[English] 日本語
Yorodumi
- PDB-7zyh: Crystal structure of human CPSF30 in complex with hFip1 -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more