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- PDB-4qmg: The Structure of MTDH-SND1 Complex Reveals Novel Cancer-Promoting... -

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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 / dense body / intercellular canaliculus / regulatory ncRNA-mediated gene silencing / micrococcal nuclease / : ...RNAi effector complex / miRNA catabolic process / regulation of cell cycle process / RISC complex binding / nuclease activity / dense body / intercellular canaliculus / 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 / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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Details

Has protein modificationY

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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: 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

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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

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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

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