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

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Basic information

Entry
Database: PDB / ID: 5xju
TitleCrystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with SmD1(1-82)/D2.R61A/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: 2.58 Å
AuthorsYi, H. / Zhang, R.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570720 China
National Natural Science Foundation of China81441109 China
CitationJournal: To Be Published
Title: Structures of 7S mutant complexes.
Authors: Yi, H. / Zhang, R.
History
DepositionMay 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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

Downloads & links

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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)83,1977
Polymers83,1977
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13860 Å2
ΔGint-64 kcal/mol
Surface area29110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.780, 112.960, 130.750
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 / Fragment: UNP residues 1-82
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: 13465.812 Da / Num. of mol.: 1 / Mutation: R61A
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: 3.76 Å3/Da / Density % sol: 67.27 %
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: 2.58→66.77 Å / Num. obs: 31276 / % possible obs: 99.9 % / Redundancy: 12.9 % / Net I/σ(I): 13.5

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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: 2.58→66.77 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.879 / SU B: 9.704 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.547 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 1395 5.1 %RANDOM
Rwork0.2055 ---
obs0.2082 25970 70.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 185.51 Å2 / Biso mean: 54.285 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å20 Å2
2---0.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.58→66.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4959 0 0 0 4959
Num. residues----621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195039
X-RAY DIFFRACTIONr_bond_other_d0.0020.025009
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.9746795
X-RAY DIFFRACTIONr_angle_other_deg0.932311506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7195610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.07924.502231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.49315953
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9151537
X-RAY DIFFRACTIONr_chiral_restr0.0990.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021120
LS refinement shellResolution: 2.585→2.652 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 3 -
Rwork0.276 94 -
all-97 -
obs--3.42 %

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