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- PDB-6u6n: Structure of the trimeric globular domain of Adiponectin mutant -... -

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Basic information

Entry
Database: PDB / ID: 6u6n
TitleStructure of the trimeric globular domain of Adiponectin mutant - D187A Q188A
ComponentsAdiponectin
KeywordsHORMONE / globular domain
Function / homology
Function and homology information


negative regulation of intracellular protein transport / positive regulation of lipid transporter activity / positive regulation of metanephric podocyte development / positive regulation of renal albumin absorption / negative regulation of metanephric mesenchymal cell migration / response to linoleic acid / positive regulation of glycogen (starch) synthase activity / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / positive regulation of myeloid cell apoptotic process / negative regulation of macrophage differentiation ...negative regulation of intracellular protein transport / positive regulation of lipid transporter activity / positive regulation of metanephric podocyte development / positive regulation of renal albumin absorption / negative regulation of metanephric mesenchymal cell migration / response to linoleic acid / positive regulation of glycogen (starch) synthase activity / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / positive regulation of myeloid cell apoptotic process / negative regulation of macrophage differentiation / AMPK inhibits chREBP transcriptional activation activity / detection of oxidative stress / positive regulation of signal transduction / negative regulation of granulocyte differentiation / negative regulation of hormone secretion / low-density lipoprotein particle clearance / negative regulation of protein autophosphorylation / sialic acid binding / negative regulation of heterotypic cell-cell adhesion / response to sucrose / negative regulation of vascular associated smooth muscle cell migration / collagen trimer / negative regulation of low-density lipoprotein receptor activity / negative regulation of DNA biosynthetic process / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of monocyte chemotactic protein-1 production / negative regulation of synaptic transmission / positive regulation of cAMP-dependent protein kinase activity / negative regulation of phagocytosis / negative regulation of cold-induced thermogenesis / positive regulation of fatty acid metabolic process / fatty acid beta-oxidation / negative regulation of fat cell differentiation / positive regulation of protein kinase A signaling / fatty acid oxidation / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of macrophage derived foam cell differentiation / negative regulation of tumor necrosis factor production / regulation of glucose metabolic process / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of cholesterol efflux / response to tumor necrosis factor / negative regulation of gluconeogenesis / response to glucose / brown fat cell differentiation / negative regulation of canonical NF-kappaB signal transduction / cellular response to cAMP / response to glucocorticoid / cellular response to epinephrine stimulus / negative regulation of blood pressure / protein serine/threonine kinase activator activity / negative regulation of cell migration / response to nutrient / response to activity / negative regulation of MAP kinase activity / negative regulation of receptor binding / generation of precursor metabolites and energy / cytokine activity / protein localization to plasma membrane / positive regulation of interleukin-8 production / positive regulation of glucose import / response to bacterium / hormone activity / negative regulation of ERK1 and ERK2 cascade / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / circadian rhythm / cellular response to insulin stimulus / glucose metabolic process / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / glucose homeostasis / positive regulation of cold-induced thermogenesis / gene expression / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / response to hypoxia / positive regulation of protein phosphorylation / signaling receptor binding / negative regulation of DNA-templated transcription / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular region
Similarity search - Function
C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPascolutti, R. / Kruse, A.C. / Erlandson, S.C. / Burri, D.J. / Zheng, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)DP5OD021345 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Mapping and engineering the interaction between adiponectin and T-cadherin.
Authors: Pascolutti, R. / Erlandson, S.C. / Burri, D.J. / Zheng, S. / Kruse, A.C.
History
DepositionAug 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Adiponectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2972
Polymers16,2611
Non-polymers351
Water19811
1
C: Adiponectin
hetero molecules

C: Adiponectin
hetero molecules

C: Adiponectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8906
Polymers48,7833
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4810 Å2
ΔGint-39 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.704, 75.704, 48.865
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11C-301-

