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- PDB-6g6s: Crystal structure of human Acinus RNA recognition motif domain -

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Basic information

Entry
Database: PDB / ID: 6g6s
TitleCrystal structure of human Acinus RNA recognition motif domain
ComponentsApoptotic chromatin condensation inducer in the nucleus
KeywordsRNA BINDING PROTEIN / Acinus / apoptosis / RRM domain / splicing factor
Function / homology
Function and homology information


ASAP complex / apoptotic chromosome condensation / positive regulation of monocyte differentiation / Apoptotic cleavage of cellular proteins / negative regulation of mRNA splicing, via spliceosome / RNA splicing / erythrocyte differentiation / mRNA processing / nucleic acid binding / nuclear speck ...ASAP complex / apoptotic chromosome condensation / positive regulation of monocyte differentiation / Apoptotic cleavage of cellular proteins / negative regulation of mRNA splicing, via spliceosome / RNA splicing / erythrocyte differentiation / mRNA processing / nucleic acid binding / nuclear speck / positive regulation of apoptotic process / nucleolus / enzyme binding / ATP hydrolysis activity / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Acin1, RNSP1-SAP18 binding (RSB) motif / Acinus, RNA recognition motif / RNSP1-SAP18 binding (RSB) motif / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Apoptotic chromatin condensation inducer in the nucleus
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsFernandes, H. / Czapinska, H. / Grudziaz, K. / Bujnicki, J.M. / Nowacka, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre (NCN)2012/04/S/NZ1/00729 to MN Poland
CitationJournal: PeerJ / Year: 2018
Title: Crystal structure of human Acinus RNA recognition motif domain.
Authors: Fernandes, H. / Czapinska, H. / Grudziaz, K. / Bujnicki, J.M. / Nowacka, M.
History
DepositionApr 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptotic chromatin condensation inducer in the nucleus
B: Apoptotic chromatin condensation inducer in the nucleus


Theoretical massNumber of molelcules
Total (without water)21,3462
Polymers21,3462
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-4 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.359, 67.911, 80.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Apoptotic chromatin condensation inducer in the nucleus / Acinus


Mass: 10673.157 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACIN1, ACINUS, KIAA0670 / Plasmid: pGEX4T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UKV3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 1.93 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Ammonium acetate, 100 mM Tris-HCl pH 8.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.65→80.07 Å / Num. obs: 19003 / % possible obs: 91.6 % / Redundancy: 4.76 % / CC1/2: 0.999 / Rrim(I) all: 0.071 / Net I/σ(I): 16.3
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
4.91-80.0746.18640.9990.024197.7
3.49-4.946.7314550.9990.029199.5
2.85-3.4834.9418480.9990.044199.6
2.47-2.8423.1121590.9970.072199.8
2.21-2.4616.7316260.9940.103166.9
2.02-2.211.5326560.9910.1531100
1.87-2.016.2420640.9740.277171
1.75-1.863.3131000.9070.5211100
1.65-1.741.9732280.7430.864198.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x1f

2x1f


Resolution: 1.65→80.07 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.445 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.118
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 947 5 %RANDOM
Rwork0.1852 ---
obs0.1872 18053 91.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 54.33 Å2 / Biso mean: 22.967 Å2 / Biso min: 13.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.49 Å20 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 1.65→80.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 0 194 1674
Biso mean---30.17 -
Num. residues----186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191528
X-RAY DIFFRACTIONr_bond_other_d0.0020.021423
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9462079
X-RAY DIFFRACTIONr_angle_other_deg1.02733301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9415190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.1723.82468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19315261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.541158
X-RAY DIFFRACTIONr_chiral_restr0.1090.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021687
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02317
LS refinement shellResolution: 1.648→1.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 66 -
Rwork0.29 1398 -
all-1464 -
obs--96.63 %
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)
12.6111-0.22020.09531.220.04430.86780.06710.05310.0621-0.0969-0.0378-0.010.10890.0423-0.02930.0720.01680.01950.0130.0050.012412.17795.66413.0264
23.22010.12970.6681.4689-0.04812.79970.0185-0.0093-0.0461-0.0081-0.03970.14140.093-0.17450.02130.0117-0.0198-0.00850.03590.0080.023919.6115-10.642915.3797
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1006 - 1100
2X-RAY DIFFRACTION2B1008 - 1098

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