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- PDB-4ra0: An engineered Axl 'decoy receptor' effectively silences the Gas6-... -

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Basic information

Entry
Database: PDB / ID: 4ra0
TitleAn engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis
Components
  • Growth arrest-specific protein 6
  • Tyrosine-protein kinase receptor UFO
KeywordsSIGNALING PROTEIN / Axl / Gas6 / cancer / metastasis
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 / hematopoietic stem cell migration to bone marrow / positive regulation of glomerular filtration / positive regulation of natural killer cell differentiation / B cell chemotaxis / ovulation cycle / negative regulation of lymphocyte activation ...negative regulation of oligodendrocyte apoptotic process / negative regulation of renal albumin absorption / cellular response to vitamin K / forebrain cell migration / hematopoietic stem cell migration to bone marrow / positive regulation of glomerular filtration / positive regulation of natural killer cell differentiation / B cell chemotaxis / ovulation cycle / negative regulation of lymphocyte activation / positive regulation of pinocytosis / myeloid cell apoptotic process / extracellular matrix assembly / cellular response to interferon-alpha / positive regulation of dendritic cell chemotaxis / neutrophil clearance / negative regulation of macrophage cytokine production / positive regulation of cytokine-mediated signaling pathway / natural killer cell differentiation / negative regulation of interleukin-1 production / dendritic cell differentiation / secretion by cell / negative regulation of myeloid cell apoptotic process / positive regulation of viral life cycle / negative regulation of dendritic cell apoptotic process / negative regulation of biomineral tissue development / negative regulation of fibroblast apoptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / fibroblast apoptotic process / positive regulation of protein kinase activity / activation of protein kinase B activity / apoptotic cell clearance / enzyme-linked receptor protein signaling pathway / phosphatidylserine binding / erythrocyte homeostasis / cell-substrate adhesion / vagina development / negative regulation of type II interferon production / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / animal organ regeneration / vascular endothelial growth factor receptor signaling pathway / positive regulation of TOR signaling / blood vessel remodeling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / phagocytosis / negative regulation of endothelial cell apoptotic process / negative regulation of tumor necrosis factor-mediated signaling pathway / Removal of aminoterminal propeptides from gamma-carboxylated proteins / cell maturation / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / platelet alpha granule lumen / establishment of localization in cell / cell surface receptor protein tyrosine kinase signaling pathway / viral genome replication / positive regulation of protein export from nucleus / cellular response to starvation / Cell surface interactions at the vascular wall / protein localization to plasma membrane / Post-translational protein phosphorylation / cellular response to glucose stimulus / receptor protein-tyrosine kinase / platelet activation / positive regulation of protein phosphorylation / receptor tyrosine kinase binding / VEGFA-VEGFR2 Pathway / Golgi lumen / cellular response to growth factor stimulus / cellular response to xenobiotic stimulus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of fibroblast proliferation / calcium ion transmembrane transport / neuron migration / blood coagulation / Platelet degranulation / nervous system development / cell migration / actin cytoskeleton / virus receptor activity / cellular response to lipopolysaccharide / protein tyrosine kinase activity / neuron apoptotic process / spermatogenesis / negative regulation of neuron apoptotic process / protein phosphorylation / protein-macromolecule adaptor activity / positive regulation of ERK1 and ERK2 cascade / receptor-mediated virion attachment to host cell / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / signaling receptor complex / endoplasmic reticulum lumen / inflammatory response / receptor ligand activity / fusion of virus membrane with host plasma membrane / signaling receptor binding / innate immune response
Similarity search - Function
: / Laminin G domain / Complement Clr-like EGF domain / Complement Clr-like EGF-like / EGF-like, conserved site / Human growth factor-like EGF / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain ...: / Laminin G domain / Complement Clr-like EGF domain / Complement Clr-like EGF-like / EGF-like, conserved site / Human growth factor-like EGF / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / : / Calcium-binding EGF domain / Coagulation factor-like, Gla domain superfamily / Immunoglobulin domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / 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 / Fibronectin type III domain / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / : / 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 / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Immunoglobulins / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Tyrosine-protein kinase receptor UFO / Growth arrest-specific protein 6 / Isoform 1 of Growth arrest-specific protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsKariolis, M.S. / Kapur, S. / Mathews, I.I. / Cochran, J.R.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis.
Authors: Kariolis, M.S. / Miao, Y.R. / Jones, D.S. / Kapur, S. / Mathews, I.I. / Giaccia, A.J. / Cochran, J.R.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_ref_seq_dif / 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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)132,49313
Polymers131,2194
Non-polymers1,2749
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.370, 112.370, 361.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: 44441.895 Da / Num. of mol.: 2 / Fragment: UNP residues 322-721
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAS6, AXLLG / Cell line (production host): HEK / Production host: Homo Sapiens (human) / References: UniProt: Q14393-2, UniProt: Q14393*PLUS
#2: Protein Tyrosine-protein kinase receptor UFO / AXL oncogene


