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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 / 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 / phosphatidylserine binding / enzyme-linked receptor protein signaling pathway / cell-substrate adhesion / 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 / positive regulation of phagocytosis / Removal of aminoterminal propeptides from gamma-carboxylated proteins / 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 / cellular response to hydrogen peroxide / VEGFA-VEGFR2 Pathway / 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
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
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
Water0
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 / Nickel


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


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

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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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