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- PDB-4dkk: The X-ray Crystal Structure of the Human STAU1 SSM-'RBD'5 Domain-... -

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Basic information

Entry
Database: PDB / ID: 4dkk
TitleThe X-ray Crystal Structure of the Human STAU1 SSM-'RBD'5 Domain-Swapped Dimer
ComponentsDouble-stranded RNA-binding protein Staufen homolog 1
KeywordsRNA BINDING PROTEIN / RBD / Beta Sheet / Swapping-motif / Dimerization / Protein binding
Function / homology
Function and homology information


lncRNA-mediated post-transcriptional gene silencing / anterograde dendritic transport of messenger ribonucleoprotein complex / : / modification of postsynaptic structure / intracellular mRNA localization / protein localization to synapse / protein phosphatase 1 binding / positive regulation by virus of viral protein levels in host cell / microtubule associated complex / germ cell development ...lncRNA-mediated post-transcriptional gene silencing / anterograde dendritic transport of messenger ribonucleoprotein complex / : / modification of postsynaptic structure / intracellular mRNA localization / protein localization to synapse / protein phosphatase 1 binding / positive regulation by virus of viral protein levels in host cell / microtubule associated complex / germ cell development / positive regulation of viral genome replication / rough endoplasmic reticulum / dendrite cytoplasm / positive regulation of long-term synaptic potentiation / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / double-stranded RNA binding / cellular response to oxidative stress / cell body / neuron projection / mRNA binding / neuronal cell body / glutamatergic synapse / dendrite / endoplasmic reticulum / RNA binding / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1360 / Staufen 1, third double-stranded RNA binding domain / Staufen, C-terminal / Staufen C-terminal domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1360 / Staufen 1, third double-stranded RNA binding domain / Staufen, C-terminal / Staufen C-terminal domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Double-stranded RNA-binding protein Staufen homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsGleghorn, M.L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Staufen1 dimerizes through a conserved motif and a degenerate dsRNA-binding domain to promote mRNA decay.
Authors: Gleghorn, M.L. / Gong, C. / Kielkopf, C.L. / Maquat, L.E.
History
DepositionFeb 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double-stranded RNA-binding protein Staufen homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7013
Polymers12,4761
Non-polymers2252
Water1,13563
1
A: Double-stranded RNA-binding protein Staufen homolog 1
hetero molecules

A: Double-stranded RNA-binding protein Staufen homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4016
Polymers24,9522
Non-polymers4494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2820 Å2
ΔGint-19 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.741, 45.741, 86.086
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Double-stranded RNA-binding protein Staufen homolog 1


Mass: 12476.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAU, STAU1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95793
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7 / Details: citrate anion
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.8 Å3/Da / Density % sol: 31.84 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Drop:130 mM citric acid pH 2.5, 26% (w/v) PEG 6000 (final pH of 4), Reservoir:100 mM citric acid pH 2.5, 35% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97932 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 17, 2010
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 10665 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Rsym value: 0.085 / Net I/σ(I): 28.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 10.6 / Rsym value: 0.263 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.701→31.346 Å / SU ML: 0.14 / σ(F): 1.95 / Phase error: 18.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 1046 9.87 %
Rwork0.1632 --
obs0.1668 10601 99.91 %
all-10613 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3978 Å20 Å2-0 Å2
2--0.3978 Å2-0 Å2
3----0.7956 Å2
Refinement stepCycle: LAST / Resolution: 1.701→31.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 14 63 889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011900
X-RAY DIFFRACTIONf_angle_d1.4861226
X-RAY DIFFRACTIONf_dihedral_angle_d15.014366
X-RAY DIFFRACTIONf_chiral_restr0.077141
X-RAY DIFFRACTIONf_plane_restr0.007160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.701-1.79020.21611400.17621316X-RAY DIFFRACTION100
1.7902-1.90240.23631380.17031349X-RAY DIFFRACTION100
1.9024-2.04930.21411630.16261311X-RAY DIFFRACTION100
2.0493-2.25540.19031610.14641331X-RAY DIFFRACTION100
2.2554-2.58170.1881410.15641379X-RAY DIFFRACTION100
2.5817-3.25210.22491670.1691373X-RAY DIFFRACTION100
3.2521-31.35170.18431360.16531496X-RAY DIFFRACTION100
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)
16.8947-1.76431.16837.9168-0.50296.30810.0144-0.6401-0.65180.7126-0.0037-0.2060.515-0.4885-0.04650.2274-0.0449-0.00710.16350.00990.1123-10.9229-6.461-17.1041
20.13980.1637-0.37544.272-0.96561.52330.4242-0.8041-0.59141.12010.3119-0.95651.10180.6452-0.50650.65170.0662-0.24960.32830.07260.50441.9658-8.3034-13.8027
32.75160.16361.59092.30861.10416.6872-0.08360.0024-0.0112-0.04040.0585-0.0903-0.2614-0.05650.02820.06560.0145-0.01260.08840.00520.1256.268913.7762-7.6656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 365 through 389 )
2X-RAY DIFFRACTION2chain 'A' and (resid 390 through 407 )
3X-RAY DIFFRACTION3chain 'A' and (resid 408 through 476 )

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