[English] 日本語
Yorodumi
- PDB-4ra0: An engineered Axl 'decoy receptor' effectively silences the Gas6-... -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of lymphocyte activation / positive regulation of pinocytosis ...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 / negative regulation of lymphocyte activation / positive regulation of pinocytosis / positive regulation of dendritic cell chemotaxis / extracellular matrix assembly / myeloid cell apoptotic process / cellular response to interferon-alpha / 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 / 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 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / fibroblast apoptotic process / apoptotic cell clearance / ovulation cycle / erythrocyte homeostasis / phosphatidylserine binding / enzyme-linked receptor protein signaling pathway / cell-substrate adhesion / negative regulation of interleukin-6 production / vagina development / positive regulation of protein kinase activity / negative regulation of type II interferon production / blood vessel remodeling / negative regulation of tumor necrosis factor production / animal organ regeneration / positive regulation of TOR signaling / negative regulation of tumor necrosis factor-mediated signaling pathway / activation of protein kinase B activity / phagocytosis / vascular endothelial growth factor receptor signaling pathway / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / negative regulation of endothelial cell apoptotic process / cell maturation / positive regulation of phagocytosis / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / cell surface receptor protein tyrosine kinase signaling pathway / viral genome replication / platelet alpha granule lumen / cellular response to starvation / positive regulation of protein export from nucleus / protein localization to plasma membrane / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / cellular response to glucose stimulus / establishment of localization in cell / receptor protein-tyrosine kinase / calcium ion transmembrane transport / receptor tyrosine kinase binding / cellular response to growth factor stimulus / platelet activation / VEGFA-VEGFR2 Pathway / Golgi lumen / positive regulation of protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron migration / positive regulation of fibroblast proliferation / blood coagulation / cellular response to xenobiotic stimulus / cell migration / Platelet degranulation / nervous system development / actin cytoskeleton / cellular response to lipopolysaccharide / virus receptor activity / protein tyrosine kinase activity / protein-macromolecule adaptor activity / spermatogenesis / neuron apoptotic process / negative regulation of neuron apoptotic process / cell surface receptor signaling pathway / receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein phosphorylation / receptor ligand activity / inflammatory response / endoplasmic reticulum lumen / signaling receptor binding / innate immune response / fusion of virus membrane with host plasma membrane
Similarity search - Function
: / Laminin G domain / Complement Clr-like EGF 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 ...: / Laminin G domain / Complement Clr-like EGF 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 / 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 / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / 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. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Concanavalin A-like lectin/glucanase domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Jelly Rolls / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Details

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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
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