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- PDB-2c5d: Structure of a minimal Gas6-Axl complex -

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Basic information

Entry
Database: PDB / ID: 2c5d
TitleStructure of a minimal Gas6-Axl complex
Components
  • GROWTH-ARREST-SPECIFIC PROTEIN 6 PRECURSOR
  • TYROSINE-PROTEIN KINASE RECEPTOR UFO
KeywordsSIGNALING PROTEIN/RECEPTOR / GROWTH REGULATION-COMPLEX / VITAMIN K-DEPENDENT PROTEIN / LAMININ G-LIKE DOMAIN / RECEPTOR TYROSINE KINASE / IMMUNOGLOBULIN-LIKE DOMAIN / GROWTH REGULATION / EGF-LIKE DOMAIN / RECEPTOR / SIGNALING PROTEIN-RECEPTOR complex
Function / homology
Function and homology information


negative regulation of oligodendrocyte apoptotic process / negative regulation of renal albumin absorption / negative regulation of fibroblast apoptotic process / cellular response to vitamin K / hematopoietic stem cell migration to bone marrow / positive regulation of natural killer cell differentiation / positive regulation of glomerular filtration / B cell chemotaxis / positive regulation of cytokine-mediated signaling pathway / cellular response to interferon-alpha ...negative regulation of oligodendrocyte apoptotic process / negative regulation of renal albumin absorption / negative regulation of fibroblast apoptotic process / cellular response to vitamin K / hematopoietic stem cell migration to bone marrow / positive regulation of natural killer cell differentiation / positive regulation of glomerular filtration / B cell chemotaxis / positive regulation of cytokine-mediated signaling pathway / cellular response to interferon-alpha / positive regulation of pinocytosis / natural killer cell differentiation / positive regulation of dendritic cell chemotaxis / extracellular matrix assembly / negative regulation of dendritic cell apoptotic process / negative regulation of interleukin-1 production / dendritic cell differentiation / positive regulation of viral life cycle / negative regulation of biomineral tissue development / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / activation of protein kinase B activity / apoptotic cell clearance / phosphatidylserine binding / negative regulation of interleukin-6 production / cell maturation / negative regulation of type II interferon production / positive regulation of protein kinase activity / negative regulation of endothelial cell apoptotic process / animal organ regeneration / negative regulation of tumor necrosis factor production / vascular endothelial growth factor receptor signaling pathway / positive regulation of TOR signaling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Dengue Virus Attachment and Entry / negative regulation of tumor necrosis factor-mediated signaling pathway / Removal of aminoterminal propeptides from gamma-carboxylated proteins / phagocytosis / positive regulation of protein export from nucleus / transmembrane receptor protein tyrosine kinase activity / positive regulation of phagocytosis / platelet alpha granule lumen / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of fibroblast proliferation / viral genome replication / protein localization to plasma membrane / Cell surface interactions at the vascular wall / cellular response to xenobiotic stimulus / cellular response to glucose stimulus / Post-translational protein phosphorylation / platelet activation / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / positive regulation of protein phosphorylation / VEGFA-VEGFR2 Pathway / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / calcium ion transmembrane transport / Platelet degranulation / cell migration / nervous system development / cellular response to lipopolysaccharide / virus receptor activity / protein tyrosine kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor-mediated virion attachment to host cell / protein-macromolecule adaptor activity / protein phosphorylation / signaling receptor complex / cell surface receptor signaling pathway / endoplasmic reticulum lumen / receptor ligand activity / fusion of virus membrane with host plasma membrane / signaling receptor binding / innate immune response / negative regulation of DNA-templated transcription / positive regulation of gene expression / calcium ion binding / negative regulation of apoptotic process / symbiont entry into host cell / cell surface / signal transduction / : / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytoplasm
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 / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Calcium-binding EGF-like 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. / Fibronectin type 3 domain / EGF-like 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 / 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
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSasaki, T. / Knyazev, P.G. / Clout, N.J. / Cheburkin, Y. / Goehring, W. / Ullrich, A. / Timpl, R. / Hohenester, E.
Citation
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of a C-Terminal Fragment of Growth Arrest-Specific Protein Gas6
Authors: Sasaki, T. / Knyazev, P.G. / Cheburkin, Y. / Goehring, W. / Tisi, D. / Ullrich, A. / Timpl, R. / Hohenester, E.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Ligand Recognition and Homophilic Interactions in Tyro3
Authors: Heiring, C. / Dahlback, B. / Muller, Y.A.
History
DepositionOct 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_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.src_method / _entity.type / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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 PRECURSOR
B: GROWTH-ARREST-SPECIFIC PROTEIN 6 PRECURSOR
C: TYROSINE-PROTEIN KINASE RECEPTOR UFO
D: TYROSINE-PROTEIN KINASE RECEPTOR UFO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,62011
Polymers135,4784
Non-polymers1,1427
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)292.951, 292.951, 63.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.07122, 0.99736, 0.01392), (0.99745, -0.07115, -0.0052), (-0.00419, 0.01426, -0.99989)-1.68797, 1.21185, 183.00417
2given(0.07122, 0.99736, 0.01392), (0.99745, -0.07115, -0.0052), (-0.00419, 0.01426, -0.99989)-1.68797, 1.21185, 183.00417

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein GROWTH-ARREST-SPECIFIC PROTEIN 6 PRECURSOR / GAS-6


Mass: 46615.352 Da / Num. of mol.: 2 / Fragment: LG DOMAINS, RESIDUES 207-624
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: Q14393
#2: Protein TYROSINE-PROTEIN KINASE RECEPTOR UFO / AXL ONCOGENE


Mass: 21123.408 Da / Num. of mol.: 2 / Fragment: IG DOMAINS, RESIDUES 26-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PASK-IBA12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P30530, EC: 2.7.1.112

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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, 5 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NI / NICKEL (II) ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Details

Has protein modificationY

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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: 5.3 Å3/Da / Density % sol: 78 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9794
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 47655 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.3
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1H30 AND 1RHF

1h30

1rhf


Resolution: 3.3→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 2384 5 %RANDOM
Rwork0.2409 ---
obs0.2409 47648 99.9 %-
Solvent computationSolvent model: FLAT / Bsol: 10 Å2 / ksol: 0.209994 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.163 Å2-6.701 Å20 Å2
2---7.163 Å20 Å2
3---14.325 Å2
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8814 0 65 0 8879
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.721.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it3.142
X-RAY DIFFRACTIONc_scangle_it3.52.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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