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- PDB-4dou: Crystal Structure of a Single-chain Trimer of Human Adiponectin G... -

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Basic information

Entry
Database: PDB / ID: 4dou
TitleCrystal Structure of a Single-chain Trimer of Human Adiponectin Globular Domain
ComponentsAdiponectin
KeywordsHORMONE / Single-chain globular domain / Calcium binding / C1Q-like domain / growth factor / serum
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 / negative regulation of protein autophosphorylation / low-density lipoprotein particle clearance / sialic acid binding / negative regulation of heterotypic cell-cell adhesion / negative regulation of vascular associated smooth muscle cell migration / response to sucrose / collagen trimer / negative regulation of low-density lipoprotein receptor activity / negative regulation of DNA biosynthetic process / positive regulation of monocyte chemotactic protein-1 production / negative regulation of platelet-derived growth factor receptor signaling pathway / 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 / negative regulation of fat cell differentiation / fatty acid beta-oxidation / 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 / negative regulation of MAP kinase activity / negative regulation of receptor binding / response to activity / generation of precursor metabolites and energy / cytokine activity / positive regulation of interleukin-8 production / protein localization to plasma membrane / 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 / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / 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 Å
AuthorsMin, X. / Walker, N.P. / Wang, Z.
CitationJournal: Febs Lett. / Year: 2012
Title: Crystal structure of a single-chain trimer of human adiponectin globular domain.
Authors: Min, X. / Lemon, B. / Tang, J. / Liu, Q. / Zhang, R. / Walker, N. / Li, Y. / Wang, Z.
History
DepositionFeb 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2May 31, 2017Group: Structure summary
Revision 1.3Sep 13, 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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adiponectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,54911
Polymers51,0031
Non-polymers54610
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.310, 49.630, 50.460
Angle α, β, γ (deg.)117.23, 101.68, 105.31
Int Tables number1
Space group name H-MP1
DetailsTHE GLOBULAR PROTEIN HAS A TRIMERIC SYMMETRY

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Components

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Protein , 1 types, 1 molecules A

#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 / 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: 51003.242 Da / Num. of mol.: 1 / Fragment: unp residues 104-244
Source method: isolated from a genetically manipulated source
Details: three copies of human adiponectin globular domain sequences (Pro104 to Asn244) are joined in tandem
Source: (gene. exp.) Homo sapiens (human)
Gene: ADIPOQ, ACDC, ACRP30, APM1, GBP28, ACDC, ACRP30, adiponectin, ADIPOQ, APM1, GBP28
Production host: homo sapiens (human) / References: UniProt: Q15848

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Non-polymers , 5 types, 168 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHREE COPIES OF HUMAN ADIPONECTIN GLOBULAR DOMAIN SEQUENCES (PRO104 TO ASN244) ARE JOINED IN TANDEM

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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: 1.88 Å3/Da / Density % sol: 34.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 22% PEG3350, 0.1M Bis-Tris, and 25% PEG200, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: mirrors
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→43.2 Å / Num. all: 22892 / Num. obs: 72800 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3 / Num. unique all: 2655 / % possible all: 72.2

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C28

1c28


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 11.965 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25693 1166 5.1 %RANDOM
Rwork0.19992 ---
obs0.2029 21717 90.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.485 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20.57 Å2-0.5 Å2
2---1.52 Å2-0.16 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 30 158 3472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223413
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9284617
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92824.497189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8315528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.282159
X-RAY DIFFRACTIONr_chiral_restr0.080.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022678
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4071.51977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.72923179
X-RAY DIFFRACTIONr_scbond_it1.11131436
X-RAY DIFFRACTIONr_scangle_it1.6454.51435
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 62 -
Rwork0.235 1141 -
obs--65.13 %
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)
11.7102-0.4590.05563.97211.73544.5244-0.01690.22540.1364-0.28360.0105-0.3687-0.38620.17090.00640.0394-0.0150.01510.04450.02910.06179.7507-20.6857-5.5564
21.77250.84110.89634.18921.49082.71080.0308-0.0110.02480.2581-0.01210.4724-0.0625-0.3519-0.01870.02850.02470.03620.06080.02910.0948-9.3897-22.5671.0321
31.2857-0.3491-0.04324.3021.54812.56590.0082-0.1868-0.05790.4580.0026-0.14870.21940.0984-0.01090.0547-0.0043-0.01610.04430.02380.02265.8749-32.442211.1525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A108 - 123
2X-RAY DIFFRACTION1A128 - 216
3X-RAY DIFFRACTION1A220 - 245
4X-RAY DIFFRACTION2A246 - 261
5X-RAY DIFFRACTION2A269 - 386
6X-RAY DIFFRACTION3A391 - 404
7X-RAY DIFFRACTION3A407 - 525

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