[English] 日本語
Yorodumi
- PDB-4qmg: The Structure of MTDH-SND1 Complex Reveals Novel Cancer-Promoting... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qmg
TitleThe Structure of MTDH-SND1 Complex Reveals Novel Cancer-Promoting Interactions
Components
  • Protein LYRIC
  • Staphylococcal nuclease domain-containing protein 1
KeywordsTRANSCRIPTION / SN domains / oligonucleotide/oligosaccharide binding-fold (OB-fold) / DNA/RNA-binding / miRNA-mediated silencing / nuclease / breast cancer / tumorigenesis / SND1 / MTDH
Function / homology
Function and homology information


RNAi effector complex / miRNA catabolic process / regulation of cell cycle process / RISC complex binding / nuclease activity / intercellular canaliculus / dense body / regulatory ncRNA-mediated gene silencing / micrococcal nuclease / : ...RNAi effector complex / miRNA catabolic process / regulation of cell cycle process / RISC complex binding / nuclease activity / intercellular canaliculus / dense body / regulatory ncRNA-mediated gene silencing / micrococcal nuclease / : / mRNA catabolic process / bicellular tight junction / NF-kappaB binding / positive regulation of autophagy / RNA endonuclease activity / lipopolysaccharide-mediated signaling pathway / transcription coregulator activity / positive regulation of NF-kappaB transcription factor activity / fibrillar center / positive regulation of angiogenesis / osteoblast differentiation / Signaling by BRAF and RAF1 fusions / melanosome / double-stranded RNA binding / endonuclease activity / nuclear membrane / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / nuclear body / apical plasma membrane / cadherin binding / regulation of transcription by RNA polymerase II / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Protein LYRIC / : / Lysine-rich CEACAM1 co-isolated protein family / RNA-induced silencing complex, nuclease component Tudor-SN / : / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 ...Protein LYRIC / : / Lysine-rich CEACAM1 co-isolated protein family / RNA-induced silencing complex, nuclease component Tudor-SN / : / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Staphylococcal nuclease domain-containing protein 1 / Protein LYRIC
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.701 Å
AuthorsGuo, F. / Stanevich, V. / Wan, L. / Satyshur, K. / Kang, Y. / Xing, Y.
CitationJournal: Cell Rep / Year: 2014
Title: Structural Insights into the Tumor-Promoting Function of the MTDH-SND1 Complex.
Authors: Guo, F. / Wan, L. / Zheng, A. / Stanevich, V. / Wei, Y. / Satyshur, K.A. / Shen, M. / Lee, W. / Kang, Y. / Xing, Y.
History
DepositionJun 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Staphylococcal nuclease domain-containing protein 1
F: Protein LYRIC
B: Staphylococcal nuclease domain-containing protein 1
G: Protein LYRIC
C: Staphylococcal nuclease domain-containing protein 1
H: Protein LYRIC
D: Staphylococcal nuclease domain-containing protein 1
I: Protein LYRIC
E: Staphylococcal nuclease domain-containing protein 1
J: Protein LYRIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,06524
Polymers206,55210
Non-polymers1,51314
Water5,224290
1
A: Staphylococcal nuclease domain-containing protein 1
F: Protein LYRIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5394
Polymers41,3102
Non-polymers2292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-40 kcal/mol
Surface area17030 Å2
MethodPISA
2
B: Staphylococcal nuclease domain-containing protein 1
G: Protein LYRIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7246
Polymers41,3102
Non-polymers4134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-44 kcal/mol
Surface area17010 Å2
MethodPISA
3
C: Staphylococcal nuclease domain-containing protein 1
H: Protein LYRIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5394
Polymers41,3102
Non-polymers2292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-47 kcal/mol
Surface area16810 Å2
MethodPISA
4
D: Staphylococcal nuclease domain-containing protein 1
I: Protein LYRIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6315
Polymers41,3102
Non-polymers3213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-45 kcal/mol
Surface area17310 Å2
MethodPISA
5
E: Staphylococcal nuclease domain-containing protein 1
J: Protein LYRIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6315
Polymers41,3102
Non-polymers3213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-44 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.830, 65.715, 135.841
Angle α, β, γ (deg.)90.00, 96.31, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Protein/peptide , 2 types, 10 molecules ABCDEFGHIJ

#1: Protein
Staphylococcal nuclease domain-containing protein 1 / 100 kDa coactivator / EBNA2 coactivator p100 / Tudor domain-containing protein 11 / p100 co-activator


