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- PDB-6c90: Human Mtr4 helicase in complex with ZCCHC8-CTD -

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Basic information

Entry
Database: PDB / ID: 6c90
TitleHuman Mtr4 helicase in complex with ZCCHC8-CTD
Components
  • Exosome RNA helicase MTR4,Exosome RNA helicase MTR4
  • Zinc finger CCHC domain-containing protein 8
KeywordsHYDROLASE/RNA binding protein / HYDROLASE / NEXT / EXOSOME / NUCLEOTIDE-BINDING / ATPASE / RNA / HELICASE / TRANSLOCASE / RNA BINDING PROTEIN / HYDROLASE-RNA binding protein complex
Function / homology
Function and homology information


: / snRNA catabolic process / TRAMP complex / RNA catabolic process / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / rRNA processing ...: / snRNA catabolic process / TRAMP complex / RNA catabolic process / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / rRNA processing / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / DNA damage response / nucleolus / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
rRNA-processing arch domain / Mtr4-like, beta-barrel domain / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / PSP, proline-rich / PSP ...rRNA-processing arch domain / Mtr4-like, beta-barrel domain / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / MALONATE ION / L(+)-TARTARIC ACID / Exosome RNA helicase MTR4 / Zinc finger CCHC domain-containing protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPuno, M.R. / Lima, C.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118080 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis for MTR4-ZCCHC8 interactions that stimulate the MTR4 helicase in the nuclear exosome-targeting complex.
Authors: Puno, M.R. / Lima, C.D.
History
DepositionJan 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exosome RNA helicase MTR4,Exosome RNA helicase MTR4
B: Zinc finger CCHC domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,11110
Polymers89,0762
Non-polymers1,0348
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-40 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.635, 147.635, 101.589
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Exosome RNA helicase MTR4,Exosome RNA helicase MTR4 / ATP-dependent RNA helicase DOB1 / ATP-dependent RNA helicase SKIV2L2 / Superkiller viralicidic ...ATP-dependent RNA helicase DOB1 / ATP-dependent RNA helicase SKIV2L2 / Superkiller viralicidic activity 2-like 2 / TRAMP-like complex helicase


Mass: 83205.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTREX, DOB1, KIAA0052, MTR4, SKIV2L2 / Production host: Escherichia coli (E. coli) / References: UniProt: P42285, RNA helicase
#2: Protein Zinc finger CCHC domain-containing protein 8 / TRAMP-like complex RNA-binding factor ZCCHC8


Mass: 5870.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZCCHC8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NZY4

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Non-polymers , 5 types, 246 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.6 M sodium-potassium (L)-tartrate, 0.1 M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→73.8 Å / Num. obs: 63653 / % possible obs: 99.25 % / Redundancy: 4.6 % / Biso Wilson estimate: 39.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 6188 / CC1/2: 0.47 / % possible all: 96.99

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XGJ

2xgj


Resolution: 2.2→73.8 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 24.81
RfactorNum. reflection% reflection
Rfree0.2214 3118 4.9 %
Rwork0.1903 --
obs0.1918 63650 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→73.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5853 0 67 238 6158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026106
X-RAY DIFFRACTIONf_angle_d0.5088252
X-RAY DIFFRACTIONf_dihedral_angle_d14.153725
X-RAY DIFFRACTIONf_chiral_restr0.039922
X-RAY DIFFRACTIONf_plane_restr0.0031066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1974-2.23180.32321140.3162633X-RAY DIFFRACTION94
2.2318-2.26840.32311390.30522774X-RAY DIFFRACTION99
2.2684-2.30750.33911380.29552740X-RAY DIFFRACTION99
2.3075-2.34950.32231480.28842728X-RAY DIFFRACTION99
2.3495-2.39470.32841450.282701X-RAY DIFFRACTION99
2.3947-2.44350.30711500.26612729X-RAY DIFFRACTION99
2.4435-2.49670.3091280.2552784X-RAY DIFFRACTION100
2.4967-2.55480.29191350.24122748X-RAY DIFFRACTION99
2.5548-2.61860.29481410.23242727X-RAY DIFFRACTION99
2.6186-2.68940.25561410.22242749X-RAY DIFFRACTION100
2.6894-2.76860.24751190.22282771X-RAY DIFFRACTION99
2.7686-2.8580.28071250.22662760X-RAY DIFFRACTION99
2.858-2.96010.2731300.21672770X-RAY DIFFRACTION100
2.9601-3.07860.23451560.21972769X-RAY DIFFRACTION99
3.0786-3.21870.2331610.20552705X-RAY DIFFRACTION99
3.2187-3.38850.23971760.18082745X-RAY DIFFRACTION100
3.3885-3.60070.21631580.16462750X-RAY DIFFRACTION100
3.6007-3.87880.17871390.15242770X-RAY DIFFRACTION100
3.8788-4.26910.16141210.13932793X-RAY DIFFRACTION100
4.2691-4.88670.15791600.12812755X-RAY DIFFRACTION100
4.8867-6.15640.19231340.15962817X-RAY DIFFRACTION100
6.1564-79.59040.191600.18432815X-RAY DIFFRACTION99

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