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- PDB-5vxz: High-affinity AXL decoy receptor -

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Basic information

Entry
Database: PDB / ID: 5vxz
TitleHigh-affinity AXL decoy receptor
Components
  • Growth arrest-specific protein 6
  • Tyrosine-protein kinase receptor UFO
KeywordsTRANSFERASE / engineered decoy receptor / human cancers
Function / homology
Function and homology information


negative regulation of oligodendrocyte apoptotic process / negative regulation of renal albumin absorption / cellular response to vitamin K / forebrain cell migration / positive regulation of glomerular filtration / positive regulation of natural killer cell differentiation / hematopoietic stem cell migration to bone marrow / B cell chemotaxis / negative regulation of lymphocyte activation / cellular response to interferon-alpha ...negative regulation of oligodendrocyte apoptotic process / negative regulation of renal albumin absorption / cellular response to vitamin K / forebrain cell migration / positive regulation of glomerular filtration / positive regulation of natural killer cell differentiation / hematopoietic stem cell migration to bone marrow / B cell chemotaxis / negative regulation of lymphocyte activation / cellular response to interferon-alpha / positive regulation of dendritic cell chemotaxis / positive regulation of pinocytosis / myeloid cell apoptotic process / extracellular matrix assembly / negative regulation of macrophage cytokine production / positive regulation of cytokine-mediated signaling pathway / neutrophil clearance / natural killer cell differentiation / dendritic cell differentiation / : / negative regulation of interleukin-1 production / secretion by cell / positive regulation of viral life cycle / negative regulation of myeloid cell apoptotic process / negative regulation of biomineral tissue development / negative regulation of dendritic cell apoptotic process / negative regulation of fibroblast apoptotic process / apoptotic cell clearance / erythrocyte homeostasis / ovulation cycle / fibroblast apoptotic process / enzyme-linked receptor protein signaling pathway / cell-substrate adhesion / phosphatidylserine binding / myosin heavy chain binding / negative regulation of interleukin-6 production / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / vagina development / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / response to axon injury / positive regulation of TOR signaling / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of protein kinase activity / blood vessel remodeling / animal organ regeneration / vascular endothelial growth factor receptor signaling pathway / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / phosphatidylinositol 3-kinase binding / phagocytosis / negative regulation of endothelial cell apoptotic process / Removal of aminoterminal propeptides from gamma-carboxylated proteins / positive regulation of phagocytosis / cell maturation / cellular response to starvation / activation of protein kinase B activity / transmembrane receptor protein tyrosine kinase activity / viral genome replication / substrate adhesion-dependent cell spreading / positive regulation of protein export from nucleus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / platelet alpha granule lumen / protein localization to plasma membrane / establishment of localization in cell / calcium ion transmembrane transport / Cell surface interactions at the vascular wall / cellular response to glucose stimulus / cell surface receptor protein tyrosine kinase signaling pathway / Post-translational protein phosphorylation / neuron migration / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / platelet activation / cellular response to growth factor stimulus / VEGFA-VEGFR2 Pathway / cellular response to hydrogen peroxide / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of fibroblast proliferation / blood coagulation / cell migration / actin cytoskeleton / cellular response to xenobiotic stimulus / Platelet degranulation / virus receptor activity / protein-macromolecule adaptor activity / nervous system development / spermatogenesis / protein tyrosine kinase activity / neuron apoptotic process / cellular response to lipopolysaccharide / negative regulation of neuron apoptotic process / receptor-mediated virion attachment to host cell / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / receptor complex
Similarity search - Function
Complement Clr-like EGF domain / Laminin G domain / Complement Clr-like EGF-like / Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / Laminin G domain profile. / Laminin G domain / Laminin G domain / Calcium-binding EGF domain ...Complement Clr-like EGF domain / Laminin G domain / Complement Clr-like EGF-like / Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / Laminin G domain profile. / Laminin G domain / Laminin G domain / Calcium-binding EGF domain / Coagulation factor-like, Gla domain superfamily / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Immunoglobulin domain / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / Jelly Rolls - #200 / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / 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. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Jelly Rolls / 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
Tyrosine-protein kinase receptor UFO / Growth arrest-specific protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMathrews, I.I. / Kapur, S. / Kariolis, M.S. / Cochran, J.R.
CitationJournal: J. Clin. Invest. / Year: 2017
Title: Inhibition of the GAS6/AXL pathway augments the efficacy of chemotherapies.
Authors: Kariolis, M.S. / Miao, Y.R. / Diep, A. / Nash, S.E. / Olcina, M.M. / Jiang, D. / Jones, D.S. / Kapur, S. / Mathews, I.I. / Koong, A.C. / Rankin, E.B. / Cochran, J.R. / Giaccia, A.J.
History
DepositionMay 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth arrest-specific protein 6
B: Growth arrest-specific protein 6
C: Tyrosine-protein kinase receptor UFO
D: Tyrosine-protein kinase receptor UFO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,25710
Polymers110,2584
Non-polymers1,0006
Water3,405189
1
A: Growth arrest-specific protein 6
C: Tyrosine-protein kinase receptor UFO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6295
Polymers55,1292
Non-polymers5003
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-16 kcal/mol
Surface area21780 Å2
MethodPISA
2
B: Growth arrest-specific protein 6
D: Tyrosine-protein kinase receptor UFO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6295
Polymers55,1292
Non-polymers5003
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-15 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.220, 80.470, 249.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Growth arrest-specific protein 6 / GAS-6 / AXL receptor tyrosine kinase ligand


