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- PDB-2xs5: Crystal structure of the RRM domain of mouse Deleted in azoosperm... -

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Basic information

Entry
Database: PDB / ID: 2xs5
TitleCrystal structure of the RRM domain of mouse Deleted in azoospermia- like in complex with Mvh RNA, UGUUC
Components
  • 5'-R(*UP*GP*UP*UP*CP)-3'
  • DELETED IN AZOOSPERMIA-LIKE
KeywordsRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX / TRANSLATION REGULATION
Function / homology
Function and homology information


female meiosis II / translation activator activity / positive regulation of meiotic nuclear division / oocyte maturation / germ cell development / positive regulation of translational initiation / mRNA 3'-UTR binding / spermatogenesis / ribosome / protein-containing complex ...female meiosis II / translation activator activity / positive regulation of meiotic nuclear division / oocyte maturation / germ cell development / positive regulation of translational initiation / mRNA 3'-UTR binding / spermatogenesis / ribosome / protein-containing complex / identical protein binding / nucleus / cytoplasm
Similarity search - Function
DAZ, RNA recognition motif, vertebrates / DAZ domain / Daz repeat / DAZ domain profile. / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...DAZ, RNA recognition motif, vertebrates / DAZ domain / Daz repeat / DAZ domain profile. / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / RNA / Deleted in azoospermia-like
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJenkins, H.T. / Edwards, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Kinked Beta-Strands Mediate High-Affinity Recognition of Mrna Targets by the Germ-Cell Regulator Dazl
Authors: Jenkins, H.T. / Edwards, T.A.
History
DepositionSep 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: DELETED IN AZOOSPERMIA-LIKE
B: DELETED IN AZOOSPERMIA-LIKE
C: 5'-R(*UP*GP*UP*UP*CP)-3'
D: 5'-R(*UP*GP*UP*UP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7495
Polymers22,6424
Non-polymers1061
Water4,306239
1
A: DELETED IN AZOOSPERMIA-LIKE
C: 5'-R(*UP*GP*UP*UP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)11,3212
Polymers11,3212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-11.2 kcal/mol
Surface area5740 Å2
MethodPISA
2
B: DELETED IN AZOOSPERMIA-LIKE
D: 5'-R(*UP*GP*UP*UP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4273
Polymers11,3212
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-8.5 kcal/mol
Surface area5840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.605, 77.538, 37.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9987, -0.05053, -0.000232), (-0.05052, -0.9987, 0.007928), (-0.000632, -0.007906, -1)
Vector: -0.07941, -5.122, 18.76)

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Components

#1: Protein DELETED IN AZOOSPERMIA-LIKE / DAZ-LIKE AUTOSOMAL / DELETED IN AZOOSPERMIA-LIKE 1


Mass: 9797.299 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET-SUMO-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA-2 PLYSS / References: UniProt: Q64368
#2: RNA chain 5'-R(*UP*GP*UP*UP*CP)-3' / MVH 3'-UTR


Mass: 1523.928 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.76 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growDetails: 0.1 M MAGNESIUM ACETATE, 18% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2010
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→27.07 Å / Num. obs: 29634 / % possible obs: 98.7 % / Observed criterion σ(I): 6 / Redundancy: 4.9 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XS2

2xs2


Resolution: 1.6→27.07 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.234 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22418 1500 5.1 %RANDOM
Rwork0.18848 ---
obs0.19033 28134 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.648 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å20 Å2
2---1.27 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 184 7 239 1733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221601
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5112.1052200
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4045187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11422.78761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54215270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.481512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021131
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.2628
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21079
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2172
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9061.5847
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41221388
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3143754
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5264.5800
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 97 -
Rwork0.281 2026 -
obs--96.32 %
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)
13.48251.3406-0.45963.2062-0.21033.06360.0504-0.05710.0551-0.0673-0.04320.1222-0.0628-0.0196-0.00710.00470.002-0.00250.03730.00660.044317.76988.232415.0124
20.23960.2449-0.51823.1369-1.59992.9844-0.03910.0343-0.06220.03250.05570.15440.0222-0.1566-0.01670.0122-0.00540.00810.0464-0.00360.06112.76174.64979.236
30.4142-0.316-0.79921.20160.45051.68550.0357-0.0275-0.0173-0.0589-0.0015-0.0736-0.15510.0519-0.03430.1141-0.01070.00580.10150.00150.095419.112711.577711.2211
43.95580.74-0.41821.26610.5322.2759-0.052-0.0646-0.00710.0190.07610.25-0.0052-0.1624-0.02410.052-0.01970.00820.05860.03080.074312.454312.432916.8512
51.6029-0.2594-0.03132.3116-0.38542.0396-0.0423-0.03050.0620.04270.00830.1838-0.0339-0.15370.0340.01010.0075-0.00620.0202-0.00640.029213.5051-13.79557.3108
60.12540.10330.02224.8302-3.35382.4461-0.0407-0.0480.05510.04980.08860.0463-0.0854-0.1136-0.04790.09310.00940.01190.07180.00210.092315.3638-9.138.0016
70.4650.47340.34971.0026-0.08121.2459-0.0018-0.03660.06690.02620.034-0.01030.105-0.0217-0.03220.08750.01420.00320.0912-0.00660.092917.6981-17.89847.1639
87.65450.2599-0.5181.91591.01412.10630.04950.118-0.044-0.0529-0.09140.312-0.0369-0.30220.04180.03150.0128-0.00810.04920.00450.063211.6258-17.84541.8883
91.9686-2.1171-1.25626.55471.9152.5523-0.0408-0.1913-0.21840.4831-0.14850.16170.17710.05310.18940.0718-0.00830.00330.08040.0220.084117.50262.855421.7172
102.30550.33951.03182.35891.18952.30340.00490.1350.2227-0.4415-0.03780.0038-0.1330.05180.03290.09060.00810.01720.06780.01590.096718.4451-8.9254-2.476
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 50
2X-RAY DIFFRACTION2A51 - 78
3X-RAY DIFFRACTION3A79 - 97
4X-RAY DIFFRACTION4A98 - 117
5X-RAY DIFFRACTION5B34 - 61
6X-RAY DIFFRACTION6B62 - 77
7X-RAY DIFFRACTION7B78 - 99
8X-RAY DIFFRACTION8B100 - 117
9X-RAY DIFFRACTION9C1 - 5
10X-RAY DIFFRACTION10D1 - 5

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