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- PDB-7k95: Crystal structure of human CPSF30 in complex with hFip1 -

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Basic information

Entry
Database: PDB / ID: 7k95
TitleCrystal structure of human CPSF30 in complex with hFip1
Components
  • Isoform 2 of Cleavage and polyadenylation specificity factor subunit 4
  • Pre-mRNA 3'-end-processing factor FIP1
KeywordsNUCLEAR PROTEIN / mRNA processing
Function / homology
Function and homology information


: / : / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / Inhibition of Host mRNA Processing and RNA Silencing / tRNA splicing, via endonucleolytic cleavage and ligation / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript ...: / : / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / Inhibition of Host mRNA Processing and RNA Silencing / tRNA splicing, via endonucleolytic cleavage and ligation / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / tRNA processing in the nucleus / RNA Polymerase II Transcription Termination / termination of RNA polymerase II transcription / : / mRNA export from nucleus / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / sequence-specific double-stranded DNA binding / intracellular membrane-bounded organelle / RNA binding / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
Pre-mRNA polyadenylation factor Fip1 domain / Fip1 motif / Zinc-finger CCCH domain / Zinc-finger containing family / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / zinc finger ...Pre-mRNA polyadenylation factor Fip1 domain / Fip1 motif / Zinc-finger CCCH domain / Zinc-finger containing family / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Cleavage and polyadenylation specificity factor subunit 4 / Pre-mRNA 3'-end-processing factor FIP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHamilton, K. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)R35GM118093 United States
CitationJournal: Genes Dev. / Year: 2020
Title: Molecular mechanism for the interaction between human CPSF30 and hFip1.
Authors: Hamilton, K. / Tong, L.
History
DepositionSep 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Cleavage and polyadenylation specificity factor subunit 4
B: Pre-mRNA 3'-end-processing factor FIP1
C: Pre-mRNA 3'-end-processing factor FIP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5465
Polymers17,4153
Non-polymers1312
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-11 kcal/mol
Surface area8450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.040, 79.040, 48.662
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Isoform 2 of Cleavage and polyadenylation specificity factor subunit 4 / Cleavage and polyadenylation specificity factor 30 kDa subunit / CPSF 30 kDa subunit / NS1 effector ...Cleavage and polyadenylation specificity factor 30 kDa subunit / CPSF 30 kDa subunit / NS1 effector domain-binding protein 1 / Neb-1 / No arches homolog


Mass: 7157.448 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF4, CPSF30, NAR, NEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95639-2
#2: Protein/peptide Pre-mRNA 3'-end-processing factor FIP1 / hFip1 / FIP1-like 1 protein / Factor interacting with PAP / Rearranged in hypereosinophilia


Mass: 5128.710 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FIP1L1, FIP1, RHE / Production host: Escherichia coli (E. coli) / References: UniProt: Q6UN15
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 0.1 M sodium malonate, 16% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→48.66 Å / Num. obs: 13793 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.013 / Rrim(I) all: 0.048 / Net I/σ(I): 30.9 / Num. measured all: 174010
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.9410.90.8748690.7880.91799.9
9.11-48.6611.60.0341370.9990.03598.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDS20180808data reduction
Aimless0.7.4data scaling
SHELXphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.9→39.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2194 / WRfactor Rwork: 0.1865 / FOM work R set: 0.8693 / SU B: 4.954 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1257 / SU Rfree: 0.1187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 690 5 %RANDOM
Rwork0.1793 ---
obs0.1811 13086 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.09 Å2 / Biso mean: 52.784 Å2 / Biso min: 29.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å20 Å2
2--0.2 Å20 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 1.9→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 2 82 1127
Biso mean--41.38 53.98 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131088
X-RAY DIFFRACTIONr_bond_other_d0.0030.017954
X-RAY DIFFRACTIONr_angle_refined_deg1.9841.6781463
X-RAY DIFFRACTIONr_angle_other_deg1.4341.6062212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0885120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47920.5869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79815180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3931510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021200
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02270
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 52 -
Rwork0.262 943 -
all-995 -
obs--99.7 %
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)
12.72411.47690.17773.51161.69244.5172-0.01810.1698-0.28270.02970.1010.03040.6291-0.1062-0.08280.1555-0.0121-0.02260.0179-0.00470.077936.75657.657212.1428
23.56730.3616-0.25074.4069-0.84953.8372-0.12760.08850.28340.21170.21530.69580.01-0.7225-0.08770.11210.0231-0.04030.1581-0.01240.208128.369616.040315.13
34.51520.7848-0.62965.2834-1.0373.65290.05370.3410.175-0.3628-0.017-0.83950.060.9281-0.03670.1859-0.02310.02210.3147-0.0230.185552.916520.53779.089
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A121 - 173
2X-RAY DIFFRACTION2B162 - 200
3X-RAY DIFFRACTION3C161 - 191

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