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- PDB-5lxr: Structure of the minimal RBM7 - ZCCHC8 Complex -

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Basic information

Entry
Database: PDB / ID: 5lxr
TitleStructure of the minimal RBM7 - ZCCHC8 Complex
Components
  • RNA-binding protein 7
  • Zinc finger CCHC domain-containing protein 8
KeywordsRNA BINDING PROTEIN / NEXT Complex RRM RBM7 ZCCHC8
Function / homology
Function and homology information


: / snRNA catabolic process / TRAMP complex / snRNA binding / regulation of alternative mRNA splicing, via spliceosome / pre-mRNA intronic binding / 14-3-3 protein binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / meiotic cell cycle ...: / snRNA catabolic process / TRAMP complex / snRNA binding / regulation of alternative mRNA splicing, via spliceosome / pre-mRNA intronic binding / 14-3-3 protein binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / meiotic cell cycle / mRNA splicing, via spliceosome / single-stranded RNA binding / nuclear body / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
RBM7, RNA recognition motif / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...RBM7, RNA recognition motif / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / zinc finger / Zinc knuckle / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / SAMARIUM (III) ION / Zinc finger CCHC domain-containing protein 8 / RNA-binding protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsFalk, S. / Finogenova, K. / Benda, C. / Conti, E.
Funding support Germany, 4items
OrganizationGrant numberCountry
European Research Council294371 Germany
Marie CurieITN RNPNet Germany
German Research FoundationSFB646 Germany
German Research FoundationSFB1035 Germany
CitationJournal: Nat Commun / Year: 2016
Title: Structure of the RBM7-ZCCHC8 core of the NEXT complex reveals connections to splicing factors.
Authors: Falk, S. / Finogenova, K. / Melko, M. / Benda, C. / Lykke-Andersen, S. / Jensen, T.H. / Conti, E.
History
DepositionSep 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 2.0May 8, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein 7
B: Zinc finger CCHC domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,93710
Polymers15,1312
Non-polymers8068
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-30 kcal/mol
Surface area6890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.519, 79.519, 87.609
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-101-

SM

21B-521-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein RNA-binding protein 7 / RNA-binding motif protein 7


Mass: 10032.661 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y580
#2: Protein/peptide Zinc finger CCHC domain-containing protein 8 / TRAMP-like complex RNA-binding factor ZCCHC8


Mass: 5097.909 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) / Strain (production host): BL21(DE3) / References: UniProt: Q6NZY4

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Non-polymers , 4 types, 72 molecules

#3: Chemical ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Sm
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris-Propane pH 6.5 0.2 M NaBr 18% (v/v) PEG3350 7% (w/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.6 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 2→87.61 Å / Num. obs: 11470 / % possible obs: 98.8 % / Redundancy: 134.8 % / CC1/2: 1 / Rmerge(I) obs: 0.187 / Net I/σ(I): 26.6
Reflection shellResolution: 2→2.08 Å / CC1/2: 0.341 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
XDSdata reduction
XDSdata scaling
AutoSol1.10.1phasing
RefinementMethod to determine structure: SAD / Resolution: 2→87.61 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 -5 %random selection
Rwork0.2022 ---
obs-11470 98.8 %-
Refinement stepCycle: LAST / Resolution: 2→87.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 8 64 1019
LS refinement shellResolution: 2→2.08 Å

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