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

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Basic information

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


Inhibition of Host mRNA Processing and RNA Silencing / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / tRNA processing in the nucleus / RNA Polymerase II Transcription Termination / Processing of Capped Intron-Containing Pre-mRNA / mRNA processing / sequence-specific double-stranded DNA binding ...Inhibition of Host mRNA Processing and RNA Silencing / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / tRNA processing in the nucleus / RNA Polymerase II Transcription Termination / Processing of Capped Intron-Containing Pre-mRNA / mRNA processing / sequence-specific double-stranded DNA binding / intracellular membrane-bounded organelle / RNA binding / zinc ion binding / nucleoplasm
Similarity search - Function
Zinc-finger CCCH domain / Zinc-finger containing family / CPSF complex subunit CPSF4-like / 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 CCCH domain / Zinc-finger containing family / CPSF complex subunit CPSF4-like / 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 / Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMuckenfuss, L.M. / Jinek, M. / Migenda Herranz, A.C. / Clerici, 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 24, 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 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cleavage and polyadenylation specificity factor subunit 4
B: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
C: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
D: Cleavage and polyadenylation specificity factor subunit 4
E: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
F: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
G: Cleavage and polyadenylation specificity factor subunit 4
H: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
I: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
J: Cleavage and polyadenylation specificity factor subunit 4
K: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
L: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,38020
Polymers92,85712
Non-polymers5238
Water1,76598
1
A: Cleavage and polyadenylation specificity factor subunit 4
B: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
C: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3455
Polymers23,2143
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Cleavage and polyadenylation specificity factor subunit 4
E: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
F: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3455
Polymers23,2143
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Cleavage and polyadenylation specificity factor subunit 4
H: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
I: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3455
Polymers23,2143
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Cleavage and polyadenylation specificity factor subunit 4
K: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
L: Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3455
Polymers23,2143
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.127, 115.125, 66.444
Angle α, β, γ (deg.)90.000, 116.781, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 123 through 169 or resid 1001 through 1002))
d_2ens_1(chain "D" and (resid 123 through 169 or resid 1001 through 1002))
d_3ens_1(chain "G" and resid 123 through 1002)
d_4ens_1(chain "J" and (resid 123 through 169 or resid 1001 through 1002))
d_1ens_2(chain "B" and resid 148 through 182)
d_2ens_2chain "E"
d_3ens_2(chain "H" and resid 148 through 182)
d_4ens_2chain "K"
d_1ens_3(chain "C" and resid 129 through 180)
d_2ens_3chain "F"
d_3ens_3(chain "I" and resid 129 through 180)
d_4ens_3(chain "L" and resid 129 through 180)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPPHEA2 - 48
d_12ens_1ZNZNB
d_21ens_1ASPPHEF1 - 47
d_22ens_1ZNZNG
d_31ens_1ASPPHEK3 - 49
d_32ens_1ZNZNL
d_41ens_1ASPPHEP1 - 47
d_42ens_1ZNZNQ
d_11ens_2LYSMETD2 - 36
d_21ens_2LYSMETI1 - 35
d_31ens_2LYSMETN1 - 35
d_41ens_2LYSMETS1 - 35
d_11ens_3ALAILEE1 - 52
d_21ens_3ALAILEJ1 - 52
d_31ens_3ALAILEO2 - 53
d_41ens_3ALAILET3 - 54

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.997803280571, -0.0637806974475, -0.0179063093413), (-0.0633831450009, -0.997747736823, 0.0219551951746), (-0.019266297281, -0.0207720075694, -0.999598586179)-2.49796323191, -73.1132936395, -1.68842349914
2given(-0.995807449046, 0.0868745407859, 0.0286415535097), (0.0864255475656, 0.996120661199, -0.0165605875774), (-0.0299691366608, -0.0140157945249, -0.999452554327)56.9532265313, -0.58716884791, -1.33557015728
3given(-0.999887971639, 0.0029441267102, 0.014675704039), (-0.00293192153936, -0.999995338014, 0.000853104129741), (0.0146781472678, 0.000809980545106, 0.999891942124)53.3391390133, -73.160689244, -0.107329656098
4given(0.997376315468, -0.0708151390887, -0.0150233624326), (-0.0705761280607, -0.997379913814, 0.0158845103299), (-0.0161088637366, -0.0147825436349, -0.999760961887)-2.98509394604, -72.8440297673, -1.50701691521
5given(-0.99827513904, 0.0564635043083, 0.0160816496418), (0.0561277140253, 0.998210687465, -0.0206180296824), (-0.0172170407523, -0.0196798402158, -0.999658080244)55.5445229236, 0.00700685105384, -1.85486622684
6given(-0.999674928482, 0.0247892150272, 0.00596088771851), (-0.0248504217846, -0.999636841691, -0.010423112364), (0.00570034219896, -0.0105678546811, 0.999927910675)54.6596181974, -72.8010002506, -0.559171389967
7given(0.999056279157, -0.0434032233721, -0.00164659563481), (-0.0434153190285, -0.999023415636, -0.0082051864694), (-0.00128885605411, 0.00826893053871, -0.999964981206)-1.54471429187, -73.2024611327, -0.582483457703
8given(-0.997390791238, 0.0658362833743, 0.0296174500046), (0.066451523302, 0.99758332082, 0.0202907139558), (-0.0282100089359, 0.0222058959163, -0.999355338997)56.2020819218, 0.074619428344, 0.166404051483
9given(-0.999995134378, -0.000946910729018, -0.00297230216509), (0.00100429622241, -0.999811976294, -0.0193650057536), (-0.00295340637011, -0.0193678966027, 0.999808062566)53.4244695888, -73.226570754, -0.83995003446

