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- PDB-6b3x: Crystal structure of CstF-50 in complex with CstF-77 -

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Basic information

Entry
Database: PDB / ID: 6b3x
TitleCrystal structure of CstF-50 in complex with CstF-77
Components
  • Cleavage stimulation factor subunit 1
  • Cleavage stimulation factor subunit 3
KeywordsGENE REGULATION / WD40 fold / Scaffold protein
Function / homology
Function and homology information


mRNA cleavage stimulating factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / RNA 3'-end processing / Processing of Intronless Pre-mRNAs / mRNA 3'-end processing / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / termination of RNA polymerase II transcription / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway ...mRNA cleavage stimulating factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / RNA 3'-end processing / Processing of Intronless Pre-mRNAs / mRNA 3'-end processing / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / termination of RNA polymerase II transcription / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / mRNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Cleavage stimulation factor subunit 1, dimerisation domain / CSTF1, dimerization domain superfamily / Cleavage stimulation factor subunit 1, dimerisation domain / mRNA 3'-end-processing protein Rna14-like / Suppressor of forked / Suppressor of forked protein (Suf) / : / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Tetratricopeptide-like helical domain superfamily ...Cleavage stimulation factor subunit 1, dimerisation domain / CSTF1, dimerization domain superfamily / Cleavage stimulation factor subunit 1, dimerisation domain / mRNA 3'-end-processing protein Rna14-like / Suppressor of forked / Suppressor of forked protein (Suf) / : / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Tetratricopeptide-like helical domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Cleavage stimulation factor subunit 1 / Cleavage stimulation factor subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYang, W. / Hsu, P. / Yang, F. / Song, J.E. / Varani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM064440 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Reconstitution of the CstF complex unveils a regulatory role for CstF-50 in recognition of 3'-end processing signals.
Authors: Yang, W. / Hsu, P.L. / Yang, F. / Song, J.E. / Varani, G.
History
DepositionSep 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cleavage stimulation factor subunit 1
B: Cleavage stimulation factor subunit 3


Theoretical massNumber of molelcules
Total (without water)42,6962
Polymers42,6962
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-16 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.863, 74.491, 95.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cleavage stimulation factor subunit 1 / / CF-1 50 kDa subunit / Cleavage stimulation factor 50 kDa subunit / CstF-50


Mass: 40331.270 Da / Num. of mol.: 1 / Fragment: UNP residues 80-431
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSTF1 / Production host: unidentified baculovirus / References: UniProt: Q05048
#2: Protein/peptide Cleavage stimulation factor subunit 3 / / CF-1 77 kDa subunit / Cleavage stimulation factor 77 kDa subunit / CstF-77


Mass: 2364.739 Da / Num. of mol.: 1 / Fragment: UNP residues 581-600 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12996
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.81 Å3/Da / Density % sol: 32.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1M MES pH6.0-6.5, 1.6-1.9M ammonium sulfate, 2-5% PEG400, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 14491 / % possible obs: 98.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 29.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 696 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Generated from HHPred derived alignment

Resolution: 2.3→47 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / SU B: 17.617 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.555 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26154 721 5.1 %RANDOM
Rwork0.21409 ---
obs0.21651 13548 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.078 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2---3.15 Å20 Å2
3---4.17 Å2
Refinement stepCycle: 1 / Resolution: 2.3→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2708 0 0 102 2810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022770
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0761.9393752
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63623.158133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20515458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.41522
X-RAY DIFFRACTIONr_chiral_restr0.0710.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212118
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 43 -
Rwork0.319 845 -
obs--93.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3771-0.2946-0.05480.7646-0.07180.4269-0.00180.0498-0.00160.06960.0091-0.022-0.01470.0086-0.00730.03210.0013-0.04230.01380.00320.071913.473528.667821.6532
27.97331.2709-2.15780.4544-0.27690.60440.1375-0.0786-0.1076-0.0115-0.1099-0.1361-0.06760.0046-0.02760.08850.00940.00940.06340.01480.06830.875447.497621.4754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A78 - 427
2X-RAY DIFFRACTION2B581 - 594

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