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- PDB-5xjr: Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39... -

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Basic information

Entry
Database: PDB / ID: 5xjr
TitleCrystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with SmD1(1-82)/D2/F/E/G from Human
Components
  • (Small nuclear ribonucleoprotein ...) x 5
  • Gem-associated protein 2
  • Survival motor neuron protein
KeywordsSPLICING
Function / homology
Function and homology information


: / Gemini of Cajal bodies / SMN complex / U7 snRNP / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / U1 snRNP binding / RNA splicing, via transesterification reactions ...: / Gemini of Cajal bodies / SMN complex / U7 snRNP / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / U1 snRNP binding / RNA splicing, via transesterification reactions / methylosome / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type precatalytic spliceosome / P granule / telomerase holoenzyme complex / commitment complex / U2-type prespliceosome assembly / U2-type spliceosomal complex / U2-type catalytic step 2 spliceosome / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U4 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / U5 snRNP / spliceosomal snRNP assembly / Cajal body / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / DNA-templated transcription termination / mRNA splicing, via spliceosome / Z disc / cytoplasmic ribonucleoprotein granule / mRNA processing / nervous system development / snRNP Assembly / perikaryon / SARS-CoV-2 modulates host translation machinery / neuron projection / nuclear body / axon / nucleolus / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Gem-associated protein 2 / Gemin2/Brr1 / Survival motor neuron (SMN) interacting protein 1 (SIP1) / : / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / SMN complex subunit Smn1 / : / Survival motor neuron, Tudor domain ...Gem-associated protein 2 / Gemin2/Brr1 / Survival motor neuron (SMN) interacting protein 1 (SIP1) / : / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / SMN complex subunit Smn1 / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Small nuclear ribonucleoprotein D1 / SH3 type barrels. - #100 / Small nuclear ribonucleoprotein Sm D2 / Tudor domain / Tudor domain / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Gem-associated protein 2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Survival motor neuron protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsYi, H. / Zhang, R.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Negative cooperativity between Gemin2 and RNA provides insights into RNA selection and the SMN complex's release in snRNP assembly.
Authors: Yi, H. / Mu, L. / Shen, C. / Kong, X. / Wang, Y. / Hou, Y. / Zhang, R.
History
DepositionMay 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
2: Gem-associated protein 2
A: Small nuclear ribonucleoprotein Sm D1
B: Small nuclear ribonucleoprotein Sm D2
E: Small nuclear ribonucleoprotein E
F: Small nuclear ribonucleoprotein F
G: Small nuclear ribonucleoprotein G
M: Survival motor neuron protein


Theoretical massNumber of molelcules
Total (without water)83,2837
Polymers83,2837
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-68 kcal/mol
Surface area28620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.960, 114.120, 130.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Small nuclear ribonucleoprotein ... , 5 types, 5 molecules ABEFG

#2: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 9300.950 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62314
#3: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD2, SNRPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62316
#4: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPE / Production host: Escherichia coli (E. coli) / References: UniProt: P62304
#5: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPF, PBSCF / Production host: Escherichia coli (E. coli) / References: UniProt: P62306
#6: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPG, PBSCG / Production host: Escherichia coli (E. coli) / References: UniProt: P62308

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Protein / Protein/peptide , 2 types, 2 molecules 2M

#1: Protein Gem-associated protein 2 / Gemin-2 / Component of gems 2 / Survival of motor neuron protein-interacting protein 1 / SMN- ...Gemin-2 / Component of gems 2 / Survival of motor neuron protein-interacting protein 1 / SMN-interacting protein 1


Mass: 27323.041 Da / Num. of mol.: 1 / Fragment: UNP residues 40-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN2, SIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14893
#7: Protein/peptide Survival motor neuron protein / Component of gems 1 / Gemin-1


Mass: 4047.395 Da / Num. of mol.: 1 / Fragment: UNP residues 26-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMN1, SMN, SMNT, SMN2, SMNC / Production host: Escherichia coli (E. coli) / References: UniProt: Q16637

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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: 3.7 Å3/Da / Density % sol: 66.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1% PEG8000, 100mM Tris.HCl / PH range: 7.5-8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.1→60 Å / Num. obs: 21992 / % possible obs: 97 % / Redundancy: 12.4 % / Net I/σ(I): 10.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S6N

3s6n
PDB Unreleased entry


Resolution: 3.12→60 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.859 / SU B: 40.003 / SU ML: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 953 5.1 %RANDOM
Rwork0.1684 ---
obs0.1721 17815 83.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 258.08 Å2 / Biso mean: 54.465 Å2 / Biso min: 8.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 3.12→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4890 0 0 0 4890
Num. residues----612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194984
X-RAY DIFFRACTIONr_bond_other_d0.0020.024967
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9746719
X-RAY DIFFRACTIONr_angle_other_deg1.094311406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6655602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.99724.405227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.515945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6791537
X-RAY DIFFRACTIONr_chiral_restr0.0740.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215519
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021108
X-RAY DIFFRACTIONr_rigid_bond_restr4.97439951
X-RAY DIFFRACTIONr_sphericity_bonded21.46259873
LS refinement shellResolution: 3.123→3.204 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 13 -
Rwork0.314 239 -
all-252 -
obs--15.06 %

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