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- PDB-5h3u: Sm RNA bound to GEMIN5-WD -

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Basic information

Entry
Database: PDB / ID: 5h3u
TitleSm RNA bound to GEMIN5-WD
Components
  • Gem-associated protein 5
  • RNA (5'-R(*AP*AP*UP*UP*UP*UP*UP*GP*AP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / GEMIN5 SMN complex Sm Site WD-40 domain / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


SMN-Gemin2 complex / Gemini of coiled bodies / SMN complex / U4atac snRNA binding / snRNA binding / RNA 7-methylguanosine cap binding / U4 snRNA binding / SMN-Sm protein complex / spliceosomal snRNP assembly / U1 snRNA binding ...SMN-Gemin2 complex / Gemini of coiled bodies / SMN complex / U4atac snRNA binding / snRNA binding / RNA 7-methylguanosine cap binding / U4 snRNA binding / SMN-Sm protein complex / spliceosomal snRNP assembly / U1 snRNA binding / mRNA 3'-UTR binding / mRNA splicing, via spliceosome / ribosome binding / regulation of translation / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / protein-containing complex assembly / nuclear body / translation / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / MIOS, WD40 repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site ...: / MIOS, WD40 repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
RNA / Gem-associated protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsBharath, S.R. / Tang, X. / Song, H.
CitationJournal: Cell Res. / Year: 2016
Title: Structural basis for specific recognition of pre-snRNA by Gemin5
Authors: Tang, X. / Bharath, S.R. / Piao, S. / Tan, V.Q. / Bowler, M.W. / Song, H.
History
DepositionOct 27, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 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
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: Gem-associated protein 5
B: Gem-associated protein 5
C: RNA (5'-R(*AP*AP*UP*UP*UP*UP*UP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,8064
Polymers167,7143
Non-polymers921
Water2,036113
1
A: Gem-associated protein 5
C: RNA (5'-R(*AP*AP*UP*UP*UP*UP*UP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5113
Polymers85,4192
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-12 kcal/mol
Surface area25890 Å2
MethodPISA
2
B: Gem-associated protein 5


Theoretical massNumber of molelcules
Total (without water)82,2951
Polymers82,2951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.836, 92.083, 110.801
Angle α, β, γ (deg.)90.00, 99.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gem-associated protein 5 / Gemin5


Mass: 82295.203 Da / Num. of mol.: 2 / Fragment: UNP residues 1-740
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TEQ6
#2: RNA chain RNA (5'-R(*AP*AP*UP*UP*UP*UP*UP*GP*AP*C)-3')


Mass: 3123.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris propane, 0.2 M Na/K phosphate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→48.88 Å / Num. obs: 51715 / % possible obs: 96.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 40.6 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.6
Reflection shellResolution: 2.49→2.57 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.6 / CC1/2: 0.605 / % possible all: 78.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2386: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YMU

2ymu


Resolution: 2.499→48.877 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2561 2585 5.01 %
Rwork0.2016 --
obs0.2042 51648 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.499→48.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10288 141 6 113 10548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910905
X-RAY DIFFRACTIONf_angle_d1.01314945
X-RAY DIFFRACTIONf_dihedral_angle_d17.5886305
X-RAY DIFFRACTIONf_chiral_restr0.0591676
X-RAY DIFFRACTIONf_plane_restr0.0071852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4993-2.54740.3121060.28512351X-RAY DIFFRACTION84
2.5474-2.59940.31941590.29122679X-RAY DIFFRACTION99
2.5994-2.65590.33511360.26922808X-RAY DIFFRACTION99
2.6559-2.71770.37511550.26872739X-RAY DIFFRACTION99
2.7177-2.78560.32941570.26212733X-RAY DIFFRACTION99
2.7856-2.86090.31341610.25262743X-RAY DIFFRACTION99
2.8609-2.94510.32741610.24742723X-RAY DIFFRACTION99
2.9451-3.04010.28691430.23782746X-RAY DIFFRACTION99
3.0401-3.14880.25381500.22012756X-RAY DIFFRACTION99
3.1488-3.27480.28011450.21462757X-RAY DIFFRACTION99
3.2748-3.42380.2721400.19722757X-RAY DIFFRACTION99
3.4238-3.60430.27941510.2062682X-RAY DIFFRACTION97
3.6043-3.830.25181190.1912706X-RAY DIFFRACTION95
3.83-4.12560.23751430.17522762X-RAY DIFFRACTION99
4.1256-4.54050.2041440.15692776X-RAY DIFFRACTION99
4.5405-5.19690.16671260.14932783X-RAY DIFFRACTION99
5.1969-6.54510.24571310.19432799X-RAY DIFFRACTION98
6.5451-48.88640.24261580.20262763X-RAY DIFFRACTION97
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)
12.301-0.84560.4222.8009-0.35222.91030.10230.2011-0.0641-0.2669-0.1545-0.22230.1040.21080.02120.22340.00940.02630.26650.01250.2684-43.5256-17.238337.1771
23.3545-0.2654-0.19231.3204-0.02380.6788-0.0681-0.34350.21430.07180.07920.3523-0.065-0.1796-0.01430.31190.0221-0.0570.3487-0.04510.3862-78.71842.109249.4661
32.95871.68881.10842.73311.07172.4855-0.0783-0.09-0.2142-0.18730.1014-0.2249-0.17480.1112-0.00170.50260.0615-0.06410.3422-0.03150.4247-40.530229.736614.8581
42.6325-0.40161.21471.45490.03822.133-0.08670.1823-0.0936-0.17730.2235-0.05950.1249-0.1048-0.1520.6876-0.0816-0.1380.41540.03520.3539-74.24814.0939-4.6057
54.5526-5.3793-1.53597.5218-0.30935.0496-0.69620.6428-0.4820.88640.81890.8586-0.5237-0.14490.13280.89340.061-0.13960.8386-0.00510.8067-62.3311-19.82649.4263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 356 )
2X-RAY DIFFRACTION2chain 'A' and (resid 357 through 722 )
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 399 )
4X-RAY DIFFRACTION4chain 'B' and (resid 400 through 722 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 7 )

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