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- PDB-5h3s: apo form of GEMIN5-WD -

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Basic information

Entry
Database: PDB / ID: 5h3s
Titleapo form of GEMIN5-WD
ComponentsGem-associated protein 5
KeywordsRNA BINDING PROTEIN / GEMIN5 / SMN complex / WD40 domain
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 / Trp-Asp (WD) repeats signature. ...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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Gem-associated protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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

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Assembly

Deposited unit
A: Gem-associated protein 5
B: Gem-associated protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,6833
Polymers164,5902
Non-polymers921
Water0
1
A: Gem-associated protein 5


Theoretical massNumber of molelcules
Total (without water)82,2951
Polymers82,2951
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gem-associated protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3872
Polymers82,2951
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.503, 91.373, 112.571
Angle α, β, γ (deg.)90.00, 100.55, 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1 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: 3→29.37 Å / Num. obs: 30421 / % possible obs: 99 % / Redundancy: 5.8 % / Biso Wilson estimate: 74.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Net I/σ(I): 11.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.2 / CC1/2: 0.769 / % possible all: 99.6

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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: 3→29.366 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2606 1479 4.87 %
Rwork0.2006 --
obs0.2037 30397 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→29.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9749 0 6 0 9755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410041
X-RAY DIFFRACTIONf_angle_d0.68813767
X-RAY DIFFRACTIONf_dihedral_angle_d12.7675759
X-RAY DIFFRACTIONf_chiral_restr0.0491573
X-RAY DIFFRACTIONf_plane_restr0.0051745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.09680.34041360.29192625X-RAY DIFFRACTION99
3.0968-3.20730.28581580.25542619X-RAY DIFFRACTION99
3.2073-3.33560.30631440.23942593X-RAY DIFFRACTION99
3.3356-3.48710.27571180.22412631X-RAY DIFFRACTION99
3.4871-3.67070.25371370.19972549X-RAY DIFFRACTION97
3.6707-3.90020.25761230.2062621X-RAY DIFFRACTION99
3.9002-4.20050.25391310.19132652X-RAY DIFFRACTION100
4.2005-4.62180.23831200.16332646X-RAY DIFFRACTION100
4.6218-5.28720.22151340.15792658X-RAY DIFFRACTION100
5.2872-6.64850.27221360.21132648X-RAY DIFFRACTION99
6.6485-29.36720.26021420.20632676X-RAY DIFFRACTION98
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)
12.2361-1.25450.26623.0434-0.55692.45440.13850.0720.1236-0.7797-0.2023-0.51810.21720.11240.04090.39990.00970.16560.40920.00150.491332.3165-9.376438.0352
21.9271-0.0224-0.38082.7230.35251.2867-0.0256-0.14620.0056-0.14390.10990.6779-0.0376-0.1751-0.03110.2862-0.0012-0.09510.54550.03090.6757-4.13319.905749.2454
31.93960.54840.00881.65070.28651.75660.0931-0.10150.0565-0.3957-0.0495-0.1261-0.09080.0389-0.05711.20940.11880.04130.4791-0.01660.585637.083336.99617.3374
41.6951-0.18011.06390.8821-0.52761.40040.16920.0354-0.0328-0.3230.0194-0.00990.484-0.1464-0.15591.56070.0082-0.21650.52590.04590.43473.686720.353-4.3243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 376 )
2X-RAY DIFFRACTION2chain 'A' and (resid 377 through 722 )
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 376 )
4X-RAY DIFFRACTION4chain 'B' and (resid 377 through 722 )

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