735-0.17030.93520.84310.10760.36740.1780.1802-0.4027-0.28141.11460.29320.06381.16920.29830.845226.03925.7627-14.0646
41.9516-0.63241.16285.1727-0.3043.4469-0.13760.07781.3724-0.7391-0.3103-0.7067-1.48970.53420.4271.39430.27260.07891.2210.41361.519722.104414.002828.8927
52.3726-1.82040.78974.8542-0.85375.03-0.2779-0.4736-0.1557-0.10770.1557-0.22220.06980.4056-0.02610.95270.17130.13071.08850.3040.95424.82542.389628.3886
63.6226-0.0055-0.28394.464-1.3996.299-0.39320.1135-0.5741-0.07160.59490.48551.7059-1.072-0.1021.35290.00790.23821.55350.29841.077719.4147-8.9257-4.1427
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 441 through 562 )
2X-RAY DIFFRACTION2chain 'A' and (resid 563 through 645 )
3X-RAY DIFFRACTION3chain 'A' and (resid 646 through 735 )
4X-RAY DIFFRACTION4chain 'B' and (resid 540 through 574 )
5X-RAY DIFFRACTION5chain 'B' and (resid 575 through 645 )
6X-RAY DIFFRACTION6chain 'B' and (resid 646 through 731 )

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