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- PDB-4xos: ANP32A LRR domain -

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Basic information

Entry
Database: PDB / ID: 4xos
TitleANP32A LRR domain
ComponentsAcidic leucine-rich nuclear phosphoprotein 32 family member A
KeywordsANTITUMOR PROTEIN / leucine rich repeat tumor suppressor / Component of the SET complex
Function / homology
Function and homology information


HuR (ELAVL1) binds and stabilizes mRNA / nucleocytoplasmic transport / histone binding / regulation of apoptotic process / intracellular signal transduction / perinuclear region of cytoplasm / endoplasmic reticulum / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Acidic leucine-rich nuclear phosphoprotein 32 / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Acidic leucine-rich nuclear phosphoprotein 32 family member A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.559 Å
AuthorsZamora-Caballero, S. / Bravo, J.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBES-2010-030116 Spain
Spanish Ministry of Economy and CompetitivenessSAF2012-31405 Spain
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: High-resolution crystal structure of the leucine-rich repeat domain of the human tumour suppressor PP32A (ANP32A).
Authors: Zamora-Caballero, S. / Siauciunaite-Gaubard, L. / Bravo, J.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_validate_symm_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_symm_contact.auth_seq_id_1 / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: Acidic leucine-rich nuclear phosphoprotein 32 family member A
B: Acidic leucine-rich nuclear phosphoprotein 32 family member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8006
Polymers34,5452
Non-polymers2554
Water2,936163
1
A: Acidic leucine-rich nuclear phosphoprotein 32 family member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4003
Polymers17,2731
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acidic leucine-rich nuclear phosphoprotein 32 family member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4003
Polymers17,2731
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.040, 50.880, 63.020
Angle α, β, γ (deg.)90.00, 110.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acidic leucine-rich nuclear phosphoprotein 32 family member A / Acidic nuclear phosphoprotein pp32 / pp32 / Leucine-rich acidic nuclear protein / LANP / Mapmodulin ...Acidic nuclear phosphoprotein pp32 / pp32 / Leucine-rich acidic nuclear protein / LANP / Mapmodulin / Potent heat-stable protein phosphatase 2A inhibitor I1PP2A / Putative HLA-DR-associated protein I / PHAPI


Mass: 17272.689 Da / Num. of mol.: 2 / Fragment: UNP residues 1-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANP32A, C15orf1, LANP, MAPM, PHAP1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon + RIPL / References: UniProt: P39687
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.33 % / Description: 2D plate
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3000, 0.1M Hepes pH 7.5, 0.2M NaCl / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97947 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.559→45.088 Å / Num. obs: 36978 / % possible obs: 90.9 % / Redundancy: 2 % / Biso Wilson estimate: 17.07 Å2 / Rmerge(I) obs: 0.072 / Net I/av σ(I): 7 / Net I/σ(I): 45.06
Reflection shellResolution: 1.559→1.615 Å / Redundancy: 2 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 1.7 / % possible all: 87.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2je0

2je0


Resolution: 1.559→45.088 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1929 1853 5.01 %
Rwork0.1603 --
obs0.162 36950 90.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.559→45.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 14 163 2597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072503
X-RAY DIFFRACTIONf_angle_d1.0663378
X-RAY DIFFRACTIONf_dihedral_angle_d12.128992
X-RAY DIFFRACTIONf_chiral_restr0.042391
X-RAY DIFFRACTIONf_plane_restr0.005441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.559-1.60120.28231530.25162459X-RAY DIFFRACTION84
1.6012-1.64830.26521340.23622687X-RAY DIFFRACTION90
1.6483-1.70150.26781390.22642665X-RAY DIFFRACTION89
1.7015-1.76230.25411200.20542671X-RAY DIFFRACTION90
1.7623-1.83290.22531250.18742657X-RAY DIFFRACTION89
1.8329-1.91630.21061400.16442701X-RAY DIFFRACTION91
1.9163-2.01730.19131450.15482719X-RAY DIFFRACTION91
2.0173-2.14370.20061400.15012688X-RAY DIFFRACTION91
2.1437-2.30920.18771260.14872711X-RAY DIFFRACTION90
2.3092-2.54160.19581520.15432757X-RAY DIFFRACTION92
2.5416-2.90930.19661560.16192736X-RAY DIFFRACTION92
2.9093-3.66520.19531570.14922831X-RAY DIFFRACTION94
3.6652-45.10690.14991660.14162815X-RAY DIFFRACTION92
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)
10.0991-0.0388-0.02690.2521-0.01830.07170.0258-0.088-0.09120.10420.0796-0.0540.16130.01560.00490.16070.0206-0.01480.18160.03040.14596.9592-10.4678-21.9769
20.2393-0.10810.12570.2156-0.00760.266-0.0173-0.1031-0.07740.04260.00850.12080.0978-0.15590.00060.1335-0.02180.00270.15320.00640.1349-0.0919-4.9037-27.044
30.06620.0899-0.02020.2061-0.01280.08570.0863-0.0845-0.00570.0302-0.06760.1464-0.0363-0.27910.01570.12980.0058-0.0110.1583-0.00540.13230.03583.3293-28.6983
40.41390.0904-0.09450.77320.02110.37260.03340.02980.1218-0.04240.04820.2164-0.1201-0.1910.06560.12490.0290.00010.16660.00830.1696-3.867712.8934-32.1857
50.03430.0313-0.00610.0508-0.00940.01850.0174-0.0120.26570.24280.0676-0.0666-0.1044-0.04180.00050.13920.02320.00920.1389-0.02790.190.861819.9906-28.1408
60.3125-0.176-0.1730.6303-0.15910.21740.0363-0.0398-0.12820.04790.02680.23560.0688-0.09960.00560.1645-0.0136-0.00740.14790.01260.150415.4703-5.61743.1377
70.08170.01840.04950.2557-0.03990.072-0.00680.0102-0.0298-0.01310.04260.2360.0935-0.24930.01290.17280.01470.00640.13740.00580.14313.51464.8629-1.5398
80.2144-0.0476-0.01470.4649-0.05830.57580.01750.0169-0.0024-0.00530.03880.3021-0.0336-0.220.01670.14150.0161-0.00170.14230.01760.17129.327211.1986-3.8474
90.49730.2709-0.34780.4196-0.06490.32870.07750.10090.2234-0.0932-0.04780.1139-0.2829-0.203-0.0340.16780.0464-0.00810.1230.00640.138113.332621.7555-7.3548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 138 )
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 149 )
6X-RAY DIFFRACTION6chain 'B' and (resid -2 through 63 )
7X-RAY DIFFRACTION7chain 'B' and (resid 64 through 79 )
8X-RAY DIFFRACTION8chain 'B' and (resid 80 through 123 )
9X-RAY DIFFRACTION9chain 'B' and (resid 124 through 149 )

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