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- PDB-4nbo: Human steroid receptor RNA activator protein carboxy-terminal domain -

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Basic information

Entry
Database: PDB / ID: 4nbo
TitleHuman steroid receptor RNA activator protein carboxy-terminal domain
ComponentsSteroid receptor RNA activator 1
KeywordsTRANSCRIPTION / 5-helix bundle
Function / homology
Function and homology information


steroid receptor RNA activator RNA binding / SCAR complex / negative regulation of myoblast differentiation / intercellular bridge / cellular response to estrogen stimulus / regulation of mitotic cell cycle / nuclear receptor coactivator activity / microtubule cytoskeleton / regulation of apoptotic process / cell differentiation ...steroid receptor RNA activator RNA binding / SCAR complex / negative regulation of myoblast differentiation / intercellular bridge / cellular response to estrogen stimulus / regulation of mitotic cell cycle / nuclear receptor coactivator activity / microtubule cytoskeleton / regulation of apoptotic process / cell differentiation / transcription coactivator activity / ribonucleoprotein complex / apoptotic process / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Steroid receptor RNA activator 1 / RNA Binding Protein, Prp18; Chain A / Functional domain of the splicing factor Prp18 / SRA1/Sec31 / Steroid receptor RNA activator (SRA1) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Steroid receptor RNA activator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.807 Å
AuthorsMckay, D.B. / Xi, L. / Barthel, K.K.B. / Cech, T.C.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structure and function of steroid receptor RNA activator protein, the proposed partner of SRA noncoding RNA.
Authors: McKay, D.B. / Xi, L. / Barthel, K.K. / Cech, T.R.
History
DepositionOct 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Steroid receptor RNA activator 1
B: Steroid receptor RNA activator 1


Theoretical massNumber of molelcules
Total (without water)25,4872
Polymers25,4872
Non-polymers00
Water0
1
A: Steroid receptor RNA activator 1


Theoretical massNumber of molelcules
Total (without water)12,7441
Polymers12,7441
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Steroid receptor RNA activator 1


Theoretical massNumber of molelcules
Total (without water)12,7441
Polymers12,7441
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.901, 85.901, 100.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Steroid receptor RNA activator 1 / Steroid receptor RNA activator protein / SRAP


Mass: 12743.624 Da / Num. of mol.: 2 / Fragment: UNP residues 106-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PP7684, sra, SRA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HD15

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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: 3.63 Å3/Da / Density % sol: 66.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.4-2.0 Malonate(Na+), 0.1 M Mops as precipitant, stabilized in 2.4 M Malonate, 0.1 M MOPS pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2013
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 9705 / Num. obs: 9695 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rsym value: 0.059
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 8 % / Num. unique all: 463 / Rsym value: 0.295 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YRU

2yru


Resolution: 2.807→39.489 Å / SU ML: 0.52 / σ(F): 1.34 / Phase error: 27.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 479 4.97 %5% of data
Rwork0.2452 ---
obs0.2468 9632 99.55 %-
all-9676 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.663 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2601 Å20 Å20 Å2
2---0.2601 Å2-0 Å2
3---0.5203 Å2
Refinement stepCycle: LAST / Resolution: 2.807→39.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 0 0 1640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041664
X-RAY DIFFRACTIONf_angle_d0.7522238
X-RAY DIFFRACTIONf_dihedral_angle_d17.502640
X-RAY DIFFRACTIONf_chiral_restr0.038254
X-RAY DIFFRACTIONf_plane_restr0.002284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8066-3.21260.39021570.29852981X-RAY DIFFRACTION100
3.2126-4.04690.29071550.24942996X-RAY DIFFRACTION99
4.0469-39.49320.23921670.22643176X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.2226 Å / Origin y: 33.8795 Å / Origin z: -17.7535 Å
111213212223313233
T0.3651 Å2-0.0664 Å20.0669 Å2-0.3185 Å2-0.0691 Å2--0.3401 Å2
L1.904 °2-1.0024 °20.9596 °2-3.4092 °2-0.3697 °2--2.455 °2
S0.0528 Å °0.0522 Å °0.1397 Å °0.224 Å °-0.0224 Å °-0.0545 Å °-0.1946 Å °0.2092 Å °-0.0286 Å °
Refinement TLS groupSelection details: all

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