CL

21C-409-

HOH

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Components

#1: Protein Adiponectin / / 30 kDa adipocyte complement-related protein / Adipocyte complement-related 30 kDa protein / ACRP30 ...30 kDa adipocyte complement-related protein / Adipocyte complement-related 30 kDa protein / ACRP30 / Adipocyte / C1q and collagen domain-containing protein / Adipose most abundant gene transcript 1 protein / apM-1 / Gelatin-binding protein


Mass: 16261.047 Da / Num. of mol.: 1 / Mutation: D187A, Q188A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADIPOQ, ACDC, ACRP30, APM1, GBP28 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / References: UniProt: Q15848
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.86 Å3/Da / Density % sol: 33.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M sodium nitrate, 0.1 M MES pH 5.5, 20% PEG 3350
PH range: 5-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2018
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 29889 / % possible obs: 99.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 47.68 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.73 / Net I/σ(I): 12.42
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 3.04 % / Mean I/σ(I) obs: 1.59 / Num. unique obs: 865 / CC1/2: 0.71 / Rrim(I) all: 0.66 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U66

6u66


Resolution: 2.15→39.18 Å / SU ML: 0.351 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 32.0923
RfactorNum. reflection% reflection
Rfree0.2556 1136 10.28 %
Rwork0.2096 --
obs0.2142 11051 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 68.12 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 1 11 1004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00181020
X-RAY DIFFRACTIONf_angle_d0.43271385
X-RAY DIFFRACTIONf_chiral_restr0.0429148
X-RAY DIFFRACTIONf_plane_restr0.0031176
X-RAY DIFFRACTIONf_dihedral_angle_d10.2007576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.250.41081330.36591083X-RAY DIFFRACTION83.98
2.25-2.370.32341370.3331210X-RAY DIFFRACTION95.13
2.37-2.510.32391290.30571260X-RAY DIFFRACTION99.5
2.51-2.710.32271340.28781320X-RAY DIFFRACTION99.86
2.71-2.980.3191610.25971230X-RAY DIFFRACTION99.78
2.98-3.410.26421560.21811269X-RAY DIFFRACTION99.65
3.41-4.30.22231560.17541257X-RAY DIFFRACTION99.93
4.3-39.180.20851300.15941286X-RAY DIFFRACTION99.3
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)
13.67151948038-2.76439152452-4.478589822157.90813870924.230920886029.24127722810.3799522579180.360024470358-0.322642224319-1.19667027683-0.322166221459-0.864893368279-0.9407584748780.611986040073-0.03668535274230.533287292253-0.001331251931060.08352483401580.5329701827310.02054186928120.7598961991216.3063018049-2.784511336937.76570578223
23.205616766591.03265141785-1.213974913923.457025804221.193295773296.26066258386-0.09418841862330.0467918351982-0.252432042644-0.130584979667-0.081582393439-0.3582052754360.3106981942450.2664607602260.2127487235290.2997600948460.011457096489-0.0001036148838730.3202443525030.01584945252270.61871654345610.7508866072-9.1185741110411.4374282403
33.70874802272-3.09665881728-3.927948322896.490568659623.95760036574.47800712420.4753112181132.24964496430.159361776306-3.85675085671-0.748984912658-0.49111099112-2.20481465367-0.1368232963-0.05042634174491.243703834320.1008697073850.06908113202811.292103767660.006763630502520.63235446873613.736935472-2.45528301902-3.98454908867
42.42013814807-1.148969081781.999477889378.07747682578-1.92270482141.92473959579-0.0645851193137-0.232887947924-0.05087874606760.8363864573510.2580552738180.156324065474-0.422891036695-0.512537706711-0.2302954858830.3927836431320.0126739119012-0.01710100289010.439544969508-0.1906626909750.6129203128724.79142039169-6.1040898816222.821046153
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 112 through 133 )
2X-RAY DIFFRACTION2chain 'C' and (resid 134 through 216 )
3X-RAY DIFFRACTION3chain 'C' and (resid 217 through 232 )
4X-RAY DIFFRACTION4chain 'C' and (resid 233 through 244 )

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