Mass: 43871.297 Da / Num. of mol.: 2 / Fragment: residues 324-718
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAS6, AXLLG / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q14393
#2: Protein Tyrosine-protein kinase receptor UFO / AXL oncogene


Mass: 11257.501 Da / Num. of mol.: 2 / Fragment: residues 34-135 / Mutation: A72V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AXL, UFO / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P30530, receptor protein-tyrosine kinase

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Sugars , 1 types, 2 molecules

#3: 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.: 2
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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Non-polymers , 3 types, 193 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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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: 3.52 Å3/Da / Density % sol: 65.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.4 / Details: 0.7 M Li2SO4, 0.1 M Tris.HCl (pH 8.4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2014 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→38.61 Å / Num. obs: 69824 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 59.364 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2% possible all
2.3-2.364.10.8861.670.68297.9
2.36-2.420.7182.080.78499
2.42-2.490.6672.940.86699.6
2.49-2.570.6264.320.9499.9
2.57-2.660.4845.540.95799.9
2.66-2.750.357.420.97599.9
2.75-2.850.2738.920.98399.9
2.85-2.970.20612.090.993100
2.97-3.10.15615.440.995100
3.1-3.250.11121.130.997100
3.25-3.430.08626.990.99899.8
3.43-3.640.06832.930.998100
3.64-3.890.05938.680.99999.9
3.89-4.20.05144.680.999100
4.2-4.60.04449.460.99999.8
4.6-5.140.04349.540.99999.6
5.14-5.940.04447.520.99999.5
5.94-7.270.04549.980.99999.9
7.27-10.290.03552.720.99999.4
10.290.0354.69197.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C5D

2c5d


Resolution: 2.3→38.61 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.025 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.197
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 3492 5 %RANDOM
Rwork0.1984 ---
obs0.2008 66331 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 168.6 Å2 / Biso mean: 61.421 Å2 / Biso min: 20.66 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å20 Å20 Å2
2--2.58 Å20 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 2.3→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7448 0 61 194 7703
Biso mean--75.59 48.82 -
Num. residues----956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197676
X-RAY DIFFRACTIONr_bond_other_d0.0010.027362
X-RAY DIFFRACTIONr_angle_refined_deg1.9951.96910460
X-RAY DIFFRACTIONr_angle_other_deg0.9263.00216834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8095948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91623.43344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.442151234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6831564
X-RAY DIFFRACTIONr_chiral_restr0.1270.21210
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021766
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 250 -
Rwork0.326 4744 -
all-4994 -
obs--97.84 %
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)
12.82851.4137-1.71411.1337-0.21872.2067-0.15560.1814-0.5247-0.0348-0.072-0.28460.0984-0.29470.22750.3608-0.0286-0.03940.09110.01370.405525.75-2.53332.6573
20.6377-0.45730.3210.9221-0.6610.8564-0.0797-0.0641-0.0659-0.02830.0609-0.0814-0.0449-0.06220.01870.1491-0.005-0.04060.1663-0.03630.366222.43332.039260.0232
35.11882.314-1.97392.6323-0.02983.43520.11710.0608-0.15390.1920.0537-0.2341-0.23160.0009-0.17080.443-0.00320.06180.0017-0.01520.243753.037720.3106-8.2955
45.0559-3.47552.25054.9865-2.12371.1531-0.7352-0.93050.26770.28730.6302-0.0674-0.2952-0.36930.1050.19810.1895-0.07050.3613-0.06360.2855-2.440329.600954.6072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A281 - 675
2X-RAY DIFFRACTION2B281 - 675
3X-RAY DIFFRACTION3C27 - 128
4X-RAY DIFFRACTION4D27 - 128

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