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- PDB-7zy4: Crystal structure of human CstF77 in complex with hFip1 -

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Basic information

Entry
Database: PDB / ID: 7zy4
TitleCrystal structure of human CstF77 in complex with hFip1
Components
  • Cleavage stimulation factor subunit 3
  • hFip1
KeywordsGENE REGULATION / Complex / 3' end processing / CstF / CPSF
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 / RNA Polymerase II Transcription Termination / Processing of Capped Intron-Containing Pre-mRNA / mRNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
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
Similarity search - Domain/homology
Cleavage stimulation factor subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMuckenfuss, L.M. / Jinek, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Elife / Year: 2022
Title: Fip1 is a multivalent interaction scaffold for processing factors in human mRNA 3' end biogenesis.
Authors: Muckenfuss, L.M. / Migenda Herranz, A.C. / Boneberg, F.M. / Clerici, M. / Jinek, M.
History
DepositionMay 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cleavage stimulation factor subunit 3
B: Cleavage stimulation factor subunit 3
C: hFip1
D: hFip1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,10911
Polymers81,4644
Non-polymers6457
Water64936
1
A: Cleavage stimulation factor subunit 3
C: hFip1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0085
Polymers40,7322
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cleavage stimulation factor subunit 3
D: hFip1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1006
Polymers40,7322
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.612, 157.612, 161.005
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 244 through 552)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNASPA1 - 305
d_12ens_1GOLGOLB
d_13ens_1GOLGOLC
d_14ens_1GOLGOLD
d_21ens_1GLNASPE2 - 306
d_22ens_1GOLGOLF
d_23ens_1GOLGOLG
d_24ens_1GOLGOLH

NCS oper: (Code: givenMatrix: (-0.982795530837, -0.18213725633, 0.0306425263796), (-0.184341994966, 0.957032937474, -0.223843663037), (0.0114443635997, -0.225641256083, -0.974143239003)Vector: 12. ...NCS oper: (Code: given
Matrix: (-0.982795530837, -0.18213725633, 0.0306425263796), (-0.184341994966, 0.957032937474, -0.223843663037), (0.0114443635997, -0.225641256083, -0.974143239003)
Vector: 12.3436814681, 2.34421588695, 10.4047139735)

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Components

#1: Protein Cleavage stimulation factor subunit 3 / / CF-1 77 kDa subunit / Cleavage stimulation factor 77 kDa subunit / CSTF 77 kDa subunit / CstF-77


Mass: 36598.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSTF3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12996
#2: Protein/peptide hFip1


Mass: 4133.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.89 Å3/Da / Density % sol: 68.4 %
Crystal growTemperature: 278.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bicine pH 9.0, 10% w/v PEG 20k, 2% v/v Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→56.31 Å / Num. obs: 38981 / % possible obs: 99.96 % / Redundancy: 40.5 % / Biso Wilson estimate: 70.93 Å2 / CC1/2: 1 / Net I/σ(I): 36
Reflection shellResolution: 2.55→2.641 Å / Redundancy: 42.3 % / Num. unique obs: 3836 / CC1/2: 0.836 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROC20211020data reduction
autoPROC20211020data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OOE

2ooe


Resolution: 2.55→56.31 Å / SU ML: 0.4593 / Cross valid method: FREE R-VALUE / Phase error: 23.6984
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2469 1916 4.9 %
Rwork0.2121 37185 -
obs0.2138 38981 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.37 Å2
Refinement stepCycle: LAST / Resolution: 2.55→56.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5219 0 42 36 5297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01275371
X-RAY DIFFRACTIONf_angle_d1.35347219
X-RAY DIFFRACTIONf_chiral_restr0.0548756
X-RAY DIFFRACTIONf_plane_restr0.01907
X-RAY DIFFRACTIONf_dihedral_angle_d15.24362029
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.62018133605 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.46881410.49242586X-RAY DIFFRACTION100
2.61-2.680.48431280.43292635X-RAY DIFFRACTION100
2.68-2.760.42211410.34972599X-RAY DIFFRACTION99.96
2.76-2.850.31881270.2862605X-RAY DIFFRACTION100
2.85-2.950.26971500.24612593X-RAY DIFFRACTION100
2.95-3.070.28651420.23922616X-RAY DIFFRACTION100
3.07-3.210.31521270.25222640X-RAY DIFFRACTION100
3.21-3.380.33741410.28692622X-RAY DIFFRACTION100
3.38-3.590.31651280.2492656X-RAY DIFFRACTION100
3.59-3.870.23741370.18632648X-RAY DIFFRACTION100
3.87-4.260.21281380.17862674X-RAY DIFFRACTION100
4.26-4.870.14511310.1582695X-RAY DIFFRACTION100
4.87-6.140.24411430.17842719X-RAY DIFFRACTION99.97
6.14-56.310.20151420.18612897X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: 2.01762852962 Å / Origin y: 45.770957828 Å / Origin z: -0.0107682085167 Å
111213212223313233
T0.51901038976 Å2-0.00803830352213 Å20.00586667437425 Å2-0.515449692414 Å20.0242783429866 Å2--0.542210925187 Å2
L1.54430060743 °20.184101863563 °21.0072648907 °2-0.0937793055355 °20.153895649296 °2--0.894132902935 °2
S0.0299845444123 Å °-0.00190447146756 Å °-0.21232026218 Å °0.00291595302125 Å °0.0683163684649 Å °-0.0356074531667 Å °-0.0590108345139 Å °0.0115894965045 Å °-0.0728221727744 Å °
Refinement TLS groupSelection details: all

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