Mass: 21167.486 Da / Num. of mol.: 2 / Fragment: UNP residues 33-227 / Mutation: G32S, D87G, V92A, G127R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AXL, UFO / Plasmid: pASK-IBA12 / Production host: Escherichia coli (E. coli)
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 , 5 types, 21 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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS STUDY USE ISOFORM 2 (Q14393-2) OF GAS

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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: 5.02 Å3/Da / Density % sol: 75.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.4 M Li2SO4, 0.1 M Tris.HCl(pH 8.5), 5% Glycerol, 2mM NiSO4 , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.03317 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2012 / Details: Rh coated flat mirror.
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 3.07→38.01 Å / Num. all: 50640 / Num. obs: 50592 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 20.4
Reflection shellResolution: 3.07→3.15 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.11 / Num. unique all: 3664 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C5D

2c5d


Resolution: 3.07→38.01 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.904 / SU B: 32.814 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.539 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24255 2526 5 %RANDOM
Rwork0.20214 ---
obs0.20416 47994 99.92 %-
all-47994 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.547 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.41 Å20 Å2
2---0.41 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 3.07→38.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8845 0 71 14 8930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0199139
X-RAY DIFFRACTIONr_bond_other_d0.0010.028695
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9712455
X-RAY DIFFRACTIONr_angle_other_deg0.7283.00219922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7851138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59923.668398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.008151438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0841568
X-RAY DIFFRACTIONr_chiral_restr0.0710.21441
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110304
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022066
LS refinement shellResolution: 3.07→3.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 182 -
Rwork0.318 3462 -
obs--100 %
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)
10.51350.0264-0.39691.08921.22061.8079-0.04260.105-0.0153-0.0269-0.08170.1159-0.0376-0.10240.12430.2868-0.02440.05370.0983-0.02640.025325.5321-35.734111.3561
20.738-0.3645-0.06042.89220.04160.91010.0447-0.0034-0.2152-0.0315-0.19450.13960.0445-0.18390.14980.0285-0.02480.00160.0689-0.04720.111539.5228-61.337167.5805
31.28950.40742.80321.17130.40866.35070.0596-0.1317-0.0710.16820.1463-0.0130.0438-0.3665-0.20590.06510.01150.04330.0496-0.00290.078514.8557-31.585962.1357
40.3986-0.85050.86132.6709-1.43142.2418-0.1298-0.00190.02730.12880.1224-0.3527-0.28680.15920.00730.1801-0.05030.10560.1518-0.00580.160450.2418-21.101436.9759
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A281 - 676
2X-RAY DIFFRACTION1A701 - 702
3X-RAY DIFFRACTION2B281 - 675
4X-RAY DIFFRACTION2B701 - 702
5X-RAY DIFFRACTION3C27 - 217
6X-RAY DIFFRACTION4D27 - 217

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