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- PDB-1c3h: ACRP30 CALCIUM COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1c3h
TitleACRP30 CALCIUM COMPLEX
Components30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR
KeywordsSIGNALING PROTEIN / ACRP30 C1Q TNF TRIMER ALL-BETA CALCIUM-BOUND
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. / Boggon, T. / Scherer, P.
CitationJournal: To Be Published
Title: ACRP30 calcium complex
Authors: Boggon, T. / Scherer, P. / Shapiro, L.
History
DepositionJul 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_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 / _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: 30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR
B: 30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR
C: 30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR
D: 30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR
E: 30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR
F: 30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2849
Polymers95,1646
Non-polymers1203
Water9,152508
1
A: 30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR
B: 30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR
C: 30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR


Theoretical massNumber of molelcules
Total (without water)47,5823
Polymers47,5823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-25 kcal/mol
Surface area17240 Å2
MethodPISA
2
D: 30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR
E: 30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR
F: 30 KD ADIPOCYTE COMPLEMENT-RELATED PROTEIN PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7026
Polymers47,5823
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-61 kcal/mol
Surface area15340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.639, 58.711, 87.315
Angle α, β, γ (deg.)70.55, 70.62, 60.14
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 15860.657 Da / Num. of mol.: 6
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M BIS-TRIS, 20MM CACL2, 2% PEG 4K, -- CRYO: 15% ETHYLENE GLYCOL, 19% SUCROSE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4CK, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.77114
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77114 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 51096 / Num. obs: 51096 / % possible obs: 93.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 24.87
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.115 / % possible all: 89.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2576 -5.0%
Rwork0.198 ---
all0.198 51096 --
obs0.198 51096 93.9 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6671 0 3 508 7182
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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