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- PDB-4uz0: Crystal Structure of apoptosis repressor with CARD (ARC) -

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Basic information

Entry
Database: PDB / ID: 4uz0
TitleCrystal Structure of apoptosis repressor with CARD (ARC)
ComponentsNUCLEOLAR PROTEIN 3Nucleolus
KeywordsAPOPTOSIS / ARC / NECROSIS / TNF
Function / homology
Function and homology information


negative regulation of muscle atrophy / inhibition of cysteine-type endopeptidase activity involved in apoptotic process / : / negative regulation of mitochondrial membrane permeability involved in apoptotic process / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / death effector domain binding / response to injury involved in regulation of muscle adaptation / regulation of non-canonical NF-kappaB signal transduction / caspase binding / mRNA splice site recognition ...negative regulation of muscle atrophy / inhibition of cysteine-type endopeptidase activity involved in apoptotic process / : / negative regulation of mitochondrial membrane permeability involved in apoptotic process / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / death effector domain binding / response to injury involved in regulation of muscle adaptation / regulation of non-canonical NF-kappaB signal transduction / caspase binding / mRNA splice site recognition / death receptor binding / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / negative regulation of cardiac muscle cell apoptotic process / negative regulation of release of cytochrome c from mitochondria / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of tumor necrosis factor-mediated signaling pathway / blood vessel remodeling / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / cardiac muscle cell apoptotic process / intrinsic apoptotic signaling pathway / RNA splicing / sarcoplasmic reticulum / response to ischemia / negative regulation of extrinsic apoptotic signaling pathway / protein complex oligomerization / response to hypoxia / calcium ion binding / nucleolus / negative regulation of apoptotic process / mitochondrion / RNA binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Death Domain, Fas / Death Domain, Fas / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.399 Å
AuthorsKim, S.H. / Jeong, J.H. / Jang, T.H. / Kim, Y.G. / Park, H.H.
Citation
Journal: Sci.Rep. / Year: 2015
Title: Crystal Structure of Caspase Recruiting Domain (Card) of Apoptosis Repressor with Card (Arc) and its Implication in Inhibition of Apoptosis.
Authors: Jang, T. / Kim, S.H. / Jeong, J. / Kim, S. / Kim, Y.G. / Park, H.H.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of the Card Domain of Apoptosis Repressor with Card (Arc).
Authors: Kim, S.H. / Park, H.H.
History
DepositionSep 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEOLAR PROTEIN 3
B: NUCLEOLAR PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5264
Polymers21,3422
Non-polymers1842
Water19811
1
A: NUCLEOLAR PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8553
Polymers10,6711
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NUCLEOLAR PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)10,6711
Polymers10,6711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.351, 99.351, 51.102
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein NUCLEOLAR PROTEIN 3 / Nucleolus / APOPTOSIS REPRESSOR WITH CARD / MUSCLE-ENRICHED CYTOPLASMIC PROTEIN / MYP / NUCLEOLAR PROTEIN OF 30 ...APOPTOSIS REPRESSOR WITH CARD / MUSCLE-ENRICHED CYTOPLASMIC PROTEIN / MYP / NUCLEOLAR PROTEIN OF 30 KDA / NOP30 / APOPTOSIS REPRESSO


Mass: 10670.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60936
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.44 Å3/Da / Density % sol: 64.26 % / Description: NONE
Crystal growpH: 8.2 / Details: 0.1 M IMIDAZOLE PH 8.2, 0.6 M DIAMMONIUM PHOSPHATE

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2014 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 11384 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 47.75 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 45.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.399→27.436 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 20.37 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2001 1116 9.9 %
Rwork0.1702 --
obs0.1731 11259 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.399→27.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 12 11 1335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081332
X-RAY DIFFRACTIONf_angle_d1.0111793
X-RAY DIFFRACTIONf_dihedral_angle_d14.444525
X-RAY DIFFRACTIONf_chiral_restr0.039206
X-RAY DIFFRACTIONf_plane_restr0.004239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3991-2.50820.26031330.1971221X-RAY DIFFRACTION95
2.5082-2.64040.21621380.18231253X-RAY DIFFRACTION98
2.6404-2.80570.21161370.18491258X-RAY DIFFRACTION99
2.8057-3.0220.2221410.19091281X-RAY DIFFRACTION99
3.022-3.32570.22881390.20421259X-RAY DIFFRACTION99
3.3257-3.80580.21461400.17081253X-RAY DIFFRACTION98
3.8058-4.79080.17151420.14641291X-RAY DIFFRACTION100
4.7908-27.43770.1831460.16261327X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.2877 Å / Origin y: 41.8666 Å / Origin z: 37.03 Å
111213212223313233
T0.3369 Å20.024 Å2-0.0443 Å2-0.3787 Å20.0053 Å2--0.3063 Å2
L2.3265 °2-1.5295 °20.2547 °2-1.745 °2-0.5442 °2--0.2105 °2
S-0.066 Å °-0.1053 Å °0.0826 Å °0.2455 Å °0.0061 Å °-0.067 Å °0.0196 Å °-0.0217 Å °-0.0004 Å °
Refinement TLS groupSelection details: ALL

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