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Components

#1: Protein
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: 7482.701 Da / Num. of mol.: 4
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: Protein
Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1 / hFip1 / FIP1-like 1 protein / Factor interacting with PAP / Rearranged in hypereosinophilia


Mass: 7865.756 Da / Num. of mol.: 8
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: Q6UN15-4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / Details: 1.626 M (NH4)SO4, 0.1 M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.2809 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2809 Å / Relative weight: 1
ReflectionResolution: 2.2→48.65 Å / Num. obs: 226720 / % possible obs: 92.25 % / Redundancy: 6 % / CC1/2: 0.998 / Net I/σ(I): 13.53
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 15294 / CC1/2: 0.557

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDS2019-03-15data reduction
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→48.65 Å / Cross valid method: FREE R-VALUE / σ(F): 15.66 / Phase error: 29.424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2644 3840 5.21 %
Rwork0.2472 69904 -
obs0.2498 73744 91.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.87 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4625 0 8 98 4731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734777
X-RAY DIFFRACTIONf_angle_d1.00766429
X-RAY DIFFRACTIONf_chiral_restr0.0537588
X-RAY DIFFRACTIONf_plane_restr0.0109840
X-RAY DIFFRACTIONf_dihedral_angle_d14.90281793
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.16004845049
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.07664242861
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.15628504486
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS1.40040361299
ens_2d_3DX-RAY DIFFRACTIONTorsion NCS1.36937882268
ens_2d_4DX-RAY DIFFRACTIONTorsion NCS1.26301404846
ens_3d_2EX-RAY DIFFRACTIONTorsion NCS1.01475027436
ens_3d_3EX-RAY DIFFRACTIONTorsion NCS1.39582164675
ens_3d_4EX-RAY DIFFRACTIONTorsion NCS1.2806632212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.32091470.32042772X-RAY DIFFRACTION70.21
2.24-2.280.29741610.3083162X-RAY DIFFRACTION77.81
2.28-2.320.32221710.30973263X-RAY DIFFRACTION80.97
2.32-2.370.33231720.30393239X-RAY DIFFRACTION80.67
2.37-2.420.28811720.31393373X-RAY DIFFRACTION83.82
2.42-2.480.33741820.33463398X-RAY DIFFRACTION83.76
2.48-2.540.3521810.33043451X-RAY DIFFRACTION85.63
2.54-2.610.37021810.3283469X-RAY DIFFRACTION85.78
2.61-2.690.33591810.32583483X-RAY DIFFRACTION86.64
2.69-2.770.34431840.31773539X-RAY DIFFRACTION86.87
2.77-2.870.32981890.29623562X-RAY DIFFRACTION88.5
2.87-2.990.27761880.27933530X-RAY DIFFRACTION88.81
2.99-3.120.27741900.26973578X-RAY DIFFRACTION89.54
3.12-3.290.25981980.26553770X-RAY DIFFRACTION92.13
3.29-3.490.281930.26173739X-RAY DIFFRACTION92.64
3.49-3.760.23871960.23093714X-RAY DIFFRACTION92.46
3.76-4.140.26231950.21253771X-RAY DIFFRACTION93.32
4.14-4.740.20092030.19693771X-RAY DIFFRACTION93.34
4.74-5.970.23461990.21073757X-RAY DIFFRACTION93.3
5.97-48.650.2811950.24973725X-RAY DIFFRACTION92.87
Refinement TLS params.Method: refined / Origin x: 26.8427481368 Å / Origin y: -36.6836251916 Å / Origin z: -0.459703028978 Å
111213212223313233
T0.383499308591 Å20.00903965134129 Å20.00334945802547 Å2-0.398363707929 Å20.00327701268292 Å2--0.246102567543 Å2
L0.478253828579 °20.152279705398 °2-0.00498572926366 °2-0.585099713692 °20.0129709679903 °2--0.133587138008 °2
S-0.00606189418842 Å °0.0692951317083 Å °0.000533468901828 Å °-0.0408478135915 Å °0.0317103089703 Å °0.0164738466774 Å °0.0261776003822 Å °0.0015723553906 Å °-0.0314070018932 Å °
Refinement TLS groupSelection details: all

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