Mass: 36918.207 Da / Num. of mol.: 5 / Fragment: SND1, UNP residues 16-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: Metadherin (MTDH) and Staphylococcal nuclease domain containing 1 (SND1), SND1, TDRD11
Plasmid: pQlink / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q7KZF4
#2: Protein/peptide
Protein LYRIC / 3D3/LYRIC / Astrocyte elevated gene-1 protein / AEG-1 / Lysine-rich CEACAM1 co-isolated protein / ...3D3/LYRIC / Astrocyte elevated gene-1 protein / AEG-1 / Lysine-rich CEACAM1 co-isolated protein / Metadherin / Metastasis adhesion protein


Mass: 4392.189 Da / Num. of mol.: 5 / Fragment: MTDH, UNP residues 386-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AEG1, LYRIC, Metadherin (MTDH), MTDH / Plasmid: pQlink / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q86UE4

-
Non-polymers , 4 types, 304 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cs
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Mix 275nl of 15mg/ml SeMet-SND1(16-339)-L21-MTDH(386-407) with 250nl of well buffer (21.6% pEG3350, 0.1M Sodium Citrate, PH8.0, 0.1M CsCl )+50nl of micro seeds., VAPOR DIFFUSION, SITTING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97849 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 59029 / Num. obs: 59029 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 46.34 Å2 / Rsym value: 0.151 / Net I/σ(I): 20.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.65 / Num. unique all: 5813 / Rsym value: 0.791 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1690)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.701→45.071 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 3875 3.39 %Random
Rwork0.1898 ---
obs0.1917 -99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.701→45.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12840 0 54 290 13184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313201
X-RAY DIFFRACTIONf_angle_d0.72317856
X-RAY DIFFRACTIONf_dihedral_angle_d13.4515008
X-RAY DIFFRACTIONf_chiral_restr0.0291907
X-RAY DIFFRACTIONf_plane_restr0.0042352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7013-2.73420.32261290.28093676X-RAY DIFFRACTION92
2.7342-2.76880.30141380.26893942X-RAY DIFFRACTION100
2.7688-2.80530.33511350.26373918X-RAY DIFFRACTION100
2.8053-2.84370.33661400.25314025X-RAY DIFFRACTION100
2.8437-2.88430.32591390.2653949X-RAY DIFFRACTION100
2.8843-2.92740.26161370.25093915X-RAY DIFFRACTION100
2.9274-2.97310.32441390.24743999X-RAY DIFFRACTION100
2.9731-3.02180.28191380.24033960X-RAY DIFFRACTION100
3.0218-3.07390.27641390.23523963X-RAY DIFFRACTION100
3.0739-3.12980.29021360.22713964X-RAY DIFFRACTION100
3.1298-3.190.31551360.22043904X-RAY DIFFRACTION100
3.19-3.25510.27951370.22493976X-RAY DIFFRACTION100
3.2551-3.32580.30671410.2153986X-RAY DIFFRACTION100
3.3258-3.40320.2931410.19693950X-RAY DIFFRACTION100
3.4032-3.48830.2551380.18753950X-RAY DIFFRACTION100
3.4883-3.58250.24621390.18123955X-RAY DIFFRACTION100
3.5825-3.68790.2331420.17834012X-RAY DIFFRACTION100
3.6879-3.80690.2231380.17133911X-RAY DIFFRACTION100
3.8069-3.94290.2271370.17263960X-RAY DIFFRACTION100
3.9429-4.10060.2261440.17533996X-RAY DIFFRACTION100
4.1006-4.28710.20421410.1593951X-RAY DIFFRACTION100
4.2871-4.5130.22431360.15463952X-RAY DIFFRACTION100
4.513-4.79540.21381350.14653923X-RAY DIFFRACTION100
4.7954-5.16520.23811400.14994004X-RAY DIFFRACTION100
5.1652-5.68410.22561370.17513928X-RAY DIFFRACTION100
5.6841-6.50450.25581410.18473984X-RAY DIFFRACTION100
6.5045-8.18690.18091450.17743957X-RAY DIFFRACTION100
8.1869-45.07710.2281370.18313859X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -24.591 Å / Origin y: -14.9862 Å / Origin z: -35.4751 Å
111213212223313233
T0.3179 Å20.0065 Å2-0.0105 Å2-0.3952 Å20.0566 Å2--0.2722 Å2
L0.0554 °20.0344 °2-0.0023 °2-0.0751 °20.1026 °2--0.0145 °2
S0.0075 Å °0.0108 Å °0.0149 Å °0.0139 Å °0.0074 Å °0.0265 Å °-0.0109 Å °-0.0666 Å °-0.0155 Å °
Refinement TLS groupSelection details: all

+
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