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- PDB-1h30: C-terminal LG domain pair of human Gas6 -

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Basic information

Entry
Database: PDB / ID: 1h30
TitleC-terminal LG domain pair of human Gas6
ComponentsGROWTH-ARREST-SPECIFIC PROTEIN
KeywordsLAMININ G-DOMAIN PROTEIN / VITAMIN K-DEPENDENT PROTEIN / AXL/SKY/MER LIGAND / LAMININ G- LIKE DOMAIN / EGF-LIKE DOMAIN / CALCIUM-BINDING
Function / homology
Function and homology information


negative regulation of oligodendrocyte apoptotic process / negative regulation of renal albumin absorption / cellular response to vitamin K / positive regulation of natural killer cell differentiation / hematopoietic stem cell migration to bone marrow / positive regulation of glomerular filtration / B cell chemotaxis / cellular response to interferon-alpha / positive regulation of dendritic cell chemotaxis / extracellular matrix assembly ...negative regulation of oligodendrocyte apoptotic process / negative regulation of renal albumin absorption / cellular response to vitamin K / positive regulation of natural killer cell differentiation / hematopoietic stem cell migration to bone marrow / positive regulation of glomerular filtration / B cell chemotaxis / cellular response to interferon-alpha / positive regulation of dendritic cell chemotaxis / extracellular matrix assembly / myeloid cell apoptotic process / positive regulation of cytokine-mediated signaling pathway / negative regulation of interleukin-1 production / dendritic cell differentiation / 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 / apoptotic cell clearance / fibroblast apoptotic process / phosphatidylserine binding / enzyme-linked receptor protein signaling pathway / cell-substrate adhesion / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of TOR signaling / positive regulation of protein kinase activity / phagocytosis / animal organ regeneration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / negative regulation of endothelial cell apoptotic process / Removal of aminoterminal propeptides from gamma-carboxylated proteins / activation of protein kinase B activity / positive regulation of phagocytosis / 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 / cellular response to growth factor stimulus / calcium ion transmembrane transport / receptor tyrosine kinase binding / Golgi lumen / positive regulation of fibroblast proliferation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron migration / blood coagulation / Platelet degranulation / cellular response to xenobiotic stimulus / positive regulation of protein phosphorylation / protein-macromolecule adaptor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor-mediated virion attachment to host cell / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / protein phosphorylation / receptor ligand activity / endoplasmic reticulum lumen / symbiont entry into host cell / signaling receptor binding / fusion of virus membrane with host plasma membrane / negative regulation of DNA-templated transcription / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / signal transduction / extracellular space / extracellular exosome / extracellular region / cytoplasm
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 / 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 / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Growth arrest-specific protein 6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsSasaki, T. / Knyazev, P.G. / Cheburkin, Y. / Gohring, W. / Tisi, D. / Ullrich, A. / Timpl, R. / Hohenester, E.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of a Carboxy-Terminal Fragment of Growth-Arrest-Specific Protein Gas6: Receptor Tyrosine Kinase Activation by Laminin G-Like Domains
Authors: Sasaki, T. / Knyazev, P.G. / Cheburkin, Y. / Gohring, W. / Tisi, D. / Ullrich, A. / Timpl, R. / Hohenester, E.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Characterization of Gas6, a Member of the Superfamily of G Domain-Containing Proteins, as a Ligand for Rse and Axl
Authors: Mark, M.R. / Chen, J. / Hammond, R.G. / Sadick, M. / Godowski, P.J.
History
DepositionAug 21, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8484
Polymers46,6151
Non-polymers2323
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)111.310, 111.310, 217.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein GROWTH-ARREST-SPECIFIC PROTEIN / GAS6


Mass: 46615.352 Da / Num. of mol.: 1 / Fragment: C-TERMINAL LG DOMAIN PAIR, RESIDUES 261-678
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE GROWTH ARREST-SPECIFIC PROTEIN IS A NEGATIVE REGULATOR IN THE BLOOD COAGULATION CASCADE.
Has protein modificationY
Sequence detailsN-TERMINAL APLA SEQUENCE IS VECTOR-DERIVED

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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: 3.62 Å3/Da / Density % sol: 65 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 Msodium HEPES1droppH7.5
20.1 M1dropNaCl
310 mM1dropCaCl2
410 mg/mlprotein1drop
50.1 Msodium HEPES1reservoirpH7.5
61.4-1.5 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorDetector: CCD / Date: Mar 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 35018 / % possible obs: 99.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 3.9 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 100 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
DMphasing
CNS1.1refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3471 10 %RANDOM
Rwork0.234 ---
obs0.234 34985 99.9 %-
Solvent computationSolvent model: FLAT / Bsol: 48.6 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.863 Å2--
2---1.863 Å2-
3---3.727 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 11 122 3182
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
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_it2.1731.5
X-RAY DIFFRACTIONc_mcangle_it3.3772
X-RAY DIFFRACTIONc_scbond_it3.1552
X-RAY DIFFRACTIONc_scangle_it4.4912.5
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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