[English] 日本語
Yorodumi
- PDB-6u6n: Structure of the trimeric globular domain of Adiponectin mutant -... -

+
Open data


ID or keywords:

Loading...

-
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


positive regulation of metanephric podocyte development / positive regulation of glycogen (starch) synthase activity / positive regulation of renal albumin absorption / negative regulation of metanephric mesenchymal cell migration / negative regulation of cholesterol import / response to linoleic acid / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / positive regulation of myeloid cell apoptotic process / adiponectin-activated signaling pathway / negative regulation of macrophage differentiation ...positive regulation of metanephric podocyte development / positive regulation of glycogen (starch) synthase activity / positive regulation of renal albumin absorption / negative regulation of metanephric mesenchymal cell migration / negative regulation of cholesterol import / response to linoleic acid / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / positive regulation of myeloid cell apoptotic process / adiponectin-activated signaling pathway / negative regulation of macrophage differentiation / AMPK inhibits chREBP transcriptional activation activity / detection of oxidative stress / negative regulation of granulocyte differentiation / positive regulation of signal transduction / negative regulation of hormone secretion / negative regulation of heterotypic cell-cell adhesion / low-density lipoprotein particle clearance / sialic acid binding / response to sucrose / collagen trimer / positive regulation of monocyte chemotactic protein-1 production / negative regulation of synaptic transmission / negative regulation of cold-induced thermogenesis / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of fatty acid metabolic process / negative regulation of phagocytosis / fatty acid beta-oxidation / negative regulation of fat cell differentiation / negative regulation of vascular associated smooth muscle cell migration / negative regulation of MAP kinase activity / fatty acid oxidation / response to tumor necrosis factor / positive regulation of cAMP/PKA signal transduction / negative regulation of vascular associated smooth muscle cell proliferation / regulation of glucose metabolic process / negative regulation of macrophage derived foam cell differentiation / negative regulation of tumor necrosis factor production / positive regulation of cholesterol efflux / negative regulation of gluconeogenesis / negative regulation of tumor necrosis factor-mediated signaling pathway / response to glucose / negative regulation of blood pressure / cellular response to epinephrine stimulus / response to nutrient / brown fat cell differentiation / response to glucocorticoid / negative regulation of cell migration / cellular response to cAMP / negative regulation of canonical NF-kappaB signal transduction / cytokine activity / protein serine/threonine kinase activator activity / response to activity / positive regulation of D-glucose import across plasma membrane / positive regulation of interleukin-8 production / generation of precursor metabolites and energy / response to bacterium / negative regulation of receptor-mediated endocytosis / circadian rhythm / hormone activity / Transcriptional regulation of white adipocyte differentiation / negative regulation of ERK1 and ERK2 cascade / negative regulation of inflammatory response / cellular response to xenobiotic stimulus / extracellular matrix / cellular response to insulin stimulus / glucose metabolic process / glucose homeostasis / positive regulation of cold-induced thermogenesis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / gene expression / response to ethanol / response to hypoxia / positive regulation of canonical NF-kappaB signal transduction / 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 ...: / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more