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

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Basic information

Entry
Database: PDB / ID: 5lxy
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


co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway / snRNA catabolic process / TRAMP complex / snRNA binding / mRNA 3'-end processing / regulation of alternative mRNA splicing, via spliceosome / pre-mRNA intronic binding / RNA processing / 14-3-3 protein binding / catalytic step 2 spliceosome ...co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway / snRNA catabolic process / TRAMP complex / snRNA binding / mRNA 3'-end processing / regulation of alternative mRNA splicing, via spliceosome / pre-mRNA intronic binding / RNA processing / 14-3-3 protein binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / 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. ...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 / Zinc finger CCHC domain-containing protein 8 / RNA-binding protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsFalk, S. / Finogenova, K. / Benda, C. / Conti, E.
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 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein 7
D: Zinc finger CCHC domain-containing protein 8
B: RNA-binding protein 7
C: Zinc finger CCHC domain-containing protein 8
E: RNA-binding protein 7
F: Zinc finger CCHC domain-containing protein 8
G: RNA-binding protein 7
H: Zinc finger CCHC domain-containing protein 8
I: RNA-binding protein 7
J: Zinc finger CCHC domain-containing protein 8
K: RNA-binding protein 7
L: Zinc finger CCHC domain-containing protein 8
M: RNA-binding protein 7
N: Zinc finger CCHC domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,63323
Polymers105,91414
Non-polymers7199
Water543
1
A: RNA-binding protein 7
D: Zinc finger CCHC domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2103
Polymers15,1312
Non-polymers801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area6400 Å2
MethodPISA
2
B: RNA-binding protein 7
C: Zinc finger CCHC domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2904
Polymers15,1312
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-12 kcal/mol
Surface area6140 Å2
MethodPISA
3
E: RNA-binding protein 7
F: Zinc finger CCHC domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2103
Polymers15,1312
Non-polymers801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-13 kcal/mol
Surface area6290 Å2
MethodPISA
4
G: RNA-binding protein 7
H: Zinc finger CCHC domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2904
Polymers15,1312
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-12 kcal/mol
Surface area5920 Å2
MethodPISA
5
I: RNA-binding protein 7
J: Zinc finger CCHC domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2103
Polymers15,1312
Non-polymers801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-13 kcal/mol
Surface area6400 Å2
MethodPISA
6
K: RNA-binding protein 7
L: Zinc finger CCHC domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2103
Polymers15,1312
Non-polymers801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-13 kcal/mol
Surface area6090 Å2
MethodPISA
7
M: RNA-binding protein 7
N: Zinc finger CCHC domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2103
Polymers15,1312
Non-polymers801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-11 kcal/mol
Surface area6160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.771, 66.575, 111.912
Angle α, β, γ (deg.)90.000, 126.570, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-103-

HOH

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Components

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


Mass: 10032.661 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM7 / Production host: Escherichia coli (E. coli) / 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.: 7
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
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.9 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 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 Å / Relative weight: 1
ReflectionResolution: 2.85→71.79 Å / Num. obs: 24933 / % possible obs: 99.8 % / Redundancy: 3.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.061 / Net I/σ(I): 8.1
Reflection shellResolution: 2.85→2.92 Å / CC1/2: 0.62 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
xia2data reduction
Aimlessdata scaling
REFMAC5.8.0135refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LXR

5lxr


Resolution: 2.85→71.79 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.829 / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1245 5 %RANDOM
Rwork0.2618 ---
obs-24232 99.78 %-
Displacement parametersBiso max: 244.62 Å2 / Biso min: 32.73 Å2
Refinement stepCycle: LAST / Resolution: 2.85→71.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5485 0 9 3 5497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195621
X-RAY DIFFRACTIONr_bond_other_d00.025034
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.977693
X-RAY DIFFRACTIONr_angle_other_deg3.767311372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1665760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.80522.529174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57315643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9521518
X-RAY DIFFRACTIONr_chiral_restr0.0380.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216486
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021294
X-RAY DIFFRACTIONr_mcbond_it5.2411.0223112
X-RAY DIFFRACTIONr_mcbond_other5.24111.0213111
X-RAY DIFFRACTIONr_mcangle_it8.0916.4913848
LS refinement shellResolution: 2.85→2.924 Å /
Num. reflection% reflection
Rwork1709 -
obs-99.78 %

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