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- PDB-6u66: Structure of the trimeric globular domain of Adiponectin -

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Basic information

Entry
Database: PDB / ID: 6u66
TitleStructure of the trimeric globular domain of Adiponectin
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: 0.99 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 29, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adiponectin
B: Adiponectin
C: Adiponectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9687
Polymers48,8253
Non-polymers1434
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-72 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.923, 49.635, 50.306
Angle α, β, γ (deg.)116.830, 100.890, 104.920
Int Tables number1
Space group name H-MP1

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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: 16275.028 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADIPOQ, ACDC, ACRP30, APM1, GBP28 / Plasmid: pMAL / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q15848
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 mM Li2SO4, 0.1 M sodium acetate pH 4.5, 50% PEG 400
PH range: 4-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2016
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: 0.989→50 Å / Num. obs: 199981 / % possible obs: 95.6 % / Redundancy: 3.95 % / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.155 / Net I/σ(I): 5.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible allRrim(I) all
0.99-1.053.9091.5450.32313950.24892.9
1.05-1.123.9390.9260.85300430.54694.51.073
1.12-1.214.020.6131.58281580.73495.10.708
1.21-1.323.9250.4882.13260560.79695.80.566
1.32-1.483.9930.353.25237550.88196.40.405
1.48-1.713.9320.2155.48210680.94896.90.25
1.71-2.094.0240.11110.82179150.98897.70.128
2.09-2.963.8980.06717.64139080.99497.90.078
2.96-40.7683.9780.03730.6376830.99898.10.042

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DOU

4dou


Resolution: 0.99→40.768 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.54
RfactorNum. reflection% reflection
Rfree0.1895 7658 1.98 %
Rwork0.1653 --
obs0.1657 198521 92.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.41 Å2 / Biso mean: 14.75 Å2 / Biso min: 5.9 Å2
Refinement stepCycle: final / Resolution: 0.99→40.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 4 537 3919
Biso mean--7.76 28.5 -
Num. residues----415
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
0.99-0.99990.39291420.3798653348
0.9999-1.01170.36391800.37781014674
1.0117-1.0240.43372310.36561171485
1.024-1.0370.37282660.35711214289
1.037-1.05060.3432340.3431248892
1.0506-1.0650.34992790.33141279093
1.065-1.08020.31492550.32011272493
1.0802-1.09640.31182550.31131283594
1.0964-1.11350.32342490.30041280194
1.1135-1.13180.30272890.28421281494
1.1318-1.15130.25252570.2741283394
1.1513-1.17220.29012530.26441296094
1.1722-1.19480.29162660.26171288694
1.1948-1.21910.27582600.25121288595
1.2191-1.24570.29782750.24861300095
1.2457-1.27460.26562820.23541290295
1.2746-1.30650.26612320.2271304595
1.3065-1.34180.23442620.21871289195
1.3418-1.38130.22672750.21441300095
1.3813-1.42590.2332540.19691293295
1.4259-1.47690.22062670.18171304495
1.4769-1.5360.19692630.16511312396
1.536-1.60590.19372580.14921319596
1.6059-1.69060.17212850.13751315396
1.6906-1.79650.14692520.12141326197
1.7965-1.93520.14512600.10751324897
1.9352-2.130.1212760.0971319997
2.13-2.43810.152610.10211323097
2.4381-3.07160.13562680.11221321297
3.0716-40.7680.11722720.11671332497

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