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- PDB-6u1u: Human Angiopoietin-Like 4 C-Terminal Domain (cANGPTL4) with Palmi... -

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Basic information

Entry
Database: PDB / ID: 6u1u
TitleHuman Angiopoietin-Like 4 C-Terminal Domain (cANGPTL4) with Palmitic Acid
ComponentsAngiopoietin-related protein 4
KeywordsSIGNALING PROTEIN / Fibrinogen-like domain / Angiogenesis / Cancer cells / Metastasis
Function / homology
Function and homology information


regulation of chylomicron remodeling / lipase inhibitor activity / lipase binding / Assembly of active LPL and LIPC lipase complexes / Regulation of CDH11 function / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of fatty acid biosynthetic process / endothelial cell apoptotic process / triglyceride homeostasis / protein unfolding ...regulation of chylomicron remodeling / lipase inhibitor activity / lipase binding / Assembly of active LPL and LIPC lipase complexes / Regulation of CDH11 function / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of fatty acid biosynthetic process / endothelial cell apoptotic process / triglyceride homeostasis / protein unfolding / enzyme inhibitor activity / negative regulation of endothelial cell apoptotic process / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation / lipid metabolic process / positive regulation of angiogenesis / blood coagulation / : / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / angiogenesis / blood microparticle / response to hypoxia / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 ...Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Angiopoietin-related protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTarver, C.L. / Yuan, Q. / Singhal, A.J. / Ramaker, R. / Cooper, S. / Pusey, M.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)5R42GM116283-03 United States
CitationJournal: To Be Published
Title: Crystal Structures of Angiopoietin-Like 4 C-Terminal Domain (cANGPTL4) Reveal a Binding Pocket with Multiple Ligands
Authors: Tarver, C.L. / Yuan, Q. / Singhal, A.J. / Ramaker, R. / Cooper, S. / Pusey, M.L.
History
DepositionAug 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 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

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Assembly

Deposited unit
A: Angiopoietin-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7152
Polymers24,4581
Non-polymers2561
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.568, 135.300, 39.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Angiopoietin-related protein 4 / Angiopoietin-like protein 4 / Hepatic fibrinogen/angiopoietin-related protein / HFARP


Mass: 24458.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ANGPTL4, ARP4, HFARP, PGAR, PP1158, PSEC0166, UNQ171/PRO197
Plasmid: pET3a / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): T7 SHuffle Cells / References: UniProt: Q9BY76
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.62 Å3/Da / Density % sol: 66.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES 7.5 0.1 M Sodium chloride 1.6 M Ammonium sulfate Palmitic Acid
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.7→42.7 Å / Num. obs: 34756 / % possible obs: 93.12 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Net I/σ(I): 15.7
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.62 / Num. unique obs: 1727 / CC1/2: 0.849 / Rpim(I) all: 0.264 / Rrim(I) all: 0.675

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.16_3549refinement
PHASERphasing
PHENIXmodel building
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EUB

6eub


Resolution: 1.75→42.7 Å / SU ML: 0.1777 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.3847
RfactorNum. reflection% reflection
Rfree0.211 1960 5.8 %
Rwork0.1943 --
obs0.1953 33820 93.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.12 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 18 124 1868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131795
X-RAY DIFFRACTIONf_angle_d1.28912428
X-RAY DIFFRACTIONf_chiral_restr0.0859241
X-RAY DIFFRACTIONf_plane_restr0.007318
X-RAY DIFFRACTIONf_dihedral_angle_d19.4635665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.26811270.22922078X-RAY DIFFRACTION85.53
1.8-1.840.21481190.20411969X-RAY DIFFRACTION83.15
1.84-1.90.2141410.19752224X-RAY DIFFRACTION91.03
1.9-1.960.21821380.19532219X-RAY DIFFRACTION92.76
1.96-2.030.19891390.18662250X-RAY DIFFRACTION93.94
2.03-2.110.19411420.1792278X-RAY DIFFRACTION94.2
2.11-2.210.21291290.17722210X-RAY DIFFRACTION90.24
2.21-2.320.21881500.1892349X-RAY DIFFRACTION96.71
2.32-2.470.21191410.19052336X-RAY DIFFRACTION96.19
2.47-2.660.22621490.19912362X-RAY DIFFRACTION96.76
2.66-2.930.2061390.19852255X-RAY DIFFRACTION92.5
2.93-3.350.22071470.19992430X-RAY DIFFRACTION98.21
3.35-4.220.19741450.18532362X-RAY DIFFRACTION94.82
4.22-42.70.21041540.20152538X-RAY DIFFRACTION96.63

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