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- PDB-1c28: THE CRYSTAL STRUCTURE OF A COMPLMENT-1Q FAMILY PROTEIN SUGGESTS A... -

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Basic information

Entry
Database: PDB / ID: 1c28
TitleTHE CRYSTAL STRUCTURE OF A COMPLMENT-1Q FAMILY PROTEIN SUGGESTS AN EVOLUTIONARY LINK TO TUMOR NECROSIS FACTOR
ComponentsPROTEIN (30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR (ACRP30))
KeywordsSERUM PROTEIN / ACRP30 C1Q TNF TRIMER ALL-BETA
Function / homology
Function and homology information


AMPK inhibits chREBP transcriptional activation activity / negative regulation of intracellular protein transport / positive regulation of metanephric podocyte development / positive regulation of renal albumin absorption / negative regulation of metanephric mesenchymal cell migration / negative regulation of cholesterol import / positive regulation of glycogen (starch) synthase activity / response to linoleic acid / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / positive regulation of myeloid cell apoptotic process ...AMPK inhibits chREBP transcriptional activation activity / negative regulation of intracellular protein transport / positive regulation of metanephric podocyte development / positive regulation of renal albumin absorption / negative regulation of metanephric mesenchymal cell migration / negative regulation of cholesterol import / positive regulation of glycogen (starch) synthase activity / response to linoleic acid / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / positive regulation of myeloid cell apoptotic process / positive regulation of cAMP-dependent protein kinase activity / adiponectin-activated signaling pathway / negative regulation of macrophage differentiation / negative regulation of protein autophosphorylation / positive regulation of signal transduction / detection of oxidative stress / negative regulation of granulocyte differentiation / negative regulation of hormone secretion / low-density lipoprotein particle clearance / negative regulation of heterotypic cell-cell adhesion / sialic acid binding / negative regulation of receptor-mediated endocytosis / response to sucrose / negative regulation of DNA biosynthetic process / collagen trimer / negative regulation of synaptic transmission / positive regulation of monocyte chemotactic protein-1 production / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of cold-induced thermogenesis / negative regulation of phagocytosis / positive regulation of fatty acid metabolic process / negative regulation of fat cell differentiation / fatty acid beta-oxidation / negative regulation of vascular associated smooth muscle cell migration / negative regulation of vascular associated smooth muscle cell proliferation / fatty acid oxidation / positive regulation of cAMP/PKA signal transduction / negative regulation of macrophage derived foam cell differentiation / regulation of glucose metabolic process / negative regulation of tumor necrosis factor production / response to tumor necrosis factor / positive regulation of cholesterol efflux / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of MAP kinase activity / negative regulation of gluconeogenesis / brown fat cell differentiation / response to glucose / response to glucocorticoid / negative regulation of canonical NF-kappaB signal transduction / negative regulation of blood pressure / cellular response to cAMP / cellular response to epinephrine stimulus / response to nutrient / protein serine/threonine kinase activator activity / negative regulation of cell migration / negative regulation of receptor binding / protein localization to plasma membrane / response to activity / cell periphery / positive regulation of interleukin-8 production / positive regulation of D-glucose import / response to bacterium / negative regulation of ERK1 and ERK2 cascade / hormone activity / negative regulation of inflammatory response / cellular response to insulin stimulus / glucose metabolic process / circadian rhythm / glucose homeostasis / cellular response to xenobiotic stimulus / positive regulation of protein phosphorylation / positive regulation of cold-induced thermogenesis / gene expression / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / response to hypoxia / signaling receptor binding / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular region / identical protein binding
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsShapiro, L. / Scherer, P.
CitationJournal: Curr.Biol. / Year: 1998
Title: The crystal structure of a complement-1q family protein suggests an evolutionary link to tumor necrosis factor.
Authors: Shapiro, L. / Scherer, P.E.
History
DepositionJul 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: PROTEIN (30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR (ACRP30))
B: PROTEIN (30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR (ACRP30))
C: PROTEIN (30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR (ACRP30))


Theoretical massNumber of molelcules
Total (without water)46,8793
Polymers46,8793
Non-polymers00
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-19 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.3, 112.3, 71.6
Angle α, β, γ (deg.)90, 90, 120
Int Tables number169
Space group name H-MP61

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Components

#1: Protein PROTEIN (30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR (ACRP30))


Mass: 15626.402 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q60994
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.8% PEG 4K, 0.1M BIS-TRIS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4.0K
Crystal grow
*PLUS
Temperature: 4. ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
21.8 %PEG40001reservoir
30.1 MBis-Tris1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→8 Å / Num. all: 29616 / Num. obs: 27888 / % possible obs: 92.82 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.05
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2 % / Rmerge(I) obs: 0.199 / % possible all: 92.2

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→8 Å / σ(F): 3 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1290 -5%
Rwork0.212 ---
obs0.212 27489 92.8 %-
all-27489 --
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 0 389 3132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.899
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.8 Å2

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