[English] 日本語
Yorodumi
- PDB-4qq6: Crystal Structure of tudor domain of SMN1 in complex with a small... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qq6
TitleCrystal Structure of tudor domain of SMN1 in complex with a small organic molecule
ComponentsSurvival motor neuron protein
KeywordsRNA BINDING PROTEIN / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Gemini of Cajal bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / Cajal body / DNA-templated transcription termination / Z disc / cytoplasmic ribonucleoprotein granule / nervous system development ...Gemini of Cajal bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / Cajal body / DNA-templated transcription termination / Z disc / cytoplasmic ribonucleoprotein granule / nervous system development / snRNP Assembly / perikaryon / SARS-CoV-2 modulates host translation machinery / neuron projection / nuclear body / axon / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / : / 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. / Tudor domain ...: / : / 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. / Tudor domain / Tudor domain / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-36X / Survival motor neuron protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLiu, Y. / Tempel, W. / Iqbal, A. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat Commun / Year: 2022
Title: A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II.
Authors: Liu, Y. / Iqbal, A. / Li, W. / Ni, Z. / Wang, Y. / Ramprasad, J. / Abraham, K.J. / Zhang, M. / Zhao, D.Y. / Qin, S. / Loppnau, P. / Jiang, H. / Guo, X. / Brown, P.J. / Zhen, X. / Xu, G. / ...Authors: Liu, Y. / Iqbal, A. / Li, W. / Ni, Z. / Wang, Y. / Ramprasad, J. / Abraham, K.J. / Zhang, M. / Zhao, D.Y. / Qin, S. / Loppnau, P. / Jiang, H. / Guo, X. / Brown, P.J. / Zhen, X. / Xu, G. / Mekhail, K. / Ji, X. / Bedford, M.T. / Greenblatt, J.F. / Min, J.
History
DepositionJun 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.type / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Survival motor neuron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5985
Polymers7,4091
Non-polymers1884
Water46826
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.789, 27.789, 112.817
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
DetailsTHE BIOLOGICAL UNIT IS UNKNOWN

-
Components

#1: Protein Survival motor neuron protein / Component of gems 1 / Gemin-1


Mass: 7409.304 Da / Num. of mol.: 1 / Fragment: unp residues 82-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMN1, SMN, SMNT, SMN2, SMNC / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q16637
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#3: Chemical ChemComp-36X / 4-methyl-2,3,4,5,6,7-hexahydrodicyclopenta[b,e]pyridin-8(1H)-imine


Mass: 188.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.7 Å3/Da / Density % sol: 27.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2M ammonium sulfate, 0.2M potassium/sodium tartrate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→37.61 Å / Num. obs: 5006 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 19.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.75-1.7910.30.8062.92917283100
8.75-37.619.20.03253.94244699.1

-
Processing

Software
NameVersionClassificationNB
Aimless0.3.3data scaling
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1MHN

1mhn


Resolution: 1.75→24.07 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2294 / WRfactor Rwork: 0.1496 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7967 / SU B: 3.803 / SU ML: 0.115 / SU R Cruickshank DPI: 0.1368 / SU Rfree: 0.1482 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Model is based on initial rigid body refinement of protein coordinates from PDB entry 1MHN. SMILES(CN1C2=C(CCC2)C(=N)C2=C1CCC2) represents the uncharged form of the ligand. Geometry ...Details: Model is based on initial rigid body refinement of protein coordinates from PDB entry 1MHN. SMILES(CN1C2=C(CCC2)C(=N)C2=C1CCC2) represents the uncharged form of the ligand. Geometry restraints for the inhibitor were prepared on the GRADE server with SMILES(C[n+]1c2CCCc2c(N)c2CCCc12). We note that mogul (CSD) inferred the type of the C1-C2 bond in refined ligand coordinates as double, which would be inconsistent with any traditional hybridization state of C1. COOT and MOLPROBITY were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 508 10.3 %RANDOM
Rwork0.1646 ---
obs0.1727 4942 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.38 Å2 / Biso mean: 26.6793 Å2 / Biso min: 14.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å2-0 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 1.75→24.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms454 0 17 26 497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02489
X-RAY DIFFRACTIONr_bond_other_d0.0010.02443
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.965671
X-RAY DIFFRACTIONr_angle_other_deg0.87431027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.883561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26125.45522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.881578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7152
X-RAY DIFFRACTIONr_chiral_restr0.1140.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02107
X-RAY DIFFRACTIONr_mcbond_it3.2132.43236
X-RAY DIFFRACTIONr_mcbond_other3.2072.433237
X-RAY DIFFRACTIONr_mcangle_it4.473.601293
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 33 -
Rwork0.246 319 -
all-352 -
obs--100 %

+
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