[English] 日本語
Yorodumi
- PDB-5xju: Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39... -

+
Open data


ID or keywords:

Loading...

-
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 ...SnRNP) x 5
  • Gem-associated protein 2
  • Survival motor neuron proteinSurvival of motor neuron
KeywordsSPLICING
Function / homology
Function and homology information


negative regulation of RNA binding / Gemini of coiled bodies / SMN complex / U7 snRNP / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / methylosome / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex ...negative regulation of RNA binding / Gemini of coiled bodies / SMN complex / U7 snRNP / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / methylosome / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / RNA splicing, via transesterification reactions / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / SMN-Sm protein complex / U2-type spliceosomal complex / telomerase holoenzyme complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / U5 snRNP / Cajal body / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / DNA-templated transcription termination / spliceosomal complex / cytoplasmic ribonucleoprotein granule / mRNA splicing, via spliceosome / mRNA processing / Z disc / snRNP Assembly / nervous system development / SARS-CoV-2 modulates host translation machinery / perikaryon / nuclear body / neuron projection / 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) / SMN complex subunit Smn1 / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain ...Gem-associated protein 2 / Gemin2/Brr1 / Survival motor neuron (SMN) interacting protein 1 (SIP1) / SMN complex subunit Smn1 / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Small nuclear ribonucleoprotein D1 / Small nuclear ribonucleoprotein Sm D2 / 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 / SH3 type barrels. - #100 / Sm-like protein Lsm6/SmF / Tudor domain / Tudor domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
Components

-
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

-
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 / Survival of motor neuron / 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more